Starting phenix.real_space_refine on Thu May 22 11:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.map" model { file = "/net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euv_19987/05_2025/9euv_19987.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 1.036 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 76 5.16 5 C 14094 2.51 5 N 3863 2.21 5 O 4258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22291 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2797, 22291 Classifications: {'peptide': 2797} Link IDs: {'PCIS': 1, 'PTRANS': 115, 'TRANS': 2680} Chain breaks: 6 Time building chain proxies: 12.42, per 1000 atoms: 0.56 Number of scatterers: 22291 At special positions: 0 Unit cell: (136.224, 218.526, 112.574, 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 76 16.00 O 4258 8.00 N 3863 7.00 C 14094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A3182 " - pdb=" SG CYS A3205 " distance=2.03 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: 5.56 Conformation dependent library (CDL) restraints added in 2.8 seconds 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 31 sheets defined 43.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 241 through 257 removed outlier: 3.820A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.265A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.738A pdb=" N PHE A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 378 removed outlier: 3.667A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.797A pdb=" N ASN A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 422 through 452 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 472 through 501 removed outlier: 3.512A pdb=" N ILE A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.534A pdb=" N MET A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.743A pdb=" N ARG A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 579 through 583 removed outlier: 4.084A pdb=" N PHE A 582 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 614 through 630 removed outlier: 3.678A pdb=" N LYS A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 3.563A pdb=" N ASP A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.776A pdb=" N GLY A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 removed outlier: 4.206A pdb=" N GLU A 777 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 841 removed outlier: 3.600A pdb=" N THR A 840 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 864 through 877 removed outlier: 5.752A pdb=" N LYS A 873 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 888 Processing helix chain 'A' and resid 892 through 909 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 952 through 966 removed outlier: 4.015A pdb=" N ASN A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 Processing helix chain 'A' and resid 1120 through 1139 removed outlier: 3.714A pdb=" N PHE A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' Processing helix chain 'A' and resid 1158 through 1166 Processing helix chain 'A' and resid 1172 through 1184 Processing helix chain 'A' and resid 1200 through 1208 Processing helix chain 'A' and resid 1209 through 1211 No H-bonds generated for 'chain 'A' and resid 1209 through 1211' Processing helix chain 'A' and resid 1212 through 1229 removed outlier: 4.311A pdb=" N SER A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Proline residue: A1221 - end of helix Processing helix chain 'A' and resid 1237 through 1246 Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.956A pdb=" N GLY A1293 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1294 " --> pdb=" O PRO A1290 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A1311 " --> pdb=" O VAL A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1323 removed outlier: 3.588A pdb=" N LEU A1323 " --> pdb=" O LEU A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1332 Processing helix chain 'A' and resid 1333 through 1347 Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.182A pdb=" N SER A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1387 Processing helix chain 'A' and resid 1388 through 1391 removed outlier: 3.732A pdb=" N GLY A1391 " --> pdb=" O GLN A1388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1391' Processing helix chain 'A' and resid 1441 through 1460 removed outlier: 4.273A pdb=" N PHE A1445 " --> pdb=" O SER A1441 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A1446 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A1449 " --> pdb=" O PHE A1445 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG A1452 " --> pdb=" O HIS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.884A pdb=" N THR A1490 " --> pdb=" O LEU A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1515 Processing helix chain 'A' and resid 1521 through 1548 removed outlier: 3.632A pdb=" N THR A1547 " --> pdb=" O ASN A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1568 Processing helix chain 'A' and resid 1606 through 1621 removed outlier: 3.518A pdb=" N ALA A1610 " --> pdb=" O SER A1606 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A1621 " --> pdb=" O MET A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1628 Processing helix chain 'A' and resid 1634 through 1639 Processing helix chain 'A' and resid 1647 through 1654 removed outlier: 3.822A pdb=" N ASN A1651 " --> pdb=" O ASP A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 removed outlier: 3.723A pdb=" N ASN A1675 " --> pdb=" O ASP A1671 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A1676 " --> pdb=" O ARG A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1689 through 1695 Processing helix chain 'A' and resid 1712 through 1716 Processing helix chain 'A' and resid 1719 through 1729 Processing helix chain 'A' and resid 1733 through 1748 Processing helix chain 'A' and resid 1757 through 1761 Processing helix chain 'A' and resid 1765 through 1767 No H-bonds generated for 'chain 'A' and resid 1765 through 1767' Processing helix chain 'A' and resid 1768 through 1799 removed outlier: 3.574A pdb=" N GLY A1788 " --> pdb=" O GLN A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1857 removed outlier: 4.130A pdb=" N VAL A1844 " --> pdb=" O VAL A1840 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A1845 " --> pdb=" O PRO A1841 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A1847 " --> pdb=" O VAL A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1883 removed outlier: 3.545A pdb=" N GLN A1883 " --> pdb=" O ARG A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1920 Processing helix chain 'A' and resid 1928 through 1944 Processing helix chain 'A' and resid 1946 through 1961 Processing helix chain 