Starting phenix.real_space_refine on Thu Nov 20 23:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.map" model { file = "/net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nju_49491/11_2025/9nju_49491.cif" } resolution = 3.94 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 24996 2.51 5 N 6500 2.21 5 O 7724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39352 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2496, 19676 Classifications: {'peptide': 2496} Link IDs: {'CIS': 7, 'PTRANS': 90, 'TRANS': 2398} Chain: "B" Number of atoms: 19676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2496, 19676 Classifications: {'peptide': 2496} Link IDs: {'CIS': 7, 'PTRANS': 90, 'TRANS': 2398} Time building chain proxies: 8.82, per 1000 atoms: 0.22 Number of scatterers: 39352 At special positions: 0 Unit cell: (218.675, 152.198, 166.193, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 7724 8.00 N 6500 7.00 C 24996 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: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9412 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 35 sheets defined 41.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.586A pdb=" N TRP A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 76' Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.644A pdb=" N ARG A 119 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 156 through 167 removed outlier: 4.399A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.706A pdb=" N SER A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.825A pdb=" N ILE A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 349 through 355 removed outlier: 4.133A pdb=" N ASN A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 375 Processing helix chain 'A' and resid 440 through 446 removed outlier: 4.546A pdb=" N THR A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.580A pdb=" N ASN A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.646A pdb=" N LYS A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 562 through 569 Processing helix chain 'A' and resid 569 through 588 removed outlier: 4.125A pdb=" N TYR A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 597 Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 608 through 630 Proline residue: A 614 - end of helix Processing helix chain 'A' and resid 642 through 651 removed outlier: 4.484A pdb=" N SER A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 685 through 692 removed outlier: 3.582A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 759 Processing helix chain 'A' and resid 788 through 798 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 862 through 877 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 897 through 908 removed outlier: 5.975A pdb=" N PHE A 904 " --> pdb=" O ASP A 900 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 925 through 932 removed outlier: 3.519A pdb=" N LYS A 929 " --> pdb=" O PRO A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 978 through 989 removed outlier: 4.148A pdb=" N ILE A 982 " --> pdb=" O GLY A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1071 removed outlier: 3.607A pdb=" N LEU A1067 " --> pdb=" O ASP A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1087 Processing helix chain 'A' and resid 1093 through 1097 Processing helix chain 'A' and resid 1127 through 1135 removed outlier: 3.831A pdb=" N PHE A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1141 removed outlier: 3.868A pdb=" N LEU A1141 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1163 Processing helix chain 'A' and resid 1251 through 1260 removed outlier: 3.514A pdb=" N ASN A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1280 removed outlier: 3.555A pdb=" N ASN A1266 " --> pdb=" O ASP A1262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A1280 " --> pdb=" O SER A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1315 removed outlier: 3.538A pdb=" N LEU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1337 through 1357 removed outlier: 4.601A pdb=" N LEU A1343 " --> pdb=" O LYS A1339 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1440 removed outlier: 4.188A pdb=" N SER A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1478 Processing helix chain 'A' and resid 1496 through 1504 Processing helix chain 'A' and resid 1550 through 1562 removed outlier: 3.791A pdb=" N LEU A1561 " --> pdb=" O LYS A1557 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1562 " --> pdb=" O LEU A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 Processing helix chain 'A' and resid 1596 through 1607 Processing helix chain 'A' and resid 1651 through 1655 removed outlier: 3.763A pdb=" N SER A1654 " --> pdb=" O ASP A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1680 Processing helix chain 'A' and resid 1699 through 1710 removed outlier: 3.534A pdb=" N LEU A1703 " --> pdb=" O ASP A1699 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A1710 " --> pdb=" O THR A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1729 through 1748 removed outlier: 4.041A pdb=" N GLN A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A1748 " --> pdb=" O ILE A1744 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1781 Processing helix chain 'A' and resid 1800 through 1807 Processing helix chain 'A' and resid 1846 through 1848 No H-bonds generated for 'chain 'A' and resid 1846 through 1848' Processing helix chain 'A' and resid 1883 through 1891 removed outlier: 3.694A pdb=" N ASN A1887 " --> pdb=" O ASN A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1899 Processing helix chain 'A' and resid 1961 through 1966 Processing helix chain 'A' and resid 1968 through 1981 Processing helix chain 'A' and resid 1999 through 2019 removed outlier: 3.643A pdb=" N HIS A2019 " --> pdb=" O GLN A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2036 through 2047 Processing helix chain 'A' and resid 2061 through 2070 removed outlier: 3.777A pdb=" N LYS A2067 " --> pdb=" O CYS A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2093 removed outlier: 4.289A pdb=" N SER A2088 " --> pdb=" O GLY A2084 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A2089 " --> pdb=" O ASP A2085 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A2092 " --> pdb=" O SER A2088 " (cutoff:3.500A) Processing helix chain 'A' and resid 2105 through 2109 removed outlier: 3.744A pdb=" N VAL A2109 " --> pdb=" O THR A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2120 removed outlier: 3.788A pdb=" N LYS A2120 " --> pdb=" O SER A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2155 removed outlier: 3.681A pdb=" N ASP A2154 " --> pdb=" O ASP A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2168 No H-bonds generated for 'chain 'A' and resid 2166 through 2168' Processing helix chain 'A' and resid 2169 through 2180 removed outlier: 4.136A pdb=" N ASN A2178 " --> pdb=" O ILE A2174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A2179 " --> pdb=" O GLU A2175 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A2180 " --> pdb=" O TYR A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2197 Processing helix chain 'A' and resid 2197 through 2206 removed outlier: 3.508A pdb=" N GLU A2206 " --> pdb=" O LEU A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2235 through 2251 removed outlier: 4.398A pdb=" N HIS A2239 " --> pdb=" O GLY A2235 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A2250 " --> pdb=" O SER A2246 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2286 Processing helix chain 'A' and resid 2287 through 2289 No H-bonds generated for 'chain 'A' and resid 2287 through 2289' Processing helix chain 'A' and resid 2300 through 2315 removed outlier: 3.519A pdb=" N CYS A2315 " --> pdb=" O VAL A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2349 Processing helix chain 'A' and resid 2351 through 2366 Processing helix chain 'A' and resid 2378 through 2383 Processing helix chain 'A' and resid 2387 through 2407 Processing helix chain 'A' and resid 2423 through 2428 Processing helix chain 'A' and resid 2428 through 2438 removed outlier: 3.760A pdb=" N ALA A2432 " --> pdb=" O ASP A2428 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A2438 " --> pdb=" O PHE A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2456 Processing helix chain 'A' and resid 2472 through 2480 Processing helix chain 'A' and resid 2482 through 2487 removed outlier: 3.999A pdb=" N LYS A2486 " --> pdb=" O GLN A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2488 through 2491 Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.577A pdb=" N TRP B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 76' Processing helix chain 'B' and resid 94 through 111 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.676A pdb=" N ARG B 119 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 156 through 167 removed outlier: 4.405A pdb=" N LEU B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 211 through 221 removed outlier: 4.698A pdb=" N SER B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.812A pdb=" N ILE B 326 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 349 through 355 removed outlier: 4.132A pdb=" N ASN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 375 Processing helix chain 'B' and resid 440 through 446 removed outlier: 4.550A pdb=" N THR B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.586A pdb=" N ASN B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.642A pdb=" N LYS B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 562 through 569 Processing helix chain 'B' and resid 569 through 588 removed outlier: 4.127A pdb=" N TYR B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 597 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 608 through 630 Proline residue: B 614 - end of helix Processing helix chain 'B' and resid 642 through 651 removed outlier: 4.477A pdb=" N SER B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 685 through 692 removed outlier: 3.560A pdb=" N TYR B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 731 Processing helix chain 'B' and resid 745 through 750 Processing helix chain 'B' and resid 751 through 759 Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 801 through 815 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 862 through 877 Processing helix chain 'B' and resid 882 through 887 Processing helix chain 'B' and resid 897 through 908 removed outlier: 5.968A pdb=" N PHE B 904 " --> pdb=" O ASP B 900 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS B 905 " --> pdb=" O ILE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 911 No H-bonds generated for 'chain 'B' and resid 909 through 911' Processing helix chain 'B' and resid 925 through 932 removed outlier: 3.520A pdb=" N LYS B 929 " --> pdb=" O PRO B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 967 Processing helix chain 'B' and resid 978 through 989 removed outlier: 4.125A pdb=" N ILE B 982 " --> pdb=" O GLY B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1071 removed outlier: 3.612A pdb=" N LEU B1067 " --> pdb=" O ASP B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1087 removed outlier: 3.502A pdb=" N VAL B1081 " --> pdb=" O THR B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1097 Processing helix chain 'B' and resid 1127 through 1135 removed outlier: 3.832A pdb=" N PHE B1135 " --> pdb=" O ILE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1141 removed outlier: 3.863A pdb=" N LEU B1141 " --> pdb=" O GLY B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1163 Processing helix chain 'B' and resid 1251 through 1260 removed outlier: 3.504A pdb=" N ASN B1255 " --> pdb=" O GLU B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1280 removed outlier: 3.554A pdb=" N ASN B1266 " --> pdb=" O ASP B1262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B1280 " --> pdb=" O SER B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1315 removed outlier: 3.540A pdb=" N LEU B1304 " --> pdb=" O ASN B1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1334 Processing