Starting phenix.real_space_refine on Sun Aug 24 20:36:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euv_19987/08_2025/9euv_19987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euv_19987/08_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_19987/08_2025/9euv_19987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euv_19987/08_2025/9euv_19987.map" model { file = "/net/cci-nas-00/data/ceres_data/9euv_19987/08_2025/9euv_19987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euv_19987/08_2025/9euv_19987.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.38, per 1000 atoms: 0.20 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: 1.51 Conformation dependent library (CDL) restraints added in 692.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.30 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: 7.14 Time building geometry restraints manager: 2.02 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- 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 : 5.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A1452 TYR 0.028 0.001 TYR A1407 PHE 0.009 0.001 PHE A 359 TRP 0.011 0.001 TRP A2046 HIS 0.013 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00197 (22727) covalent geometry : angle 0.44611 (30794) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.34804 ( 2) hydrogen bonds : bond 0.15657 ( 1024) hydrogen bonds : angle 6.06948 ( 2856) *********************** 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 : 1.147 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: 0.6054 time to fit residues: 177.2503 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 : 0.572 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 398 ASN A1772 GLN A1883 GLN A1912 GLN A2162 GLN A2289 GLN A2412 HIS A2500 GLN A3066 GLN A3125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101976 restraints weight = 32065.493| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.15 r_work: 0.2895 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 22728 Z= 0.269 Angle : 0.584 7.682 30796 Z= 0.306 Chirality : 0.046 0.175 3490 Planarity : 0.005 0.070 3971 Dihedral : 5.327 59.041 3102 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.87 % Allowed : 21.17 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 2783 helix: 1.91 (0.16), residues: 1070 sheet: 0.09 (0.22), residues: 592 loop : -0.50 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2067 TYR 0.018 0.002 TYR A3135 PHE 0.019 0.002 PHE A3144 TRP 0.016 0.002 TRP A2687 HIS 0.008 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00651 (22727) covalent geometry : angle 0.58386 (30794) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.94530 ( 2) hydrogen bonds : bond 0.04961 ( 1024) hydrogen bonds : angle 4.75094 ( 2856) *********************** 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 344 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 223 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7511 (m110) cc_final: 0.7172 (m-40) REVERT: A 471 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9155 (mp) REVERT: A 481 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8777 (tppt) REVERT: A 530 MET cc_start: 0.9454 (mtt) cc_final: 0.9254 (mtt) REVERT: A 777 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: A 779 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 1407 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8357 (p90) REVERT: A 1501 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: A 2027 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: A 2175 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.8065 (m100) REVERT: A 2265 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7908 (mptt) REVERT: A 2455 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: A 2494 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6730 (tp40) REVERT: A 2660 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7424 (mt0) REVERT: A 3062 MET cc_start: 0.7452 (tpt) cc_final: 0.7128 (tpp) REVERT: A 3093 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.6111 (ptmt) REVERT: A 3144 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.5762 (t80) outliers start: 121 outliers final: 46 residues processed: 309 average time/residue: 0.5868 time to fit residues: 208.1149 Evaluate side-chains 270 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 471 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 779 ILE 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 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1214 ASP 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 1480 CYS Chi-restraints excluded: chain A residue 1501 GLU 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 1685 ILE Chi-restraints excluded: chain A residue 1718 LEU Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1852 THR Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 2027 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 2265 LYS Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2455 GLU Chi-restraints excluded: chain A residue 2474 THR 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 2561 VAL 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 2663 CYS 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 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 3017 THR Chi-restraints excluded: chain A residue 3093 LYS Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 143 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 0.0060 chunk 245 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 chunk 182 optimal weight: 2.9990 overall best weight: 0.5254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A1356 HIS A1642 HIS A1772 GLN A1883 GLN A1912 GLN ** A2289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS A2500 GLN A2962 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104653 restraints weight = 31709.158| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.18 r_work: 0.2963 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22728 Z= 0.104 Angle : 0.452 6.628 30796 Z= 0.240 Chirality : 0.041 0.148 3490 Planarity : 0.004 0.048 3971 Dihedral : 4.765 59.373 3069 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.70 % Allowed : 22.62 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.16), residues: 2783 helix: 2.17 (0.16), residues: 1071 sheet: 0.20 (0.22), residues: 583 loop : -0.48 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2744 TYR 0.012 0.001 TYR A 397 PHE 0.009 0.001 PHE A 359 TRP 0.011 0.001 TRP A2046 HIS 0.012 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00228 (22727) covalent geometry : angle 0.45169 (30794) SS BOND : bond 0.00597 ( 1) SS BOND : angle 1.59763 ( 2) hydrogen bonds : bond 0.03745 ( 1024) hydrogen bonds : angle 4.35661 ( 2856) *********************** 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 323 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 231 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7524 (m-40) cc_final: 0.7270 (m110) REVERT: A 471 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9106 (mp) REVERT: A 1796 HIS cc_start: 0.8295 (t-90) cc_final: 0.7820 (m170) REVERT: A 2221 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7558 (mm) REVERT: A 2599 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6450 (ptp90) REVERT: A 2660 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7433 (mt0) REVERT: A 2781 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 2987 ASN cc_start: 0.6993 (p0) cc_final: 0.6722 (p0) REVERT: A 3035 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 3062 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7129 (tpp) REVERT: A 3144 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.5481 (t80) outliers start: 92 outliers final: 25 residues processed: 297 average time/residue: 0.6356 time to fit residues: 217.5988 Evaluate side-chains 247 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 886 ILE Chi-restraints excluded: chain A residue 1120 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1583 LEU 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 2221 LEU Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2358 THR 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 2599 ARG Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2758 ASN Chi-restraints excluded: chain A residue 2781 LEU 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 3017 THR Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 130 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 274 optimal weight: 0.4980 chunk 275 optimal weight: 7.9990 chunk 77 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A2289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3622 r_free = 0.3622 target = 0.138527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104043 restraints weight = 31784.353| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.19 r_work: 0.2945 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0980 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= 0.126 Angle : 0.469 6.546 30796 Z= 0.245 Chirality : 0.041 0.145 3490 Planarity : 0.004 0.046 3971 Dihedral : 4.439 59.064 3059 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.98 % Allowed : 22.33 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.16), residues: 2783 helix: 2.22 (0.16), residues: 1069 sheet: 0.15 (0.22), residues: 583 loop : -0.47 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1452 TYR 0.012 0.001 TYR A2121 PHE 0.012 0.001 PHE A 359 TRP 0.012 0.001 TRP A2046 HIS 0.011 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00294 (22727) covalent geometry : angle 0.46871 (30794) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.75412 ( 2) hydrogen bonds : bond 0.03714 ( 1024) hydrogen bonds : angle 4.22419 ( 2856) *********************** 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 327 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 228 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7611 (m-40) cc_final: 0.7370 (m110) REVERT: A 471 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9111 (mp) REVERT: A 503 GLU cc_start: 0.8095 (mp0) cc_final: 0.7856 (mm-30) REVERT: A 530 MET cc_start: 0.9469 (mtt) cc_final: 0.9216 (mtt) REVERT: A 574 MET cc_start: 0.8195 (mmp) cc_final: 0.7982 (mmp) REVERT: A 777 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 941 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 1407 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8212 (p90) REVERT: A 1826 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7119 (mm-40) REVERT: A 2221 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 2494 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6652 (tp40) REVERT: A 2525 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7423 (ttt90) REVERT: A 2554 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: A 2660 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7418 (mt0) REVERT: A 2677 GLU cc_start: 0.7721 (tt0) cc_final: 0.7455 (tt0) REVERT: A 2692 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5145 (pm20) REVERT: A 3035 THR cc_start: 0.8273 (p) cc_final: 0.7967 (p) REVERT: A 3038 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7130 (pp) REVERT: A 3062 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7068 (tpp) REVERT: A 3144 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.5485 (t80) outliers start: 99 outliers final: 47 residues processed: 295 average time/residue: 0.6330 time to fit residues: 213.5093 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 : 0.906 ------------------------------------------------------------------------------- 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 450 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 628 ILE 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 957 MET 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 1222 LEU Chi-restraints excluded: chain A residue 1407 TYR Chi-restraints excluded: chain A residue 1428 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1547 THR 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 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2364 