'A' and resid 1964 through 1982 removed outlier: 5.224A pdb=" N GLN A1979 " --> pdb=" O ASN A1975 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A1980 " --> pdb=" O SER A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2003 removed outlier: 3.615A pdb=" N THR A1989 " --> pdb=" O SER A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2029 through 2037 removed outlier: 3.767A pdb=" N ASN A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2059 removed outlier: 4.265A pdb=" N HIS A2059 " --> pdb=" O ASP A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2111 through 2120 Processing helix chain 'A' and resid 2127 through 2131 Processing helix chain 'A' and resid 2222 through 2232 Processing helix chain 'A' and resid 2379 through 2381 No H-bonds generated for 'chain 'A' and resid 2379 through 2381' Processing helix chain 'A' and resid 2406 through 2414 removed outlier: 3.519A pdb=" N LEU A2410 " --> pdb=" O GLU A2407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN A2411 " --> pdb=" O ALA A2408 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A2414 " --> pdb=" O ASN A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2452 Processing helix chain 'A' and resid 2458 through 2469 Processing helix chain 'A' and resid 2610 through 2616 Processing helix chain 'A' and resid 2642 through 2644 No H-bonds generated for 'chain 'A' and resid 2642 through 2644' Processing helix chain 'A' and resid 2742 through 2748 Processing helix chain 'A' and resid 2776 through 2787 Processing helix chain 'A' and resid 2822 through 2828 removed outlier: 3.937A pdb=" N THR A2827 " --> pdb=" O VAL A2824 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A2828 " --> pdb=" O MET A2825 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2844 Proline residue: A2839 - end of helix Processing helix chain 'A' and resid 2845 through 2849 Processing helix chain 'A' and resid 2868 through 2884 Processing helix chain 'A' and resid 2982 through 2986 Processing helix chain 'A' and resid 3056 through 3070 removed outlier: 3.558A pdb=" N GLU A3064 " --> pdb=" O TYR A3060 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A3065 " --> pdb=" O MET A3061 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A3066 " --> pdb=" O MET A3062 " (cutoff:3.500A) Processing helix chain 'A' and resid 3072 through 3086 Processing helix chain 'A' and resid 3095 through 3102 removed outlier: 3.693A pdb=" N LEU A3099 " --> pdb=" O THR A3095 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A3100 " --> pdb=" O PRO A3096 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS A3101 " --> pdb=" O GLU A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3192 through 3195 Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 510 removed outlier: 6.633A pdb=" N TYR A 345 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS A 509 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 347 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 316 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TRP A 348 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 318 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE A 319 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 652 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA4, first strand: chain 'A' and resid 657 through 658 Processing sheet with id=AA5, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AA6, first strand: chain 'A' and resid 935 through 936 Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 6.445A pdb=" N ILE A 971 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N HIS A1148 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A 973 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1188 " --> pdb=" O SER A1282 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1269 " --> pdb=" O THR A1276 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN A1278 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N GLY A1267 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA9, first strand: chain 'A' and resid 1464 through 1467 removed outlier: 4.513A pdb=" N ASN A1464 " --> pdb=" O ASP A1603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1679 through 1682 Processing sheet with id=AB2, first strand: chain 'A' and resid 1702 through 1703 Processing sheet with id=AB3, first strand: chain 'A' and resid 1814 through 1817 removed outlier: 3.714A pdb=" N GLU A1814 " --> pdb=" O ASN A1824 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG A1822 " --> pdb=" O ALA A1816 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1826 through 1827 removed outlier: 3.944A pdb=" N LEU A1833 " --> pdb=" O ILE A1827 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.585A pdb=" N LEU A2070 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A2246 " --> pdb=" O THR A2268 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER A2270 " --> pdb=" O LEU A2246 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A2248 " --> pdb=" O SER A2270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A2267 " --> pdb=" O THR A2312 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL A2314 " --> pdb=" O ASN A2267 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A2269 " --> pdb=" O VAL A2314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2139 through 2140 removed outlier: 10.743A pdb=" N TYR A2163 " --> pdb=" O GLY A2094 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER A2096 " --> pdb=" O TYR A2163 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ALA A2165 " --> pdb=" O SER A2096 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A2098 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A2162 " --> pdb=" O LEU A2197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2139 through 2140 removed outlier: 4.551A pdb=" N GLU A2095 " --> pdb=" O LYS A2080 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS A2080 " --> pdb=" O GLU A2095 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER A2097 " --> pdb=" O PHE A2078 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE A2078 " --> pdb=" O SER A2097 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY A2079 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR A2202 " --> pdb=" O GLY A2079 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A2081 " --> pdb=" O THR A2202 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A2204 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A2083 " --> pdb=" O ILE A2204 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY A2254 " --> pdb=" O THR A2304 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR A2306 " --> pdb=" O GLY A2254 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A2256 " --> pdb=" O THR A2306 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A2291 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A2304 " --> pdb=" O GLN A2289 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN A2289 " --> pdb=" O THR A2304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2168 through 2172 Processing sheet with id=AB9, first strand: chain 'A' and resid 2281 through 2283 removed outlier: 6.080A pdb=" N ASP A2321 " --> pdb=" O THR A2340 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE A2342 " --> pdb=" O ASP A2321 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A2323 " --> pdb=" O ILE A2342 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A2339 " --> pdb=" O THR A2361 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR A2363 " --> pdb=" O GLY A2339 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A2341 " --> pdb=" O THR A2363 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN A2403 " --> pdb=" O LEU A2360 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU A2362 " --> pdb=" O GLN A2403 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2331 through 2333 removed outlier: 6.369A pdb=" N GLY A2346 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU A2372 " --> pdb=" O GLY A2346 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN A2348 " --> pdb=" O GLU A2372 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE A2374 " --> pdb=" O ASN A2348 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A2350 " --> pdb=" O PHE A2374 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ARG A2418 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS A2371 " --> pdb=" O ARG A2418 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS A2420 " --> pdb=" O HIS A2371 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A2373 " --> pdb=" O HIS A2420 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE A2417 " --> pdb=" O ALA A2429 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A2425 " --> pdb=" O THR A2421 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A2426 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N SER A2472 " --> pdb=" O ILE A2436 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU A2438 " --> pdb=" O SER A2472 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A2474 " --> pdb=" O LEU A2438 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A2440 " --> pdb=" O THR A2474 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU A2476 " --> pdb=" O ILE A2440 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A2442 " --> pdb=" O GLU A2476 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG A2478 " --> pdb=" O LEU A2442 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP A2444 " --> pdb=" O ARG A2478 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A2480 " --> pdb=" O ASP A2444 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A2486 " --> pdb=" O PHE A2479 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A2485 " --> pdb=" O GLN A2498 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A2516 " --> pdb=" O GLN A2540 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A2542 " --> pdb=" O THR A2516 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A2518 " --> pdb=" O ILE A2542 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A2539 " --> pdb=" O THR A2586 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER A2588 " --> pdb=" O THR A2539 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A2541 " --> pdb=" O SER A2588 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A2564 " --> pdb=" O THR A2575 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A2563 " --> pdb=" O ILE A2626 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2383 through 2384 removed outlier: 4.553A pdb=" N ILE A2393 " --> pdb=" O LYS A2384 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2505 through 2508 removed outlier: 6.789A pdb=" N TYR A2526 " --> pdb=" O ASP A2554 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP A2606 " --> pdb=" O ILE A2602 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2637 through 2640 removed outlier: 6.921A pdb=" N TYR A2711 " --> pdb=" O ALA A2686 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A2686 " --> pdb=" O TYR A2711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A2713 " --> pdb=" O LYS A2684 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2647 through 2651 removed outlier: 3.592A pdb=" N VAL A2647 " --> pdb=" O SER A2724 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A2721 " --> pdb=" O LEU A2679 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2702 through 2704 Processing sheet with id=AC7, first strand: chain 'A' and resid 2731 through 2733 removed outlier: 6.043A pdb=" N LEU A2731 " --> pdb=" O ILE A2753 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2738 through 2741 removed outlier: 5.014A pdb=" N LEU A2763 " --> pdb=" O ASN A2858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2908 through 2912 removed outlier: 6.365A pdb=" N MET A2909 " --> pdb=" O ILE A2973 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER A2975 " --> pdb=" O MET A2909 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A2911 " --> pdb=" O SER A2975 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2936 through 2938 Processing sheet with id=AD2, first strand: chain 'A' and resid 2947 through 2950 Processing sheet with id=AD3, first strand: chain 'A' and resid 3104 through 3110 removed outlier: 3.534A pdb=" N TYR A3151 " --> pdb=" O VAL A3110 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN A3152 " --> pdb=" O ILE A3198 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A3200 " --> pdb=" O GLN A3152 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A3154 " --> pdb=" O VAL A3200 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU A3202 " --> pdb=" O TYR A3154 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG A3156 " --> pdb=" O LEU A3202 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR A3204 " --> pdb=" O ARG A3156 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A3199 " --> pdb=" O VAL A3188 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL A3188 " --> pdb=" O TYR A3199 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 3132 through 3135 removed outlier: 3.633A pdb=" N ASP A3164 " --> pdb=" O THR A3176 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2856 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: 16.25 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7390 1.34 - 1.46: 3371 1.46 - 1.58: 11828 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22727 Sorted by residual: bond pdb=" N LYS A 800 " pdb=" CA LYS A 