helix chain 'B' and resid 1337 through 1357 removed outlier: 4.605A pdb=" N LEU B1343 " --> pdb=" O LYS B1339 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B1348 " --> pdb=" O ILE B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1440 removed outlier: 4.189A pdb=" N SER B1420 " --> pdb=" O SER B1416 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B1433 " --> pdb=" O THR B1429 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1478 Processing helix chain 'B' and resid 1496 through 1504 Processing helix chain 'B' and resid 1550 through 1562 removed outlier: 3.789A pdb=" N LEU B1561 " --> pdb=" O LYS B1557 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B1562 " --> pdb=" O LEU B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1577 through 1582 Processing helix chain 'B' and resid 1589 through 1593 Processing helix chain 'B' and resid 1596 through 1607 Processing helix chain 'B' and resid 1651 through 1655 removed outlier: 3.786A pdb=" N SER B1654 " --> pdb=" O ASP B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1673 through 1680 Processing helix chain 'B' and resid 1699 through 1710 removed outlier: 3.517A pdb=" N LEU B1703 " --> pdb=" O ASP B1699 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B1710 " --> pdb=" O THR B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1729 through 1748 removed outlier: 4.013A pdb=" N GLN B1733 " --> pdb=" O GLU B1729 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN B1748 " --> pdb=" O ILE B1744 " (cutoff:3.500A) Processing helix chain 'B' and resid 1770 through 1781 Processing helix chain 'B' and resid 1800 through 1807 Processing helix chain 'B' and resid 1846 through 1848 No H-bonds generated for 'chain 'B' and resid 1846 through 1848' Processing helix chain 'B' and resid 1883 through 1891 removed outlier: 3.693A pdb=" N ASN B1887 " --> pdb=" O ASN B1883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1895 through 1899 Processing helix chain 'B' and resid 1961 through 1966 Processing helix chain 'B' and resid 1968 through 1981 Processing helix chain 'B' and resid 1999 through 2019 removed outlier: 3.644A pdb=" N HIS B2019 " --> pdb=" O GLN B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2036 through 2047 Processing helix chain 'B' and resid 2060 through 2070 removed outlier: 4.232A pdb=" N ASP B2064 " --> pdb=" O THR B2060 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B2067 " --> pdb=" O CYS B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2084 through 2093 removed outlier: 4.241A pdb=" N SER B2088 " --> pdb=" O GLY B2084 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B2089 " --> pdb=" O ASP B2085 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B2092 " --> pdb=" O SER B2088 " (cutoff:3.500A) Processing helix chain 'B' and resid 2105 through 2109 removed outlier: 3.652A pdb=" N VAL B2109 " --> pdb=" O THR B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2115 through 2120 removed outlier: 3.540A pdb=" N LYS B2120 " --> pdb=" O SER B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2138 through 2155 removed outlier: 3.682A pdb=" N ASP B2154 " --> pdb=" O ASP B2150 " (cutoff:3.500A) Processing helix chain 'B' and resid 2166 through 2168 No H-bonds generated for 'chain 'B' and resid 2166 through 2168' Processing helix chain 'B' and resid 2169 through 2180 removed outlier: 4.143A pdb=" N ASN B2178 " --> pdb=" O ILE B2174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B2179 " --> pdb=" O GLU B2175 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B2180 " --> pdb=" O TYR B2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2197 Processing helix chain 'B' and resid 2197 through 2206 removed outlier: 3.503A pdb=" N GLU B2206 " --> pdb=" O LEU B2202 " (cutoff:3.500A) Processing helix chain 'B' and resid 2235 through 2251 removed outlier: 4.380A pdb=" N HIS B2239 " --> pdb=" O GLY B2235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B2250 " --> pdb=" O SER B2246 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2286 Processing helix chain 'B' and resid 2287 through 2289 No H-bonds generated for 'chain 'B' and resid 2287 through 2289' Processing helix chain 'B' and resid 2300 through 2315 removed outlier: 3.521A pdb=" N CYS B2315 " --> pdb=" O VAL B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2340 through 2349 Processing helix chain 'B' and resid 2351 through 2366 Processing helix chain 'B' and resid 2378 through 2383 Processing helix chain 'B' and resid 2387 through 2407 Processing helix chain 'B' and resid 2423 through 2428 Processing helix chain 'B' and resid 2428 through 2438 removed outlier: 3.773A pdb=" N ALA B2432 " --> pdb=" O ASP B2428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B2438 " --> pdb=" O PHE B2434 " (cutoff:3.500A) Processing helix chain 'B' and resid 2444 through 2456 Processing helix chain 'B' and resid 2472 through 2480 Processing helix chain 'B' and resid 2482 through 2487 removed outlier: 4.010A pdb=" N LYS B2486 " --> pdb=" O GLN B2482 " (cutoff:3.500A) Processing helix chain 'B' and resid 2488 through 2491 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 6.344A pdb=" N VAL A 125 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU A 175 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE A 127 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA A 124 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY A 204 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 126 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A 206 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 128 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 246 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 18 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 252 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A 16 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS A 266 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE A 268 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A 432 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 270 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 312 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU A 345 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 467 Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 639 removed outlier: 6.558A pdb=" N VAL A 547 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 636 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 548 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 827 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 550 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 854 " --> pdb=" O PHE A 824 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 707 removed outlier: 7.006A pdb=" N VAL A 712 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR A 705 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N SER A 710 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 774 Processing sheet with id=AB1, first strand: chain 'A' and resid 942 through 943 removed outlier: 4.549A pdb=" N SER A1046 " --> pdb=" O PHE A1031 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1047 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 999 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG A1049 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 998 " --> pdb=" O GLN A1154 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN A1154 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A1000 " --> pdb=" O ARG A1152 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A1152 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS A1206 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A1153 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A1204 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP A1155 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A1202 " --> pdb=" O ASP A1155 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A1157 " --> pdb=" O ILE A1200 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A1200 " --> pdb=" O LYS A1157 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN A1204 " --> pdb=" O GLY A1187 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A1187 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS A1206 " --> pdb=" O THR A1185 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A1185 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A1188 " --> pdb=" O PHE A1177 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE A1177 " --> pdb=" O SER A1188 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASP A1190 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA A1175 " --> pdb=" O ASP A1190 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET A1192 " --> pdb=" O ALA A1173 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A1173 " --> pdb=" O MET A1192 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A1110 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS A1102 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A1112 " --> pdb=" O GLU A1100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 969 through 970 Processing sheet with id=AB3, first strand: chain 'A' and resid 1689 through 1696 removed outlier: 6.797A pdb=" N SER A1660 " --> pdb=" O ASN A1691 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A1693 " --> pdb=" O SER A1660 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N CYS A1662 " --> pdb=" O THR A1693 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A1695 " --> pdb=" O CYS A1662 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE A1664 " --> pdb=" O ILE A1695 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A1717 " --> pdb=" O ALA A1755 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A1757 " --> pdb=" O ILE A1717 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N PHE A1719 " --> pdb=" O LEU A1757 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR A1759 " --> pdb=" O PHE A1719 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N THR A1818 " --> pdb=" O THR A1788 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A1790 " --> pdb=" O THR A1818 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A1820 " --> pdb=" O SER A1790 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP A1792 " --> pdb=" O VAL A1820 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE A2372 " --> pdb=" O THR A2412 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A2414 " --> pdb=" O PHE A2372 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A2374 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TRP A2416 " --> pdb=" O LEU A2374 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER A2376 " --> pdb=" O TRP A2416 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A2227 " --> pdb=" O SER A2323 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LEU A2325 " --> pdb=" O THR A2227 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A2229 " --> pdb=" O LEU A2325 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A2262 " --> pdb=" O HIS A2292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1511 through 1516 removed outlier: 6.216A pdb=" N ILE A1449 " --> pdb=" O GLU A1487 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A1489 " --> pdb=" O ILE A1449 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A1451 " --> pdb=" O THR A1489 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP A1453 " --> pdb=" O PRO A1491 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU A1536 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS A1450 " --> pdb=" O LEU A1536 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A1538 " --> pdb=" O LYS A1450 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A1452 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER A1540 " --> pdb=" O ILE A1452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1511 through 1516 removed outlier: 6.216A pdb=" N ILE A1449 " --> pdb=" O GLU A1487 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A1489 " --> pdb=" O ILE A1449 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A1451 " --> pdb=" O THR A1489 