800 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.75e+00 bond pdb=" N THR A 798 " pdb=" CA THR A 798 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.69e+00 bond pdb=" N TYR A 801 " pdb=" CA TYR A 801 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.23e-02 6.61e+03 5.74e+00 bond pdb=" N THR A 796 " pdb=" CA THR A 796 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.39e+00 bond pdb=" N GLY A 797 " pdb=" CA GLY A 797 " ideal model delta sigma weight residual 1.445 1.476 -0.031 1.39e-02 5.18e+03 4.94e+00 ... (remaining 22722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 30464 1.79 - 3.57: 284 3.57 - 5.36: 38 5.36 - 7.14: 5 7.14 - 8.93: 3 Bond angle restraints: 30794 Sorted by residual: angle pdb=" CA THR A 795 " pdb=" C THR A 795 " pdb=" O THR A 795 " ideal model delta sigma weight residual 122.37 117.81 4.56 1.15e+00 7.56e-01 1.57e+01 angle pdb=" N GLY A1283 " pdb=" CA GLY A1283 " pdb=" C GLY A1283 " ideal model delta sigma weight residual 111.78 117.38 -5.60 1.69e+00 3.50e-01 1.10e+01 angle pdb=" CB LYS A1156 " pdb=" CG LYS A1156 " pdb=" CD LYS A1156 " ideal model delta sigma weight residual 111.30 118.79 -7.49 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CB MET A3062 " pdb=" CG MET A3062 " pdb=" SD MET A3062 " ideal model delta sigma weight residual 112.70 103.77 8.93 3.00e+00 1.11e-01 8.86e+00 angle pdb=" CA LYS A 800 " pdb=" C LYS A 800 " pdb=" O LYS A 800 " ideal model delta sigma weight residual 121.56 118.33 3.23 1.09e+00 8.42e-01 8.80e+00 ... (remaining 30789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11768 17.73 - 35.46: 1493 35.46 - 53.19: 388 53.19 - 70.92: 123 70.92 - 88.66: 23 Dihedral angle restraints: 13795 sinusoidal: 5647 harmonic: 8148 Sorted by residual: dihedral pdb=" CB CYS A3182 " pdb=" SG CYS A3182 " pdb=" SG CYS A3205 " pdb=" CB CYS A3205 " ideal model delta sinusoidal sigma weight residual -86.00 -29.83 -56.17 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA THR A2421 " pdb=" C THR A2421 " pdb=" N ARG A2422 " pdb=" CA ARG A2422 " ideal model delta harmonic sigma weight residual 180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA SER A2088 " pdb=" C SER A2088 " pdb=" N PRO A2089 " pdb=" CA PRO A2089 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 13792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2490 0.035 - 0.070: 690 0.070 - 0.104: 202 0.104 - 0.139: 103 0.139 - 0.174: 5 Chirality restraints: 3490 Sorted by residual: chirality pdb=" CB ILE A 393 " pdb=" CA ILE A 393 " pdb=" CG1 ILE A 393 " pdb=" CG2 ILE A 393 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA ILE A1154 " pdb=" N ILE A1154 " pdb=" C ILE A1154 " pdb=" CB ILE A1154 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ASN A 577 " pdb=" N ASN A 577 " pdb=" C ASN A 577 " pdb=" CB ASN A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 3487 not shown) Planarity restraints: 3971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 400 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 401 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2295 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A2296 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A2296 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2296 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A2692 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A2693 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A2693 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2693 " -0.026 5.00e-02 4.00e+02 ... (remaining 3968 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2063 2.75 - 3.28: 21196 3.28 - 3.82: 37450 3.82 - 4.36: 44629 4.36 - 4.90: 77400 Nonbonded interactions: 182738 Sorted by model distance: nonbonded pdb=" OH TYR A 306 " pdb=" O LEU A 774 " model vdw 2.208 3.040 nonbonded pdb=" OE1 GLN A1772 " pdb=" OG SER A2002 " model vdw 2.209 3.040 nonbonded pdb=" OG SER A 614 " pdb=" OD1 ASP A 617 " model vdw 2.219 3.040 nonbonded pdb=" O PRO A1197 " pdb=" OH TYR A1224 " model vdw 2.222 3.040 nonbonded pdb=" O LEU A3098 " pdb=" OG1 THR A3102 " model vdw 2.234 3.040 ... (remaining 182733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 57.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.002 0.037 22728 Z= 0.101 Angle : 0.446 8.927 30796 Z= 0.239 Chirality : 0.040 0.174 3490 Planarity : 0.004 0.103 3971 Dihedral : 17.346 88.655 8540 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 24.99 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2783 helix: 2.24 (0.16), residues: 1065 sheet: 0.31 (0.23), residues: 565 loop : -0.36 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2046 HIS 0.013 0.001 HIS A2412 PHE 0.009 0.001 PHE A 359 TYR 0.028 0.001 TYR A1407 ARG 0.004 0.000 ARG A1452 Details of bonding type rmsd hydrogen bonds : bond 0.15657 ( 1024) hydrogen bonds : angle 6.06948 ( 2856) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.34804 ( 2) covalent geometry : bond 0.00197 (22727) covalent geometry : angle 0.44611 (30794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 1603 ASP cc_start: 0.8826 (p0) cc_final: 0.8564 (p0) REVERT: A 2744 ARG cc_start: 0.7148 (mtp-110) cc_final: 0.6939 (mtp-110) outliers start: 44 outliers final: 32 residues processed: 255 average time/residue: 1.2776 time to fit residues: 377.1010 Evaluate side-chains 241 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1134 ARG Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1623 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1773 THR Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2547 ASN Chi-restraints excluded: chain A residue 2602 ILE Chi-restraints excluded: chain A residue 2645 ASN Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2708 SER Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2954 LYS Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3073 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.4980 chunk 211 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 142 optimal weight: 0.0370 chunk 112 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 253 optimal weight: 0.3980 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A1642 HIS A1772 GLN A1912 GLN A2162 GLN A2412 HIS A2500 GLN A3066 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106648 restraints weight = 31733.377| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.11 r_work: 0.2979 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22728 Z= 0.108 Angle : 0.460 6.615 30796 Z= 0.245 Chirality : 0.041 0.172 3490 Planarity : 0.004 0.067 3971 Dihedral : 4.843 55.940 3102 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.42 % Allowed : 22.17 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2783 helix: 2.31 (0.16), residues: 1060 sheet: 0.38 (0.22), residues: 586 loop : -0.32 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2746 HIS 0.009 0.001 HIS A2412 PHE 0.011 0.001 PHE A 359 TYR 0.011 0.001 TYR A2255 ARG 0.003 0.000 ARG A3107 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 1024) hydrogen bonds : angle 4.59865 ( 2856) SS BOND : bond 0.00179 ( 1) SS BOND : angle 1.38295 ( 2) covalent geometry : bond 0.00237 (22727) covalent geometry : angle 0.46016 (30794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 223 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7440 (m110) cc_final: 0.7138 (m110) REVERT: A 916 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8343 (tttt) REVERT: A 1407 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8340 (p90) REVERT: A 2799 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 2987 ASN cc_start: 0.6978 (p0) cc_final: 0.6560 (p0) REVERT: A 3035 THR cc_start: 0.8364 (p) cc_final: 0.8148 (p) REVERT: A 3190 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7114 (mt-10) outliers start: 85 outliers final: 29 residues processed: 282 average time/residue: 1.2190 time to fit residues: 400.0453 Evaluate side-chains 242 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 916 LYS Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2708 SER Chi-restraints excluded: chain A residue 2799 VAL Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3190 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 261 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1356 HIS A1772 GLN A1912 GLN A2412 HIS A2500 GLN A3125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104742 restraints weight = 31519.041| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.15 r_work: 0.2952 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22728 Z= 0.146 Angle : 0.473 6.288 30796 Z= 0.248 Chirality : 0.042 0.145 3490 Planarity : 0.004 0.049 3971 Dihedral : 4.481 56.846 3062 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.14 % Allowed : 21.77 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2783 helix: 2.25 (0.16), residues: 1066 sheet: 0.26 (0.22), residues: 585 loop : -0.42 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2687 HIS 0.010 0.001 HIS A2412 PHE 0.014 0.001 PHE A 359 TYR 0.013 0.001 TYR A2121 ARG 0.009 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1024) hydrogen bonds : angle 4.37729 ( 2856) SS BOND : bond 0.00168 ( 1) SS BOND : angle 1.62130 ( 2) covalent geometry : bond 0.00344 (22727) covalent geometry : angle 0.47236 (30794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 224 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7448 (m-40) cc_final: 0.7188 (m110) REVERT: A 948 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7820 (m-70) REVERT: A 2494 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.6629 (tp40) REVERT: A 2537 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 2599 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6424 (ptp90) REVERT: A 3007 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7949 (tmt170) REVERT: A 3144 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.5447 (t80) REVERT: A 3190 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7111 (mt-10) outliers start: 103 outliers final: 39 residues processed: 289 average time/residue: 1.3206 time to fit residues: 438.8681 Evaluate side-chains 261 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2494 GLN Chi-restraints excluded: chain A residue 2512 ARG Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2537 LEU Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2640 ASN Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2708 SER Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2881 GLU Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3190 GLU Chi-restraints excluded: chain A residue 3200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 207 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 178 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A1912 GLN A2412 HIS A2500 GLN A2962 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104855 restraints weight = 31919.155| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.13 r_work: 0.2956 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22728 Z= 0.135 Angle : 0.469 6.331 30796 Z= 0.246 Chirality : 0.041 0.145 3490 Planarity : 0.004 0.044 3971 Dihedral : 4.418 58.264 3060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.27 % Allowed : 21.49 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2783 helix: 2.26 (0.16), residues: 1067 sheet: 0.20 (0.22), residues: 585 loop : -0.45 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2046 HIS 0.010 0.001 HIS A2412 PHE 0.012 0.001 PHE A 359 TYR 0.012 0.001 TYR A2121 ARG 0.007 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1024) hydrogen bonds : angle 4.22238 ( 2856) SS BOND : bond 0.00002 ( 1) SS BOND : angle 1.83632 ( 2) covalent geometry : bond 0.00317 (22727) covalent geometry : angle 0.46851 (30794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 223 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8370 (tpp) cc_final: 0.8161 (tpp) REVERT: A 256 ASN cc_start: 0.7549 (m-40) cc_final: 0.7316 (m110) REVERT: A 777 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: A 941 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8967 (tp) REVERT: A 1407 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8192 (p90) REVERT: A 2221 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 2455 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: A 2494 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6621 (tp40) REVERT: A 2677 GLU cc_start: 0.7712 (tt0) cc_final: 0.7443 (tt0) REVERT: A 2692 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5245 (pm20) REVERT: A 2769 ARG cc_start: 0.9025 (mpp80) cc_final: 0.8805 (mpp80) REVERT: A 3007 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7867 (tmt170) REVERT: A 3038 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7101 (pp) REVERT: A 3062 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7091 (tpp) REVERT: A 3144 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.5520 (t80) outliers start: 106 outliers final: 51 residues processed: 296 average time/residue: 1.2995 time to fit residues: 445.5949 Evaluate side-chains 279 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2455 GLU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2494 GLN Chi-restraints excluded: chain A residue 2512 ARG Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2640 ASN Chi-restraints excluded: chain A residue 2645 ASN Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2824 