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP A1453 " --> pdb=" O PRO A1491 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU A1536 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS A1450 " --> pdb=" O LEU A1536 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A1538 " --> pdb=" O LYS A1450 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A1452 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER A1540 " --> pdb=" O ILE A1452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1850 through 1854 Processing sheet with id=AB7, first strand: chain 'A' and resid 1945 through 1949 removed outlier: 6.831A pdb=" N GLU A1874 " --> pdb=" O THR A1918 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A1914 " --> pdb=" O MET A1878 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR A1880 " --> pdb=" O GLU A1912 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU A1912 " --> pdb=" O THR A1880 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1945 through 1949 removed outlier: 4.534A pdb=" N ILE A2186 " --> pdb=" O ILE A1882 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS A2163 " --> pdb=" O VAL A2187 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP A2189 " --> pdb=" O LYS A2163 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A2165 " --> pdb=" O ASP A2189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2053 through 2056 removed outlier: 4.304A pdb=" N ALA A2053 " --> pdb=" O ILE A2030 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A2032 " --> pdb=" O ALA A2053 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A2055 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A1993 " --> pdb=" O LEU A2079 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A2078 " --> pdb=" O MET A2101 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B2078 " --> pdb=" O MET B2101 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B1993 " --> pdb=" O LEU B2079 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B2053 " --> pdb=" O ILE B2030 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B2032 " --> pdb=" O ALA B2053 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B2055 " --> pdb=" O ALA B2032 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2440 through 2441 removed outlier: 4.213A pdb=" N SER A2470 " --> pdb=" O LEU A2441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.355A pdb=" N VAL B 125 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU B 175 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 127 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 124 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY B 204 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 126 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 206 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY B 128 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 246 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 18 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS B 252 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE B 16 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS B 266 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 268 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER B 432 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 270 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 312 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU B 345 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AC4, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AC7, first strand: chain 'B' and resid 461 through 467 Processing sheet with id=AC8, first strand: chain 'B' and resid 779 through 780 removed outlier: 8.243A pdb=" N PHE B 773 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 637 " --> pdb=" O PHE B 773 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 547 " --> pdb=" O PRO B 634 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 636 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B 548 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 827 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 550 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 854 " --> pdb=" O PHE B 824 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 707 removed outlier: 7.010A pdb=" N VAL B 712 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 705 " --> pdb=" O SER B 710 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 710 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 942 through 943 removed outlier: 4.609A pdb=" N SER B1046 " --> pdb=" O PHE B1031 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B1047 " --> pdb=" O LEU B 999 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 999 " --> pdb=" O ASN B1047 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B1049 " --> pdb=" O PHE B 997 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 998 " --> pdb=" O GLN B1154 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B1154 " --> pdb=" O ASN B 998 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU B1000 " --> pdb=" O ARG B1152 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B1152 " --> pdb=" O GLU B1000 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B1206 " --> pdb=" O ASP B1151 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B1153 " --> pdb=" O ASN B1204 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1204 " --> pdb=" O LEU B1153 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP B1155 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B1202 " --> pdb=" O ASP B1155 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS B1157 " --> pdb=" O ILE B1200 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE B1200 " --> pdb=" O LYS B1157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN B1204 " --> pdb=" O GLY B1187 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B1187 " --> pdb=" O ASN B1204 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B1206 " --> pdb=" O THR B1185 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B1185 " --> pdb=" O LYS B1206 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER B1188 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE B1177 " --> pdb=" O SER B1188 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP B1190 " --> pdb=" O ALA B1175 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA B1175 " --> pdb=" O ASP B1190 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B1192 " --> pdb=" O ALA B1173 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B1173 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B1110 " --> pdb=" O CYS B1102 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS B1102 " --> pdb=" O PHE B1110 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS B1112 " --> pdb=" O GLU B1100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 969 through 970 Processing sheet with id=AD3, first strand: chain 'B' and resid 1689 through 1696 removed outlier: 6.803A pdb=" N SER B1660 " --> pdb=" O ASN B1691 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR B1693 " --> pdb=" O SER B1660 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS B1662 " --> pdb=" O THR B1693 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE B1695 " --> pdb=" O CYS B1662 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE B1664 " --> pdb=" O ILE B1695 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B1717 " --> pdb=" O ALA B1755 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B1757 " --> pdb=" O ILE B1717 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE B1719 " --> pdb=" O LEU B1757 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR B1759 " --> pdb=" O PHE B1719 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR B1818 " --> pdb=" O THR B1788 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER B1790 " --> pdb=" O THR B1818 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B1820 " --> pdb=" O SER B1790 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B1792 " --> pdb=" O VAL B1820 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE B2372 " --> pdb=" O THR B2412 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE B2414 " --> pdb=" O PHE B2372 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B2374 " --> pdb=" O ILE B2414 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TRP B2416 " --> pdb=" O LEU B2374 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B2376 " --> pdb=" O TRP B2416 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B2227 " --> pdb=" O SER B2323 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU B2325 " --> pdb=" O THR B2227 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B2229 " --> pdb=" O LEU B2325 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE B2262 " --> pdb=" O HIS B2292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1511 through 1516 removed outlier: 6.215A pdb=" N ILE B1449 " --> pdb=" O GLU B1487 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B1489 " --> pdb=" O ILE B1449 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B1451 " --> pdb=" O THR B1489 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP B1453 " --> pdb=" O PRO B1491 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B1536 " --> pdb=" O LEU B1448 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS B1450 " --> pdb=" O LEU B1536 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE B1538 " --> pdb=" O LYS B1450 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B1452 " --> pdb=" O ILE B1538 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N SER B1540 " --> pdb=" O ILE B1452 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1511 through 1516 removed outlier: 6.215A pdb=" N ILE B1449 " --> pdb=" O GLU B1487 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B1489 " --> pdb=" O ILE B1449 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B1451 " --> pdb=" O THR B1489 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP B1453 " --> pdb=" O PRO B1491 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B1536 " --> pdb=" O LEU B1448 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS B1450 " --> pdb=" O LEU B1536 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE B1538 " --> pdb=" O LYS B1450 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B1452 " --> pdb=" O ILE B1538 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N SER B1540 " --> pdb=" O ILE B1452 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1850 through 1854 Processing sheet with id=AD7, first strand: chain 'B' and resid 1945 through 1949 removed outlier: 6.830A pdb=" N GLU B1874 " --> pdb=" O THR B1918 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B1914 " --> pdb=" O MET B1878 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR B1880 " --> pdb=" O GLU B1912 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU B1912 " --> pdb=" O THR B1880 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1945 through 1949 removed outlier: 4.539A pdb=" N ILE B2186 " --> pdb=" O ILE B1882 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS B2163 " --> pdb=" O VAL B2187 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B2189 " --> pdb=" O LYS B2163 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B2165 " --> pdb=" O ASP B2189 " (cutoff:3.500A) 1604 hydrogen bonds defined for protein. 4515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.51 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12795 1.34 - 1.46: 8730 1.46 - 1.58: 18399 1.58 - 1.70: 2 1.70 - 1.81: 194 Bond restraints: 40120 Sorted by residual: bond pdb=" C ASN B1056 " pdb=" N PRO B1057 " ideal model delta sigma weight residual 1.331 1.304 0.027 7.90e-03 1.60e+04 1.21e+01 bond pdb=" CA TYR A2125 " pdb=" CB TYR A2125 " ideal model delta sigma weight residual 1.527 1.500 0.027 1.30e-02 5.92e+03 4.33e+00 bond pdb=" CA TYR B2125 " pdb=" CB TYR B2125 " ideal model delta sigma weight residual 1.527 1.504 0.024 1.30e-02 5.92e+03 3.29e+00 bond pdb=" CA THR B 117 " pdb=" C THR B 117 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.37e-02 5.33e+03 2.67e+00 bond pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.37e-02 5.33e+03 2.64e+00 ... (remaining 40115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 53677 2.47 - 4.94: 540 4.94 - 7.41: 57 7.41 - 9.88: 8 9.88 - 12.35: 4 Bond angle restraints: 54286 Sorted by residual: angle pdb=" N VAL A2105 " pdb=" CA VAL A2105 " pdb=" C VAL A2105 " ideal model delta sigma weight residual 113.20 107.02 6.18 9.60e-01 1.09e+00 4.14e+01 angle pdb=" CA LYS A2037 " pdb=" CB LYS A2037 " pdb=" CG LYS A2037 " ideal model delta sigma weight residual 114.10 123.89 -9.79 2.00e+00 2.50e-01 2.40e+01 angle pdb=" CA LYS B2037 " pdb=" CB LYS B2037 " pdb=" CG LYS B2037 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 angle pdb=" N ILE B1457 " pdb=" CA ILE B1457 " pdb=" C ILE B1457 " ideal model delta sigma weight residual 113.47 108.70 4.77 1.01e+00 9.80e-01 2.23e+01 angle pdb=" N ILE A1457 " pdb=" CA ILE A1457 " pdb=" C ILE A1457 " ideal model delta sigma weight residual 113.47 108.72 4.75 1.01e+00 9.80e-01 2.21e+01 ... (remaining 54281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21120 17.93 - 35.86: 2570 35.86 - 53.79: 465 53.79 - 71.71: 87 71.71 - 89.64: 58 Dihedral angle restraints: 24300 sinusoidal: 9718 harmonic: 14582 Sorted by residual: dihedral pdb=" CA TYR B 144 " pdb=" C TYR B 144 " pdb=" N ILE B 145 " pdb=" CA ILE B 145 " ideal model delta harmonic sigma weight residual -180.00 -143.21 -36.79 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA TYR A 144 " pdb=" C TYR A 144 " pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta harmonic sigma weight residual 180.00 -144.13 -35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA THR A1288 " pdb=" C THR A1288 " pdb=" N SER A1289 " pdb=" CA SER A1289 " ideal model delta harmonic sigma weight residual 0.00 28.81 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 24297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4979 0.056 - 0.112: 1107 0.112 - 0.168: 69 0.168 - 0.223: 5 0.223 - 0.279: 4 Chirality restraints: 6164 Sorted by residual: chirality pdb=" CG LEU A 874 " pdb=" CB LEU A 874 " pdb=" CD1 LEU A 874 " pdb=" CD2 LEU A 874 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA VAL A1291 " pdb=" N VAL A1291 " pdb=" C VAL A1291 " pdb=" CB VAL A1291 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL B1291 " pdb=" N VAL B1291 " pdb=" C VAL B1291 " pdb=" CB VAL B1291 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 6161 not shown) Planarity restraints: 6990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A2199 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A2200 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A2200 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2200 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 890 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 891 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 891 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 891 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 890 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 891 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 891 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 891 " 0.026 5.00e-02 4.00e+02 ... (remaining 6987 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 20563 2.97 - 3.45: 42010 3.45 - 3.93: 65280 3.93 - 4.42: 76634 4.42 - 4.90: 119639 Nonbonded interactions: 324126 Sorted by model distance: nonbonded pdb=" O THR A 177 " pdb=" OG1 THR A 177 " model vdw 2.483 3.040 nonbonded pdb=" O THR B 177 " pdb=" OG1 THR B 177 " model vdw 2.485 3.040 nonbonded pdb=" O ASP A2129 " pdb=" OD1 ASP A2129 " model vdw 2.499 3.040 nonbonded pdb=" O LEU A2114 " pdb=" OG SER B2113 " model vdw 2.499 3.040 nonbonded pdb=" OE1 GLU A2061 " pdb=" OD1 ASN B1056 " model vdw 2.522 3.040 ... (remaining 324121 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 43.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.004 0.045 40120 Z= 0.191 Angle : 0.673 12.353 54286 Z= 0.387 Chirality : 0.044 0.279 6164 Planarity : 0.004 0.048 6990 Dihedral : 16.102 89.643 14888 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.66 % Allowed : 16.92 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4988 helix: -0.28 (0.12), residues: 1860 sheet: -1.63 (0.19), residues: 732 loop : -1.54 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1049 TYR 0.016 0.001 TYR A 144 PHE 0.027 0.001 PHE B1780 TRP 0.010 0.002 TRP A 105 HIS 0.021 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00393 (40120) covalent geometry : angle 0.67284 (54286) hydrogen bonds : bond 0.16111 ( 1566) hydrogen bonds : angle 7.13836 ( 4515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 178 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: A 130 MET cc_start: 0.6421 (ptm) cc_final: 0.5297 (ptm) REVERT: A 358 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 429 MET cc_start: 0.9348 (mmm) cc_final: 0.9130 (mtt) REVERT: A 569 GLU cc_start: 0.8009 (mp0) cc_final: 0.7231 (mp0) REVERT: A 674 MET cc_start: 0.6161 (mtt) cc_final: 0.5691 (mmt) REVERT: A 750 MET cc_start: 0.7875 (ptt) cc_final: 0.7309 (ptt) REVERT: A 798 MET cc_start: 0.8404 (tpp) cc_final: 0.7566 (mmp) REVERT: A 1087 LEU cc_start: 0.9247 (tt) cc_final: 0.8790 (mm) REVERT: A 1512 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6986 (p0) REVERT: A 1736 MET cc_start: 0.8314 (tpt) cc_final: 0.7869 (tpt) REVERT: A 1780 PHE cc_start: 0.6816 (m-80) cc_final: 0.6161 (m-80) REVERT: A 2122 HIS cc_start: 0.6801 (m-70) cc_final: 0.6361 (m170) REVERT: A 2487 MET cc_start: 0.7735 (mtm) cc_final: 0.7328 (mpp) REVERT: B 108 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: B 167 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7998 (t0) REVERT: B 429 MET cc_start: 0.9338 (mmm) cc_final: 0.9089 (mtt) REVERT: B 569 GLU cc_start: 0.7991 (mp0) cc_final: 0.7216 (mp0) REVERT: B 750 MET cc_start: 0.7598 (ptt) cc_final: 0.7110 (ptt) REVERT: B 798 MET cc_start: 0.8390 (tpp) cc_final: 0.7564 (mmp) REVERT: B 1087 LEU cc_start: 0.9253 (tt) cc_final: 0.8805 (mm) REVERT: B 1736 MET cc_start: 0.8266 (tpt) cc_final: 0.7814 (tpt) REVERT: B 1863 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8135 (mm-40) REVERT: B 2487 MET cc_start: 0.7740 (mtm) cc_final: 0.7322 (mpp) outliers start: 75 outliers final: 56 residues processed: 237 average time/residue: 0.2256 time to fit residues: 93.3448 Evaluate side-chains 226 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2083 SER Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2219 HIS Chi-restraints excluded: chain A residue 2245 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1293 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1863 GLN Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 2083 SER Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2219 HIS Chi-restraints excluded: chain B residue 2245 ILE Chi-restraints excluded: chain B residue 2452 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 295 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 830 HIS ** A1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 ASN A1581 ASN A1691 ASN A1853 ASN A2019 HIS ** A2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2212 ASN A2387 GLN ** A2482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 295 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN B1423 ASN B1581 ASN B1691 ASN B1853 ASN B1959 ASN B2019 HIS ** B2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2387 GLN ** B2482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.114353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.086336 restraints weight = 131476.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085203 restraints weight = 94610.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085412 restraints weight = 73531.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085708 restraints weight = 73015.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086079 restraints weight = 56725.286| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40120 Z= 0.127 Angle : 0.555 7.643 54286 Z= 0.299 Chirality : 0.043 0.218 6164 Planarity : 0.004 0.048 6990 Dihedral : 6.739 58.054 5396 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.46 % Allowed : 16.90 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 4988 helix: -0.04 (0.12), residues: 1880 sheet: -1.52 (0.18), residues: 752 loop : -1.46 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1049 TYR 0.015 0.001 TYR A1082 PHE 0.020 0.001 PHE B1777 TRP 0.013 0.001 TRP B 558 HIS 0.008 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00273 (40120) covalent geometry : angle 0.55543 (54286) hydrogen bonds : bond 0.04497 ( 1566) hydrogen bonds : angle 5.47463 ( 4515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 207 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: A 167 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 308 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7652 (t) REVERT: A 429 MET cc_start: 0.9231 (mmm) cc_final: 0.8766 (mtt) REVERT: A 466 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 569 GLU cc_start: 0.8055 (mp0) cc_final: 0.7334 (mp0) REVERT: A 674 MET cc_start: 0.6074 (mtt) cc_final: 0.5566 (mmt) REVERT: A 750 MET cc_start: 0.7546 (ptt) cc_final: 0.6769 (ptt) REVERT: A 825 LEU cc_start: 0.8639 (tp) cc_final: 0.8389 (tp) REVERT: A 880 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 1087 LEU cc_start: 0.9086 (tt) cc_final: 0.8757 (mm) REVERT: A 1317 LEU cc_start: 0.8168 (tp) cc_final: 0.7938 (pp) REVERT: A 1478 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6110 (pp) REVERT: A 1512 ASN cc_start: 0.7452 (t0) cc_final: 0.6878 (p0) REVERT: A 1624 GLU cc_start: -0.1655 (OUTLIER) cc_final: -0.2935 (tt0) REVERT: A 1686 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: A 1736 MET cc_start: 0.8258 (tpt) cc_final: 0.7806 (tpt) REVERT: A 1780 PHE cc_start: 0.6676 (m-80) cc_final: 0.6204 (m-80) REVERT: A 2122 HIS cc_start: 0.6864 (m-70) cc_final: 0.6342 (m-70) REVERT: A 2130 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 2487 MET cc_start: 0.8212 (mtm) cc_final: 0.7808 (mpp) REVERT: B 108 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: B 308 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 340 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8897 (p) REVERT: B 429 MET cc_start: 0.9229 (mmm) cc_final: 0.8765 (mtt) REVERT: B 466 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 569 GLU cc_start: 0.8059 (mp0) cc_final: 0.7325 (mp0) REVERT: B 674 MET cc_start: 0.6564 (mmm) cc_final: 0.6268 (mmm) REVERT: B 750 MET cc_start: 0.7544 (ptt) cc_final: 0.6936 (ptt) REVERT: B 793 TYR cc_start: 0.7444 (t80) cc_final: 0.7039 (t80) REVERT: B 836 TYR cc_start: 0.7783 (m-80) cc_final: 0.7242 (m-80) REVERT: B 880 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8380 (tm-30) REVERT: B 1087 LEU cc_start: 0.9097 (tt) cc_final: 0.8775 (mm) REVERT: B 1478 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6131 (pp) REVERT: B 1624 GLU cc_start: -0.1731 (OUTLIER) cc_final: -0.2973 (tt0) REVERT: B 1686 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: B 1729 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: B 1736 MET cc_start: 0.8203 (tpt) cc_final: 0.7772 (tpt) REVERT: B 1780 PHE cc_start: 0.6850 (m-80) cc_final: 0.6464 (m-80) REVERT: B 2130 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8093 (mm) REVERT: B 2487 MET cc_start: 0.8180 (mtm) cc_final: 0.7771 (mpp) outliers start: 111 outliers final: 50 residues processed: 305 average time/residue: 0.2184 time to fit residues: 116.0311 Evaluate side-chains 234 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1293 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2130 LEU Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 70 optimal weight: 0.0970 chunk 394 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 97 optimal weight: 0.0050 chunk 365 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 372 optimal weight: 8.9990 chunk 278 optimal weight: 0.4980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS ** A1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 ASN A1512 ASN A1691 ASN A1853 ASN A1959 ASN A2019 HIS ** A2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN B 160 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN B1300 ASN B1404 ASN B1691 ASN B1853 ASN B1959 ASN B2019 HIS ** B2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN B2212 ASN B2482 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.115459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087039 restraints weight = 132232.