VAL Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2881 GLU Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3038 ILE Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 123 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 276 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 196 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A1912 GLN A2412 HIS A2500 GLN A2962 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104910 restraints weight = 31588.460| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.18 r_work: 0.2957 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22728 Z= 0.118 Angle : 0.460 6.498 30796 Z= 0.241 Chirality : 0.041 0.144 3490 Planarity : 0.004 0.057 3971 Dihedral : 4.351 58.223 3059 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.02 % Allowed : 21.89 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2783 helix: 2.31 (0.16), residues: 1067 sheet: 0.17 (0.22), residues: 585 loop : -0.44 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2046 HIS 0.011 0.001 HIS A2412 PHE 0.011 0.001 PHE A 359 TYR 0.013 0.001 TYR A 397 ARG 0.011 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1024) hydrogen bonds : angle 4.12190 ( 2856) SS BOND : bond 0.00040 ( 1) SS BOND : angle 2.00200 ( 2) covalent geometry : bond 0.00272 (22727) covalent geometry : angle 0.45992 (30794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 226 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8293 (tpp) cc_final: 0.8061 (tpp) REVERT: A 570 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8119 (t80) REVERT: A 574 MET cc_start: 0.8209 (mmp) cc_final: 0.7758 (mpm) REVERT: A 777 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: A 941 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 948 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7771 (m-70) REVERT: A 1156 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8191 (mmmm) REVERT: A 1407 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8205 (p90) REVERT: A 1603 ASP cc_start: 0.8726 (p0) cc_final: 0.8504 (p0) REVERT: A 1826 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7096 (mm-40) REVERT: A 2175 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.7896 (m100) REVERT: A 2221 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7600 (mm) REVERT: A 2455 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: A 2554 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: A 2692 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5240 (pm20) REVERT: A 2879 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6552 (mm-40) REVERT: A 2987 ASN cc_start: 0.7472 (p0) cc_final: 0.6947 (m110) REVERT: A 3007 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7896 (tmt170) REVERT: A 3038 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7106 (pp) REVERT: A 3062 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7030 (tpp) REVERT: A 3144 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.5472 (t80) REVERT: A 3203 LYS cc_start: 0.6732 (mttm) cc_final: 0.6058 (mtpt) outliers start: 100 outliers final: 44 residues processed: 293 average time/residue: 1.2827 time to fit residues: 433.1906 Evaluate side-chains 278 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2175 TRP Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2364 LEU Chi-restraints excluded: chain A residue 2455 GLU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2512 ARG Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2554 ASP Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2640 ASN Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2881 GLU Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3038 ILE Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 191 optimal weight: 0.0980 chunk 106 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 254 optimal weight: 0.0270 chunk 240 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1912 GLN ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS A2500 GLN A2962 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105146 restraints weight = 31721.234| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.16 r_work: 0.2964 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22728 Z= 0.086 Angle : 0.438 6.298 30796 Z= 0.230 Chirality : 0.040 0.155 3490 Planarity : 0.004 0.061 3971 Dihedral : 4.079 56.147 3056 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 23.22 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2783 helix: 2.42 (0.16), residues: 1059 sheet: 0.21 (0.22), residues: 585 loop : -0.42 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2746 HIS 0.012 0.001 HIS A2412 PHE 0.009 0.001 PHE A 359 TYR 0.009 0.001 TYR A1407 ARG 0.012 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 1024) hydrogen bonds : angle 3.99062 ( 2856) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.69962 ( 2) covalent geometry : bond 0.00185 (22727) covalent geometry : angle 0.43820 (30794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8350 (tpp) cc_final: 0.7954 (tpp) REVERT: A 503 GLU cc_start: 0.8035 (mp0) cc_final: 0.7806 (mm-30) REVERT: A 570 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 574 MET cc_start: 0.8217 (mmp) cc_final: 0.7653 (mpm) REVERT: A 941 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8910 (tp) REVERT: A 948 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7718 (m-70) REVERT: A 1603 ASP cc_start: 0.8580 (p0) cc_final: 0.8251 (p0) REVERT: A 1826 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7166 (mm-40) REVERT: A 1863 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7222 (ppp) REVERT: A 2221 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7608 (mm) REVERT: A 2599 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6413 (ptp90) REVERT: A 2692 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5185 (pm20) REVERT: A 2769 ARG cc_start: 0.9056 (mpp80) cc_final: 0.8843 (mpp80) REVERT: A 2879 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6650 (mm-40) REVERT: A 2987 ASN cc_start: 0.7469 (p0) cc_final: 0.6988 (m110) REVERT: A 3007 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7947 (tmt170) REVERT: A 3062 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7092 (tpp) REVERT: A 3144 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.5452 (t80) REVERT: A 3203 LYS cc_start: 0.6892 (mttm) cc_final: 0.6235 (mtpt) outliers start: 80 outliers final: 35 residues processed: 284 average time/residue: 1.2561 time to fit residues: 412.9027 Evaluate side-chains 261 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1647 ASP Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2824 VAL Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2956 