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086039 restraints weight = 95281.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086772 restraints weight = 70319.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087018 restraints weight = 60370.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087250 restraints weight = 52750.432| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 40120 Z= 0.107 Angle : 0.527 8.318 54286 Z= 0.282 Chirality : 0.042 0.193 6164 Planarity : 0.003 0.049 6990 Dihedral : 5.990 58.520 5341 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.77 % Allowed : 17.60 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: -1.19 (0.12), residues: 4988 helix: 0.20 (0.12), residues: 1868 sheet: -1.38 (0.18), residues: 768 loop : -1.34 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2132 TYR 0.014 0.001 TYR B1082 PHE 0.020 0.001 PHE B1777 TRP 0.009 0.001 TRP A 105 HIS 0.008 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00229 (40120) covalent geometry : angle 0.52735 (54286) hydrogen bonds : bond 0.03731 ( 1566) hydrogen bonds : angle 5.02108 ( 4515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 205 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: A 167 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 308 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7551 (t) REVERT: A 340 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 429 MET cc_start: 0.9243 (mmm) cc_final: 0.8810 (mtt) REVERT: A 466 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 500 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8051 (mm-40) REVERT: A 561 MET cc_start: 0.8195 (mmt) cc_final: 0.7767 (mmm) REVERT: A 569 GLU cc_start: 0.8124 (mp0) cc_final: 0.7358 (mp0) REVERT: A 674 MET cc_start: 0.6248 (mtt) cc_final: 0.5808 (mmt) REVERT: A 750 MET cc_start: 0.7649 (ptt) cc_final: 0.6932 (ptt) REVERT: A 798 MET cc_start: 0.8786 (tpp) cc_final: 0.8010 (mmp) REVERT: A 836 TYR cc_start: 0.7795 (m-80) cc_final: 0.6864 (m-10) REVERT: A 930 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: A 1087 LEU cc_start: 0.9078 (tt) cc_final: 0.8710 (mm) REVERT: A 1317 LEU cc_start: 0.7472 (tp) cc_final: 0.7268 (pp) REVERT: A 1478 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6481 (pp) REVERT: A 1512 ASN cc_start: 0.7414 (t0) cc_final: 0.6796 (p0) REVERT: A 1571 MET cc_start: 0.5702 (mtm) cc_final: 0.5151 (mpp) REVERT: A 1686 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 1736 MET cc_start: 0.8203 (tpt) cc_final: 0.7758 (tpt) REVERT: A 1759 TYR cc_start: 0.8312 (t80) cc_final: 0.8028 (t80) REVERT: A 1780 PHE cc_start: 0.6557 (m-80) cc_final: 0.6071 (m-80) REVERT: A 1807 LEU cc_start: 0.8805 (mt) cc_final: 0.8598 (mt) REVERT: A 2122 HIS cc_start: 0.6815 (m-70) cc_final: 0.6152 (m-70) REVERT: A 2130 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 2487 MET cc_start: 0.8146 (mtm) cc_final: 0.7655 (mpp) REVERT: A 2494 TYR cc_start: 0.4739 (t80) cc_final: 0.4415 (t80) REVERT: B 108 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 308 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7465 (t) REVERT: B 429 MET cc_start: 0.9251 (mmm) cc_final: 0.8788 (mtt) REVERT: B 466 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 500 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: B 561 MET cc_start: 0.8205 (mmt) cc_final: 0.7779 (mmm) REVERT: B 569 GLU cc_start: 0.8118 (mp0) cc_final: 0.7353 (mp0) REVERT: B 674 MET cc_start: 0.6433 (mmm) cc_final: 0.6056 (mmm) REVERT: B 750 MET cc_start: 0.7398 (ptt) cc_final: 0.6752 (ptt) REVERT: B 798 MET cc_start: 0.8766 (tpp) cc_final: 0.8016 (mmp) REVERT: B 836 TYR cc_start: 0.7759 (m-80) cc_final: 0.6852 (m-10) REVERT: B 880 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 930 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7631 (ttm) REVERT: B 1087 LEU cc_start: 0.9093 (tt) cc_final: 0.8652 (mm) REVERT: B 1317 LEU cc_start: 0.8151 (tp) cc_final: 0.7947 (pp) REVERT: B 1478 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6481 (pp) REVERT: B 1571 MET cc_start: 0.5460 (mtm) cc_final: 0.4979 (mpp) REVERT: B 1686 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: B 1736 MET cc_start: 0.8187 (tpt) cc_final: 0.7791 (tpt) REVERT: B 1759 TYR cc_start: 0.8304 (t80) cc_final: 0.8015 (t80) REVERT: B 1780 PHE cc_start: 0.6648 (m-80) cc_final: 0.6331 (m-80) REVERT: B 2130 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7996 (mm) REVERT: B 2338 ASP cc_start: 0.8706 (t0) cc_final: 0.8399 (t0) REVERT: B 2487 MET cc_start: 0.8049 (mtm) cc_final: 0.7782 (mpp) outliers start: 125 outliers final: 67 residues processed: 313 average time/residue: 0.2192 time to fit residues: 120.0710 Evaluate side-chains 254 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 169 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1256 PHE Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2482 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2130 LEU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2482 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 484 optimal weight: 9.9990 chunk 290 optimal weight: 8.9990 chunk 433 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 70 optimal weight: 0.0070 chunk 298 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 420 optimal weight: 20.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN A 962 HIS A1590 GLN A1635 GLN A1691 ASN A1853 ASN A2019 HIS ** A2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2212 ASN A2482 GLN B 160 ASN B 484 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B 830 HIS B 962 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1590 GLN B1635 GLN B1691 ASN ** B1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS ** B2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2212 ASN ** B2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2482 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.112332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083630 restraints weight = 131487.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082621 restraints weight = 93996.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083154 restraints weight = 71862.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083459 restraints weight = 68273.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083608 restraints weight = 54468.321| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 40120 Z= 0.255 Angle : 0.632 8.190 54286 Z= 0.335 Chirality : 0.045 0.229 6164 Planarity : 0.004 0.044 6990 Dihedral : 6.309 59.424 5331 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.83 % Allowed : 18.58 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.24 (0.12), residues: 4988 helix: 0.17 (0.12), residues: 1862 sheet: -1.23 (0.19), residues: 748 loop : -1.45 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2132 TYR 0.023 0.002 TYR B2136 PHE 0.028 0.002 PHE B1777 TRP 0.013 0.002 TRP A1042 HIS 0.013 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00563 (40120) covalent geometry : angle 0.63156 (54286) hydrogen bonds : bond 0.04164 ( 1566) hydrogen bonds : angle 5.17071 ( 4515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 183 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: A 167 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7929 (t0) REVERT: A 308 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.7550 (t) REVERT: A 340 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9049 (p) REVERT: A 429 MET cc_start: 0.9223 (mmm) cc_final: 0.8861 (mtt) REVERT: A 466 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 500 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: A 561 MET cc_start: 0.8909 (mmt) cc_final: 0.8521 (mmm) REVERT: A 569 GLU cc_start: 0.8337 (mp0) cc_final: 0.7467 (mp0) REVERT: A 750 MET cc_start: 0.7274 (ptt) cc_final: 0.6705 (ptt) REVERT: A 793 TYR cc_start: 0.7587 (t80) cc_final: 0.7236 (t80) REVERT: A 836 TYR cc_start: 0.7837 (m-80) cc_final: 0.6888 (m-10) REVERT: A 930 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7597 (ttm) REVERT: A 1087 LEU cc_start: 0.9120 (tt) cc_final: 0.8831 (mm) REVERT: A 1478 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6560 (pp) REVERT: A 1512 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6835 (p0) REVERT: A 1571 MET cc_start: 0.5896 (mtm) cc_final: 0.5322 (mpp) REVERT: A 1686 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: A 1759 TYR cc_start: 0.8217 (t80) cc_final: 0.8015 (t80) REVERT: A 2122 HIS cc_start: 0.7222 (m-70) cc_final: 0.6505 (m-70) REVERT: A 2132 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7648 (mtt180) REVERT: A 2487 MET cc_start: 0.8046 (mtm) cc_final: 0.7675 (mpp) REVERT: B 108 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 308 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.7523 (t) REVERT: B 340 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 429 MET cc_start: 0.9226 (mmm) cc_final: 0.8860 (mtt) REVERT: B 466 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 500 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8033 (mm-40) REVERT: B 561 MET cc_start: 0.8931 (mmt) cc_final: 0.8547 (mmm) REVERT: B 569 GLU cc_start: 0.8324 (mp0) cc_final: 0.7455 (mp0) REVERT: B 750 MET cc_start: 0.7204 (ptt) cc_final: 0.6572 (ptt) REVERT: B 793 TYR cc_start: 0.7662 (t80) cc_final: 0.7227 (t80) REVERT: B 836 TYR cc_start: 0.7900 (m-80) cc_final: 0.6857 (m-10) REVERT: B 930 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7597 (ttm) REVERT: B 1087 LEU cc_start: 0.9128 (tt) cc_final: 0.8844 (mm) REVERT: B 1478 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6577 (pp) REVERT: B 1512 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7122 (p0) REVERT: B 1686 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: B 1729 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: B 2338 ASP cc_start: 0.8774 (t0) cc_final: 0.8512 (t0) REVERT: B 2339 ILE cc_start: 0.8523 (mt) cc_final: 0.8320 (mt) REVERT: B 2487 MET cc_start: 0.7984 (mtm) cc_final: 0.7580 (mpp) outliers start: 173 outliers final: 108 residues processed: 340 average time/residue: 0.2216 time to fit residues: 132.0048 Evaluate side-chains 283 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 155 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1482 ASN Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1512 ASN Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1791 ILE Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2121 TYR Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2192 ASN Chi-restraints excluded: chain A residue 2219 HIS Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1293 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1512 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1635 GLN Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1691 ASN Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1791 ILE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1837 LEU Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2192 ASN Chi-restraints excluded: chain B residue 2219 HIS Chi-restraints excluded: chain B residue 2452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 221 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 332 optimal weight: 0.1980 chunk 482 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 463 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 431 optimal weight: 20.