ASP Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 262 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 247 optimal weight: 0.0060 chunk 193 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1912 GLN ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103556 restraints weight = 31799.967| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.12 r_work: 0.2927 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22728 Z= 0.142 Angle : 0.480 6.707 30796 Z= 0.250 Chirality : 0.042 0.149 3490 Planarity : 0.004 0.066 3971 Dihedral : 4.202 57.289 3056 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.50 % Allowed : 23.10 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2783 helix: 2.37 (0.16), residues: 1061 sheet: 0.18 (0.22), residues: 588 loop : -0.46 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2746 HIS 0.010 0.001 HIS A2412 PHE 0.013 0.001 PHE A 359 TYR 0.015 0.001 TYR A 306 ARG 0.013 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1024) hydrogen bonds : angle 4.05813 ( 2856) SS BOND : bond 0.00114 ( 1) SS BOND : angle 1.77585 ( 2) covalent geometry : bond 0.00334 (22727) covalent geometry : angle 0.48013 (30794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8069 (mp0) cc_final: 0.7844 (mm-30) REVERT: A 941 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8942 (tp) REVERT: A 948 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: A 1407 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8246 (p90) REVERT: A 1648 MET cc_start: 0.8266 (mtm) cc_final: 0.8057 (mtt) REVERT: A 1826 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: A 2175 TRP cc_start: 0.8469 (OUTLIER) cc_final: 0.7877 (m100) REVERT: A 2221 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7698 (mm) REVERT: A 2455 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: A 2692 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5070 (pm20) REVERT: A 2879 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6656 (mm-40) REVERT: A 2935 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.7057 (mtt-85) REVERT: A 2987 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7248 (m110) REVERT: A 3007 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7909 (tmt170) REVERT: A 3062 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7033 (tpp) REVERT: A 3144 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5467 (t80) REVERT: A 3203 LYS cc_start: 0.6989 (mttm) cc_final: 0.6279 (mtpt) outliers start: 87 outliers final: 47 residues processed: 284 average time/residue: 1.2326 time to fit residues: 406.0622 Evaluate side-chains 279 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2175 TRP Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2364 LEU Chi-restraints excluded: chain A residue 2455 GLU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2512 ARG Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2547 ASN Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2645 ASN Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2738 GLU Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2824 VAL Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2987 ASN Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 67 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1912 GLN ** A2289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102800 restraints weight = 31801.760| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.18 r_work: 0.2911 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22728 Z= 0.192 Angle : 0.527 8.698 30796 Z= 0.273 Chirality : 0.043 0.151 3490 Planarity : 0.004 0.070 3971 Dihedral : 4.441 59.564 3056 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.58 % Allowed : 23.06 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2783 helix: 2.19 (0.16), residues: 1067 sheet: 0.10 (0.22), residues: 588 loop : -0.52 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2687 HIS 0.009 0.001 HIS A2412 PHE 0.020 0.002 PHE A 920 TYR 0.016 0.002 TYR A 306 ARG 0.014 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1024) hydrogen bonds : angle 4.20944 ( 2856) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.88808 ( 2) covalent geometry : bond 0.00462 (22727) covalent geometry : angle 0.52674 (30794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 221 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: A 252 MET cc_start: 0.8096 (tpp) cc_final: 0.7873 (tpp) REVERT: A 471 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9176 (mp) REVERT: A 503 GLU cc_start: 0.8081 (mp0) cc_final: 0.7865 (mm-30) REVERT: A 941 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 948 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7800 (m-70) REVERT: A 1124 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6115 (t-90) REVERT: A 1407 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8210 (p90) REVERT: A 1826 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7136 (mm-40) REVERT: A 2175 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7957 (m100) REVERT: A 2221 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7652 (mm) REVERT: A 2455 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: A 2494 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6724 (tp40) REVERT: A 2554 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 2692 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5082 (pm20) REVERT: A 2744 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.7685 (mtp-110) REVERT: A 2769 ARG cc_start: 0.9008 (mpp80) cc_final: 0.8747 (mpp80) REVERT: A 2879 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6660 (mm-40) REVERT: A 2987 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7270 (m110) REVERT: A 3007 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7945 (tmt170) REVERT: A 3062 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6980 (tpp) REVERT: A 3144 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.5466 (t80) REVERT: A 3203 LYS cc_start: 0.6896 (mttm) cc_final: 0.6229 (mtpt) outliers start: 89 outliers final: 44 residues processed: 277 average time/residue: 1.2341 time to fit residues: 396.1260 Evaluate side-chains 275 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1843 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2175 TRP Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2364 LEU Chi-restraints excluded: chain A residue 2455 GLU Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2494 GLN Chi-restraints excluded: chain A residue 2512 ARG Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2547 ASN Chi-restraints excluded: chain A residue 2554 ASP Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2640 ASN Chi-restraints excluded: chain A residue 2645 ASN Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2738 GLU Chi-restraints excluded: chain A residue 2824 VAL Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2987 ASN Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 148 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1356 HIS A1548 ASN ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS A2500 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104968 restraints weight = 31617.935| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.11 r_work: 0.2947 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22728 Z= 0.096 Angle : 0.463 7.555 30796 Z= 0.242 Chirality : 0.041 0.195 3490 Planarity : 0.004 0.073 3971 Dihedral : 4.228 58.958 3056 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.37 % Allowed : 24.47 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2783 helix: 2.37 (0.16), residues: 1062 sheet: 0.13 (0.22), residues: 588 loop : -0.47 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2746 HIS 0.013 0.001 HIS A2412 PHE 0.010 0.001 PHE A 359 TYR 0.014 0.001 TYR A 306 ARG 0.013 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 1024) hydrogen bonds : angle 4.01485 ( 2856) SS BOND : bond 0.00088 ( 1) SS BOND : angle 1.59185 ( 2) covalent geometry : bond 0.00209 (22727) covalent geometry : angle 0.46283 (30794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9148 (mp) REVERT: A 503 GLU cc_start: 0.8010 (mp0) cc_final: 0.7781 (mm-30) REVERT: A 941 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8928 (tp) REVERT: A 1826 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7137 (mm-40) REVERT: A 2221 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7632 (mm) REVERT: A 2692 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5194 (pm20) REVERT: A 2769 ARG cc_start: 0.9035 (mpp80) cc_final: 0.8801 (mpp80) REVERT: A 2879 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6663 (mm-40) REVERT: A 2987 ASN cc_start: 0.7455 (p0) cc_final: 0.7255 (m110) REVERT: A 3007 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7957 (tmt170) REVERT: A 3062 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7045 (tpp) REVERT: A 3144 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.5313 (t80) REVERT: A 3203 LYS cc_start: 0.7059 (mttm) cc_final: 0.6394 (mtpt) outliers start: 59 outliers final: 35 residues processed: 259 average time/residue: 1.3058 time to fit residues: 390.3627 Evaluate side-chains 256 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2547 ASN Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2640 ASN Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2967 MET Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 205 optimal weight: 0.0870 chunk 234 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 182 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105295 restraints weight = 31866.750| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.12 r_work: 0.2942 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22728 Z= 0.097 Angle : 0.462 7.379 30796 Z= 0.240 Chirality : 0.041 0.189 3490 Planarity : 0.004 0.075 3971 Dihedral : 4.134 57.186 3056 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.97 % Allowed : 24.91 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2783 helix: 2.43 (0.16), residues: 1060 sheet: 0.18 (0.22), residues: 588 loop : -0.46 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2746 HIS 0.013 0.001 HIS A2412 PHE 0.010 0.001 PHE A 359 TYR 0.018 0.001 TYR A 306 ARG 0.013 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1024) hydrogen bonds : angle 3.97680 ( 2856) SS BOND : bond 0.00108 ( 1) SS BOND : angle 1.53904 ( 2) covalent geometry : bond 0.00216 (22727) covalent geometry : angle 0.46154 (30794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5566 Ramachandran restraints generated. 2783 Oldfield, 0 Emsley, 2783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9153 (mp) REVERT: A 503 GLU cc_start: 0.7982 (mp0) cc_final: 0.7749 (mm-30) REVERT: A 570 PHE cc_start: 0.8721 (t80) cc_final: 0.8134 (t80) REVERT: A 574 MET cc_start: 0.8352 (mtt) cc_final: 0.8101 (mpm) REVERT: A 941 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8913 (tp) REVERT: A 948 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7704 (m-70) REVERT: A 1648 MET cc_start: 0.8120 (mtm) cc_final: 0.7840 (mtt) REVERT: A 1826 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7158 (mm-40) REVERT: A 2221 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 2692 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5076 (pm20) REVERT: A 2769 ARG cc_start: 0.9034 (mpp80) cc_final: 0.8794 (mpp80) REVERT: A 2879 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6673 (mm-40) REVERT: A 3007 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7928 (tmt170) REVERT: A 3062 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7023 (tpp) REVERT: A 3144 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.5265 (t80) REVERT: A 3203 LYS cc_start: 0.7085 (mttm) cc_final: 0.6408 (mtpt) outliers start: 49 outliers final: 32 residues processed: 255 average time/residue: 1.2726 time to fit residues: 376.3721 Evaluate side-chains 255 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2547 ASN Chi-restraints excluded: chain A residue 2572 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2599 ARG Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER Chi-restraints excluded: chain A residue 3001 VAL Chi-restraints excluded: chain A residue 3007 ARG Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2987 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104272 restraints weight = 31781.424| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.17 r_work: 0.2930 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22728 Z= 0.110 Angle : 0.472 7.635 30796 Z= 0.245 Chirality : 0.041 0.186 3490 Planarity : 0.004 0.074 3971 Dihedral : 4.147 59.458 3056 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.13 % Allowed : 24.71 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2783 helix: 2.41 (0.16), residues: 1061 sheet: 0.18 (0.22), residues: 588 loop : -0.46 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2746 HIS 0.013 0.001 HIS A2412 PHE 0.011 0.001 PHE A 359 TYR 0.022 0.001 TYR A 306 ARG 0.016 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 1024) hydrogen bonds : angle 3.97962 ( 2856) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.53917 ( 2) covalent geometry : bond 0.00253 (22727) covalent geometry : angle 0.47136 (30794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15851.02 seconds wall clock time: 273 minutes 24.65 seconds (16404.65 seconds total)