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS A1404 ASN A1635 GLN A1691 ASN A1853 ASN ** A1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 HIS ** A2111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2462 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1635 GLN B1691 ASN ** B1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS B2111 ASN ** B2122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2462 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.113773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085553 restraints weight = 130873.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084070 restraints weight = 97285.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.084691 restraints weight = 73737.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084880 restraints weight = 63916.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086105 restraints weight = 54300.612| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40120 Z= 0.146 Angle : 0.567 13.527 54286 Z= 0.300 Chirality : 0.043 0.259 6164 Planarity : 0.004 0.046 6990 Dihedral : 6.121 59.568 5331 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.39 % Allowed : 19.88 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.11 (0.12), residues: 4988 helix: 0.25 (0.12), residues: 1866 sheet: -1.12 (0.19), residues: 730 loop : -1.37 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2132 TYR 0.015 0.001 TYR B1082 PHE 0.041 0.001 PHE A1780 TRP 0.010 0.001 TRP B 105 HIS 0.009 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00324 (40120) covalent geometry : angle 0.56736 (54286) hydrogen bonds : bond 0.03804 ( 1566) hydrogen bonds : angle 4.99989 ( 4515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 174 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 308 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.7482 (t) REVERT: A 340 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9049 (p) REVERT: A 429 MET cc_start: 0.9234 (mmm) cc_final: 0.8714 (mtt) REVERT: A 466 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 500 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7820 (mm-40) REVERT: A 561 MET cc_start: 0.8096 (mmt) cc_final: 0.7566 (mmm) REVERT: A 569 GLU cc_start: 0.8168 (mp0) cc_final: 0.7383 (mp0) REVERT: A 750 MET cc_start: 0.7341 (ptt) cc_final: 0.6863 (ptt) REVERT: A 798 MET cc_start: 0.8585 (tpp) cc_final: 0.7877 (tpp) REVERT: A 836 TYR cc_start: 0.7819 (m-80) cc_final: 0.6772 (m-80) REVERT: A 1087 LEU cc_start: 0.9010 (tt) cc_final: 0.8775 (mm) REVERT: A 1478 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6498 (pp) REVERT: A 1571 MET cc_start: 0.5642 (mtm) cc_final: 0.5139 (mpp) REVERT: A 1686 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: A 2085 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 2092 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.9084 (ttm110) REVERT: A 2130 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 2132 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7058 (mtt180) REVERT: A 2487 MET cc_start: 0.8027 (mtm) cc_final: 0.7688 (mpp) REVERT: B 108 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: B 308 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7451 (t) REVERT: B 340 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9038 (p) REVERT: B 429 MET cc_start: 0.9246 (mmm) cc_final: 0.8707 (mtt) REVERT: B 466 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8460 (p) REVERT: B 500 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7910 (mm-40) REVERT: B 561 MET cc_start: 0.8116 (mmt) cc_final: 0.7583 (mmm) REVERT: B 569 GLU cc_start: 0.8156 (mp0) cc_final: 0.7382 (mp0) REVERT: B 674 MET cc_start: 0.6777 (mmm) cc_final: 0.6575 (mmm) REVERT: B 750 MET cc_start: 0.7130 (ptt) cc_final: 0.6607 (ptt) REVERT: B 793 TYR cc_start: 0.7551 (t80) cc_final: 0.7137 (t80) REVERT: B 836 TYR cc_start: 0.7785 (m-80) cc_final: 0.6710 (m-10) REVERT: B 1087 LEU cc_start: 0.9024 (tt) cc_final: 0.8782 (mm) REVERT: B 1478 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6506 (pp) REVERT: B 1571 MET cc_start: 0.5316 (mtm) cc_final: 0.4769 (mpp) REVERT: B 1686 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: B 1729 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 2122 HIS cc_start: 0.7220 (m-70) cc_final: 0.6592 (m-70) REVERT: B 2338 ASP cc_start: 0.8768 (t0) cc_final: 0.8521 (t0) REVERT: B 2339 ILE cc_start: 0.8615 (mt) cc_final: 0.8390 (mt) REVERT: B 2487 MET cc_start: 0.8190 (mtm) cc_final: 0.7683 (mpp) outliers start: 153 outliers final: 107 residues processed: 316 average time/residue: 0.2225 time to fit residues: 122.9009 Evaluate side-chains 284 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 159 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1482 ASN Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2085 ASP Chi-restraints excluded: chain A residue 2092 ARG Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2482 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1293 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1466 LEU Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1635 GLN Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1691 ASN Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2245 ILE Chi-restraints excluded: chain B residue 2382 ILE Chi-restraints excluded: chain B residue 2482 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 111 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 395 optimal weight: 9.9990 chunk 459 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 175 optimal weight: 20.0000 chunk 392 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 429 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS A1635 GLN A1691 ASN A2019 HIS A2111 ASN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1635 GLN B1691 ASN ** B1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS ** B2122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.114123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085361 restraints weight = 131035.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084541 restraints weight = 94837.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084894 restraints weight = 70425.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085253 restraints weight = 65512.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085587 restraints weight = 54216.282| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40120 Z= 0.138 Angle : 0.559 13.510 54286 Z= 0.294 Chirality : 0.043 0.232 6164 Planarity : 0.003 0.045 6990 Dihedral : 5.983 59.188 5327 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.26 % Allowed : 19.93 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.01 (0.12), residues: 4988 helix: 0.37 (0.12), residues: 1858 sheet: -1.11 (0.19), residues: 728 loop : -1.32 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2132 TYR 0.014 0.001 TYR B1082 PHE 0.027 0.001 PHE A2149 TRP 0.011 0.001 TRP A 105 HIS 0.008 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00307 (40120) covalent geometry : angle 0.55875 (54286) hydrogen bonds : bond 0.03694 ( 1566) hydrogen bonds : angle 4.93331 ( 4515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 176 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 308 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.7529 (t) REVERT: A 340 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9027 (p) REVERT: A 429 MET cc_start: 0.9235 (mmm) cc_final: 0.8748 (mtt) REVERT: A 466 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 500 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: A 561 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7510 (mmm) REVERT: A 569 GLU cc_start: 0.8202 (mp0) cc_final: 0.7374 (mp0) REVERT: A 674 MET cc_start: 0.6672 (mtt) cc_final: 0.5702 (mmt) REVERT: A 750 MET cc_start: 0.7481 (ptt) cc_final: 0.7025 (ptt) REVERT: A 793 TYR cc_start: 0.7805 (t80) cc_final: 0.7407 (t80) REVERT: A 836 TYR cc_start: 0.7774 (m-80) cc_final: 0.6723 (m-10) REVERT: A 1087 LEU cc_start: 0.9065 (tt) cc_final: 0.8743 (mm) REVERT: A 1478 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6535 (pp) REVERT: A 1571 MET cc_start: 0.5712 (mtm) cc_final: 0.5193 (mpp) REVERT: A 1686 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: A 1783 PHE cc_start: 0.7380 (m-80) cc_final: 0.6993 (m-80) REVERT: A 2085 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 2092 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9014 (ttm110) REVERT: A 2487 MET cc_start: 0.8041 (mtm) cc_final: 0.7644 (mpp) REVERT: B 108 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: B 308 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7477 (t) REVERT: B 340 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9022 (p) REVERT: B 429 MET cc_start: 0.9247 (mmm) cc_final: 0.8728 (mtt) REVERT: B 466 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 500 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: B 569 GLU cc_start: 0.8185 (mp0) cc_final: 0.7361 (mp0) REVERT: B 674 MET cc_start: 0.7122 (mmm) cc_final: 0.6782 (mmm) REVERT: B 750 MET cc_start: 0.7240 (ptt) cc_final: 0.6770 (ptt) REVERT: B 798 MET cc_start: 0.8345 (tpp) cc_final: 0.7552 (mmp) REVERT: B 836 TYR cc_start: 0.7746 (m-80) cc_final: 0.6672 (m-10) REVERT: B 880 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 1087 LEU cc_start: 0.9070 (tt) cc_final: 0.8743 (mm) REVERT: B 1478 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6556 (pp) REVERT: B 1571 MET cc_start: 0.5463 (mtm) cc_final: 0.4891 (mpp) REVERT: B 1644 MET cc_start: 0.6662 (mpp) cc_final: 0.6152 (mpp) REVERT: B 1686 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: B 1729 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: B 2092 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.9099 (ttm110) REVERT: B 2122 HIS cc_start: 0.7286 (m-70) cc_final: 0.7086 (m-70) REVERT: B 2339 ILE cc_start: 0.8603 (mt) cc_final: 0.8375 (mt) REVERT: B 2487 MET cc_start: 0.8195 (mtm) cc_final: 0.7620 (mpp) outliers start: 147 outliers final: 106 residues processed: 306 average time/residue: 0.2244 time to fit residues: 119.1438 Evaluate side-chains 286 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 161 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2085 ASP Chi-restraints excluded: chain A residue 2092 ARG Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2482 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1466 LEU Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1635 GLN Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1691 ASN Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2092 ARG Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2382 ILE Chi-restraints excluded: chain B residue 2482 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 198 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 483 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 410 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS A1512 ASN ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 GLN ** A1870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 ASN A2019 HIS A2044 GLN A2257 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1460 ASN B1635 GLN ** B1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS B2257 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.111978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.083728 restraints weight = 131537.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082668 restraints weight = 93956.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082991 restraints weight = 70127.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083451 restraints weight = 60993.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083535 restraints weight = 53493.171| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 40120 Z= 0.254 Angle : 0.645 13.240 54286 Z= 0.338 Chirality : 0.045 0.273 6164 Planarity : 0.004 0.045 6990 Dihedral : 6.201 58.913 5327 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.88 % Allowed : 20.28 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.21 (0.12), residues: 4988 helix: 0.20 (0.12), residues: 1872 sheet: -1.22 (0.19), residues: 738 loop : -1.46 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.023 0.002 TYR B2136 PHE 0.050 0.002 PHE B1780 TRP 0.013 0.002 TRP A1042 HIS 0.008 0.001 HIS A2182 Details of bonding type rmsd covalent geometry : bond 0.00563 (40120) covalent geometry : angle 0.64527 (54286) hydrogen bonds : bond 0.04087 ( 1566) hydrogen bonds : angle 5.13742 ( 4515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 162 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 308 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.7499 (t) REVERT: A 340 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9055 (p) REVERT: A 429 MET cc_start: 0.9227 (mmm) cc_final: 0.8775 (mtt) REVERT: A 466 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 500 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: A 569 GLU cc_start: 0.8245 (mp0) cc_final: 0.7482 (mp0) REVERT: A 674 MET cc_start: 0.6656 (mtt) cc_final: 0.5730 (mmt) REVERT: A 750 MET cc_start: 0.7450 (ptt) cc_final: 0.7022 (ptt) REVERT: A 793 TYR cc_start: 0.7610 (t80) cc_final: 0.7141 (t80) REVERT: A 798 MET cc_start: 0.8356 (tpp) cc_final: 0.7566 (mmp) REVERT: A 836 TYR cc_start: 0.7855 (m-80) cc_final: 0.6736 (m-10) REVERT: A 871 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8446 (tp) REVERT: A 1087 LEU cc_start: 0.9041 (tt) cc_final: 0.8840 (mm) REVERT: A 1478 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6579 (pp) REVERT: A 1783 PHE cc_start: 0.7381 (m-80) cc_final: 0.7016 (m-80) REVERT: A 2105 VAL cc_start: 0.8430 (t) cc_final: 0.8093 (p) REVERT: A 2130 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 2487 MET cc_start: 0.7982 (mtm) cc_final: 0.7522 (mpp) REVERT: B 108 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 130 MET cc_start: 0.6325 (ptm) cc_final: 0.5832 (ptm) REVERT: B 308 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7474 (t) REVERT: B 340 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9051 (p) REVERT: B 429 MET cc_start: 0.9221 (mmm) cc_final: 0.8752 (mtt) REVERT: B 466 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 500 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: B 569 GLU cc_start: 0.8249 (mp0) cc_final: 0.7471 (mp0) REVERT: B 674 MET cc_start: 0.6475 (mmm) cc_final: 0.6186 (mmm) REVERT: B 750 MET cc_start: 0.7204 (ptt) cc_final: 0.6638 (ptt) REVERT: B 836 TYR cc_start: 0.7831 (m-80) cc_final: 0.6689 (m-10) REVERT: B 871 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (tp) REVERT: B 1028 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8778 (ttmm) REVERT: B 1478 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6589 (pp) REVERT: B 1571 MET cc_start: 0.5511 (mtm) cc_final: 0.4966 (mpp) REVERT: B 1644 MET cc_start: 0.6512 (mpp) cc_final: 0.5993 (mpp) REVERT: B 1729 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: B 2487 MET cc_start: 0.7997 (mtm) cc_final: 0.7534 (mpp) outliers start: 175 outliers final: 127 residues processed: 325 average time/residue: 0.2159 time to fit residues: 123.0786 Evaluate side-chains 299 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 155 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1155 ASP Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1482 ASN Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2092 ARG Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2121 TYR Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2164 VAL Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2192 ASN Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2482 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1014 HIS Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1466 LEU Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1691 ASN Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1777 PHE Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2092 ARG Chi-restraints excluded: chain B residue 2097 VAL Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2164 VAL Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2192 ASN Chi-restraints excluded: chain B residue 2245 ILE Chi-restraints excluded: chain B residue 2382 ILE Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2482 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 492 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 468 optimal weight: 0.9990 chunk 273 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 391 optimal weight: 30.0000 chunk 453 optimal weight: 2.9990 chunk 471 optimal weight: 0.9990 chunk 486 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS A1635 GLN A2019 HIS ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1460 ASN B1863 GLN B2019 HIS ** B2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.112960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085160 restraints weight = 131353.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083415 restraints weight = 105144.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083721 restraints weight = 81687.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083948 restraints weight = 74120.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084600 restraints weight = 61724.877| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 40120 Z= 0.183 Angle : 0.599 14.070 54286 Z= 0.313 Chirality : 0.044 0.259 6164 Planarity : 0.004 0.059 6990 Dihedral : 6.073 59.215 5324 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.54 % Allowed : 20.95 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4988 helix: 0.25 (0.12), residues: 1872 sheet: -1.21 (0.19), residues: 734 loop : -1.40 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.020 0.001 TYR B 793 PHE 0.051 0.002 PHE B1780 TRP 0.011 0.002 TRP A 105 HIS 0.008 0.001 HIS B2122 Details of bonding type rmsd covalent geometry : bond 0.00406 (40120) covalent geometry : angle 0.59854 (54286) hydrogen bonds : bond 0.03855 ( 1566) hydrogen bonds : angle 5.03182 ( 4515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 164 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: A 173 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8823 (ptm) REVERT: A 191 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: A 308 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7574 (t) REVERT: A 340 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9035 (p) REVERT: A 358 GLU cc_start: 0.8110 (tt0) cc_final: 0.7510 (tt0) REVERT: A 429 MET cc_start: 0.9236 (mmm) cc_final: 0.8697 (mtt) REVERT: A 466 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8516 (p) REVERT: A 500 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: A 561 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: A 569 GLU cc_start: 0.8292 (mp0) cc_final: 0.7469 (mp0) REVERT: A 674 MET cc_start: 0.6664 (mtt) cc_final: 0.5783 (mmt) REVERT: A 750 MET cc_start: 0.7433 (ptt) cc_final: 0.7004 (ptt) REVERT: A 793 TYR cc_start: 0.7771 (t80) cc_final: 0.7301 (t80) REVERT: A 798 MET cc_start: 0.8378 (tpp) cc_final: 0.7415 (tpp) REVERT: A 836 TYR cc_start: 0.7804 (m-80) cc_final: 0.6677 (m-10) REVERT: A 930 MET cc_start: 0.8935 (tpp) cc_final: 0.8700 (tpp) REVERT: A 1087 LEU cc_start: 0.9094 (tt) cc_final: 0.8821 (mm) REVERT: A 1478 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6541 (pp) REVERT: A 1644 MET cc_start: 0.6385 (mpp) cc_final: 0.5840 (mpp) REVERT: A 1783 PHE cc_start: 0.7347 (m-80) cc_final: 0.6998 (m-80) REVERT: A 2092 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.9011 (ttm110) REVERT: A 2105 VAL cc_start: 0.8395 (t) cc_final: 0.8094 (p) REVERT: A 2130 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 2487 MET cc_start: 0.7963 (mtm) cc_final: 0.7487 (mpp) REVERT: B 108 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: B 173 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8867 (ptm) REVERT: B 308 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.7539 (t) REVERT: B 340 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9038 (p) REVERT: B 429 MET cc_start: 0.9235 (mmm) cc_final: 0.8699 (mtt) REVERT: B 466 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 500 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: B 569 GLU cc_start: 0.8289 (mp0) cc_final: 0.7470 (mp0) REVERT: B 674 MET cc_start: 0.6492 (mmm) cc_final: 0.6226 (mmm) REVERT: B 750 MET cc_start: 0.7330 (ptt) cc_final: 0.6898 (ptt) REVERT: B 793 TYR cc_start: 0.7015 (t80) cc_final: 0.6717 (t80) REVERT: B 798 MET cc_start: 0.8314 (tpp) cc_final: 0.7575 (mmp) REVERT: B 836 TYR cc_start: 0.7769 (m-80) cc_final: 0.6670 (m-10) REVERT: B 930 MET cc_start: 0.8800 (tpp) cc_final: 0.8341 (tpp) REVERT: B 1028 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (ttmm) REVERT: B 1478 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6565 (pp) REVERT: B 1571 MET cc_start: 0.5455 (mtm) cc_final: 0.4937 (mpp) REVERT: B 1644 MET cc_start: 0.6492 (mpp) cc_final: 0.5993 (mpp) REVERT: B 1729 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 2122 HIS cc_start: 0.6788 (m-70) cc_final: 0.6391 (m-70) REVERT: B 2487 MET cc_start: 0.7985 (mtm) cc_final: 0.7484 (mpp) outliers start: 160 outliers final: 118 residues processed: 311 average time/residue: 0.2241 time to fit residues: 122.7028 Evaluate side-chains 291 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 153 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1014 HIS Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1482 ASN Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2092 ARG Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2121 TYR Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2164 VAL Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2192 ASN Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2482 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2092 ARG Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2164 VAL Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2192 ASN Chi-restraints excluded: chain B residue 2245 ILE Chi-restraints excluded: chain B residue 2382 ILE Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2482 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 67 optimal weight: 10.0000 chunk 154 optimal weight: 40.0000 chunk 261 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS A1635 GLN ** A1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 HIS ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS ** B2257 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 = 0.3999 r_free = 0.3999 target = 0.112688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.084602 restraints weight = 131850.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083200 restraints weight = 95101.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083646 restraints weight = 73006.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083920 restraints weight = 69146.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084146 restraints weight = 56403.977| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 40120 Z= 0.191 Angle : 0.609 14.099 54286 Z= 0.317 Chirality : 0.044 0.274 6164 Planarity : 0.004 0.046 6990 Dihedral : 5.979 59.601 5320 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.19 % Allowed : 21.59 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.13 (0.12), residues: 4988 helix: 0.28 (0.12), residues: 1870 sheet: -1.20 (0.19), residues: 734 loop : -1.41 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 933 TYR 0.017 0.001 TYR B 793 PHE 0.051 0.002 PHE B1780 TRP 0.012 0.002 TRP A2243 HIS 0.009 0.001 HIS B1014 Details of bonding type rmsd covalent geometry : bond 0.00425 (40120) covalent geometry : angle 0.60887 (54286) hydrogen bonds : bond 0.03853 ( 1566) hydrogen bonds : angle 5.01022 ( 4515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 159 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: A 308 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.7572 (t) REVERT: A 340 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9042 (p) REVERT: A 358 GLU cc_start: 0.8085 (tt0) cc_final: 0.7547 (tt0) REVERT: A 429 MET cc_start: 0.9236 (mmm) cc_final: 0.8715 (mtt) REVERT: A 466 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8246 (p) REVERT: A 500 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7941 (mm-40) REVERT: A 561 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: A 569 GLU cc_start: 0.8311 (mp0) cc_final: 0.7493 (mp0) REVERT: A 674 MET cc_start: 0.6684 (mtt) cc_final: 0.5820 (mmt) REVERT: A 750 MET cc_start: 0.7442 (ptt) cc_final: 0.7014 (ptt) REVERT: A 793 TYR cc_start: 0.7788 (t80) cc_final: 0.7304 (t80) REVERT: A 836 TYR cc_start: 0.7795 (m-80) cc_final: 0.6663 (m-10) REVERT: A 871 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8424 (tp) REVERT: A 930 MET cc_start: 0.8933 (tpp) cc_final: 0.8705 (tpp) REVERT: A 951 MET cc_start: 0.8842 (mmm) cc_final: 0.8147 (mmm) REVERT: A 1087 LEU cc_start: 0.9077 (tt) cc_final: 0.8817 (mm) REVERT: A 1478 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6552 (pp) REVERT: A 1783 PHE cc_start: 0.7339 (m-80) cc_final: 0.6982 (m-80) REVERT: A 2105 VAL cc_start: 0.8291 (t) cc_final: 0.7969 (p) REVERT: A 2130 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8249 (mm) REVERT: A 2487 MET cc_start: 0.7963 (mtm) cc_final: 0.7494 (mpp) REVERT: B 108 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: B 308 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.7544 (t) REVERT: B 340 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9041 (p) REVERT: B 358 GLU cc_start: 0.8028 (tt0) cc_final: 0.7303 (tm-30) REVERT: B 429 MET cc_start: 0.9234 (mmm) cc_final: 0.8701 (mtt) REVERT: B 466 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 500 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8022 (mm-40) REVERT: B 569 GLU cc_start: 0.8309 (mp0) cc_final: 0.7479 (mp0) REVERT: B 674 MET cc_start: 0.6635 (mmm) cc_final: 0.6397 (mmm) REVERT: B 750 MET cc_start: 0.7342 (ptt) cc_final: 0.6926 (ptt) REVERT: B 793 TYR cc_start: 0.7058 (t80) cc_final: 0.6737 (t80) REVERT: B 798 MET cc_start: 0.8356 (tpp) cc_final: 0.7589 (mmp) REVERT: B 836 TYR cc_start: 0.7750 (m-80) cc_final: 0.6665 (m-10) REVERT: B 871 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 880 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 930 MET cc_start: 0.8925 (tpp) cc_final: 0.8446 (tpp) REVERT: B 951 MET cc_start: 0.8845 (mmm) cc_final: 0.8183 (mmm) REVERT: B 1028 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8659 (ttmm) REVERT: B 1478 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6573 (pp) REVERT: B 1482 ASN cc_start: 0.6540 (OUTLIER) cc_final: 0.5733 (p0) REVERT: B 1571 MET cc_start: 0.5564 (mtm) cc_final: 0.5024 (mpp) REVERT: B 1644 MET cc_start: 0.6491 (mpp) cc_final: 0.5992 (mpp) REVERT: B 1729 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: B 2122 HIS cc_start: 0.7043 (m-70) cc_final: 0.6628 (m-70) REVERT: B 2487 MET cc_start: 0.7995 (mtm) cc_final: 0.7498 (mpp) outliers start: 144 outliers final: 114 residues processed: 290 average time/residue: 0.2224 time to fit residues: 113.5828 Evaluate side-chains 292 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 159 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1192 MET Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1482 ASN Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1624 GLU Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1883 ASN Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1943 SER Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2121 TYR Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2140 ILE Chi-restraints excluded: chain A residue 2164 VAL Chi-restraints excluded: chain A residue 2187 VAL Chi-restraints excluded: chain A residue 2192 ASN Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1624 GLU Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1729 GLU Chi-restraints excluded: chain B residue 1812 THR Chi-restraints excluded: chain B residue 1883 ASN Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2132 ARG Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2164 VAL Chi-restraints excluded: chain B residue 2187 VAL Chi-restraints excluded: chain B residue 2192 ASN Chi-restraints excluded: chain B residue 2219 HIS Chi-restraints excluded: chain B residue 2245 ILE Chi-restraints excluded: chain B residue 2382 ILE Chi-restraints excluded: chain B residue 2452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 414 optimal weight: 0.0970 chunk 296 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 483 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS ** A1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 GLN ** A1995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 HIS B 160 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN B2019 HIS ** B2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.114885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086616 restraints weight = 131773.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085416 restraints weight = 97152.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086137 restraints weight = 73763.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086352 restraints weight = 69356.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086703 restraints weight = 54225.969| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40120 Z= 0.109 Angle : 0.564 14.792 54286 Z= 0.291 Chirality : 0.043 0.272 6164 Planarity : 0.003 0.045 6990 Dihedral : 5.454 54.571 5312 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.33 % Allowed : 22.45 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.12), residues: 4988 helix: 0.46 (0.12), residues: 1866 sheet: -1.07 (0.19), residues: 734 loop : -1.26 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 933 TYR 0.016 0.001 TYR B 793 PHE 0.051 0.001 PHE B1780 TRP 0.013 0.001 TRP B 105 HIS 0.006 0.001 HIS A2182 Details of bonding type rmsd covalent geometry : bond 0.00236 (40120) covalent geometry : angle 0.56368 (54286) hydrogen bonds : bond 0.03465 ( 1566) hydrogen bonds : angle 4.81198 ( 4515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 192 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: A 308 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 340 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9001 (p) REVERT: A 429 MET cc_start: 0.9261 (mmm) cc_final: 0.8690 (mtt) REVERT: A 466 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 500 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7904 (mm-40) REVERT: A 561 MET cc_start: 0.8473 (mmt) cc_final: 0.7854 (mmm) REVERT: A 674 MET cc_start: 0.6748 (mtt) cc_final: 0.5846 (mmt) REVERT: A 750 MET cc_start: 0.7436 (ptt) cc_final: 0.7056 (ptt) REVERT: A 793 TYR cc_start: 0.7909 (t80) cc_final: 0.7338 (t80) REVERT: A 798 MET cc_start: 0.8248 (tpp) cc_final: 0.7544 (mmp) REVERT: A 836 TYR cc_start: 0.7339 (m-80) cc_final: 0.6454 (m-10) REVERT: A 930 MET cc_start: 0.8865 (tpp) cc_final: 0.8622 (tpp) REVERT: A 951 MET cc_start: 0.8662 (mmm) cc_final: 0.7986 (mmm) REVERT: A 1087 LEU cc_start: 0.9031 (tt) cc_final: 0.8720 (mm) REVERT: A 1339 LYS cc_start: 0.6475 (ptmm) cc_final: 0.6182 (mmmt) REVERT: A 1478 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6491 (pp) REVERT: A 1571 MET cc_start: 0.5306 (mtm) cc_final: 0.4844 (mpp) REVERT: A 1686 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: A 1783 PHE cc_start: 0.7564 (m-80) cc_final: 0.7272 (m-80) REVERT: A 2105 VAL cc_start: 0.8253 (t) cc_final: 0.7975 (p) REVERT: A 2130 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 2487 MET cc_start: 0.8129 (mtm) cc_final: 0.7583 (mpp) REVERT: B 108 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: B 216 MET cc_start: 0.8674 (mtm) cc_final: 0.8173 (ptp) REVERT: B 308 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 327 GLU cc_start: 0.8818 (pp20) cc_final: 0.8486 (pp20) REVERT: B 340 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 429 MET cc_start: 0.9264 (mmm) cc_final: 0.8678 (mtt) REVERT: B 466 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 500 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: B 674 MET cc_start: 0.6639 (mmm) cc_final: 0.6318 (mmm) REVERT: B 750 MET cc_start: 0.7351 (ptt) cc_final: 0.6906 (ptt) REVERT: B 793 TYR cc_start: 0.7092 (t80) cc_final: 0.6804 (t80) REVERT: B 798 MET cc_start: 0.8351 (tpp) cc_final: 0.7566 (mmp) REVERT: B 836 TYR cc_start: 0.7314 (m-80) cc_final: 0.6480 (m-10) REVERT: B 951 MET cc_start: 0.8704 (mmm) cc_final: 0.8084 (mmm) REVERT: B 1028 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8535 (ttmm) REVERT: B 1478 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6505 (pp) REVERT: B 1571 MET cc_start: 0.5522 (mtm) cc_final: 0.4983 (mpp) REVERT: B 1644 MET cc_start: 0.6399 (mpp) cc_final: 0.5917 (mpp) REVERT: B 1686 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: B 2122 HIS cc_start: 0.6891 (m-70) cc_final: 0.6320 (m-70) REVERT: B 2487 MET cc_start: 0.8126 (mtm) cc_final: 0.7590 (mpp) outliers start: 105 outliers final: 72 residues processed: 287 average time/residue: 0.2262 time to fit residues: 113.8971 Evaluate side-chains 257 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 169 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 918 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1516 ARG Chi-restraints excluded: chain A residue 1614 THR Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1635 GLN Chi-restraints excluded: chain A residue 1686 GLU Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain A residue 1930 VAL Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2063 CYS Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2130 LEU Chi-restraints excluded: chain A residue 2219 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1166 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1478 LEU Chi-restraints excluded: chain B residue 1516 ARG Chi-restraints excluded: chain B residue 1614 THR Chi-restraints excluded: chain B residue 1634 VAL Chi-restraints excluded: chain B residue 1686 GLU Chi-restraints excluded: chain B residue 1930 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1992 ILE Chi-restraints excluded: chain B residue 1998 THR Chi-restraints excluded: chain B residue 2063 CYS Chi-restraints excluded: chain B residue 2121 TYR Chi-restraints excluded: chain B residue 2127 THR Chi-restraints excluded: chain B residue 2140 ILE Chi-restraints excluded: chain B residue 2219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 55 optimal weight: 10.0000 chunk 334 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 421 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 435 optimal weight: 1.9990 chunk 219 optimal weight: 0.1980 chunk 168 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 ASN ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 GLN A2019 HIS B 160 ASN B 207 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS B1056 ASN ** B1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 HIS ** B2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.111904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084465 restraints weight = 132063.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082216 restraints weight = 118016.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.082827 restraints weight = 88793.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082980 restraints weight = 78682.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083829 restraints weight = 64567.646| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 40120 Z= 0.255 Angle : 0.666 14.124 54286 Z= 0.346 Chirality : 0.046 0.264 6164 Planarity : 0.004 0.052 6990 Dihedral : 5.814 57.818 5310 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.26 % Allowed : 23.01 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.12 (0.12), residues: 4988 helix: 0.28 (0.12), residues: 1876 sheet: -1.16 (0.19), residues: 738 loop : -1.41 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 22 TYR 0.043 0.002 TYR A1458 PHE 0.053 0.002 PHE B1780 TRP 0.014 0.002 TRP A2243 HIS 0.011 0.002 HIS A1014 Details of bonding type rmsd covalent geometry : bond 0.00568 (40120) covalent geometry : angle 0.66588 (54286) hydrogen bonds : bond 0.04053 ( 1566) hydrogen bonds : angle 5.06829 ( 4515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5884.82 seconds wall clock time: 104 minutes 10.24 seconds (6250.24 seconds total)