LEU 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 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 2758 ASN 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 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 215 optimal weight: 0.0970 chunk 140 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A1912 GLN ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3641 r_free = 0.3641 target = 0.139987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105452 restraints weight = 31546.481| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.17 r_work: 0.2974 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1001 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= 0.098 Angle : 0.447 6.635 30796 Z= 0.234 Chirality : 0.040 0.144 3490 Planarity : 0.004 0.057 3971 Dihedral : 4.318 58.728 3059 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.34 % Allowed : 23.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 2783 helix: 2.35 (0.16), residues: 1061 sheet: 0.15 (0.22), residues: 585 loop : -0.46 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2744 TYR 0.010 0.001 TYR A1407 PHE 0.010 0.001 PHE A 359 TRP 0.011 0.001 TRP A2746 HIS 0.012 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00217 (22727) covalent geometry : angle 0.44650 (30794) SS BOND : bond 0.00083 ( 1) SS BOND : angle 2.14352 ( 2) hydrogen bonds : bond 0.03338 ( 1024) hydrogen bonds : angle 4.08434 ( 2856) *********************** 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 313 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 503 GLU cc_start: 0.8091 (mp0) cc_final: 0.7845 (mm-30) REVERT: A 777 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: A 1156 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8238 (mmmm) REVERT: A 1826 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7156 (mm-40) REVERT: A 2525 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7440 (ttt90) REVERT: A 2554 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: A 2599 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6422 (ptp90) REVERT: A 2660 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7452 (mt0) REVERT: A 2675 GLU cc_start: 0.6657 (mp0) cc_final: 0.6178 (mp0) REVERT: A 2677 GLU cc_start: 0.7681 (tt0) cc_final: 0.7451 (tt0) REVERT: A 2692 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.4976 (pm20) REVERT: A 2769 ARG cc_start: 0.9036 (mpp80) cc_final: 0.8794 (mpp80) REVERT: A 3038 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7131 (pp) REVERT: A 3062 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7062 (tpp) REVERT: A 3144 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.5409 (t80) outliers start: 83 outliers final: 36 residues processed: 287 average time/residue: 0.5507 time to fit residues: 182.0607 Evaluate side-chains 264 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 1120 PHE Chi-restraints excluded: chain A residue 1130 ASN 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 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 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 2692 GLU Chi-restraints excluded: chain A residue 2694 THR Chi-restraints excluded: chain A residue 2758 ASN 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 2967 MET Chi-restraints excluded: chain A residue 2988 LEU Chi-restraints excluded: chain A residue 2989 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 263 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104258 restraints weight = 31842.373| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.18 r_work: 0.2946 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1051 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= 0.134 Angle : 0.470 6.056 30796 Z= 0.245 Chirality : 0.041 0.145 3490 Planarity : 0.004 0.060 3971 Dihedral : 4.338 59.133 3058 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.94 % Allowed : 22.86 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.16), residues: 2783 helix: 2.27 (0.16), residues: 1068 sheet: 0.14 (0.22), residues: 585 loop : -0.44 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2744 TYR 0.012 0.001 TYR A2121 PHE 0.012 0.001 PHE A 359 TRP 0.012 0.001 TRP A2746 HIS 0.010 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00316 (22727) covalent geometry : angle 0.46942 (30794) SS BOND : bond 0.00088 ( 1) SS BOND : angle 2.07043 ( 2) hydrogen bonds : bond 0.03582 ( 1024) hydrogen bonds : angle 4.11894 ( 2856) *********************** 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 326 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 228 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8235 (tpp) cc_final: 0.8011 (tpp) REVERT: A 256 ASN cc_start: 0.7414 (m110) cc_final: 0.7008 (m110) REVERT: A 471 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9031 (mp) REVERT: A 503 GLU cc_start: 0.8134 (mp0) cc_final: 0.7895 (mm-30) REVERT: A 574 MET cc_start: 0.8185 (mmp) cc_final: 0.7938 (mmp) REVERT: A 777 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: A 948 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7783 (m-70) REVERT: A 1156 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8245 (mmmm) REVERT: A 1407 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8203 (p90) REVERT: A 1826 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7136 (mm-40) REVERT: A 2175 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7927 (m100) REVERT: A 2221 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 2455 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 2525 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7422 (ttt90) REVERT: A 2554 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: A 2660 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7464 (mt0) REVERT: A 2675 GLU cc_start: 0.6644 (mp0) cc_final: 0.6162 (mp0) REVERT: A 2692 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.4983 (pm20) REVERT: A 2744 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7814 (mtp-110) REVERT: A 3035 THR cc_start: 0.8293 (p) cc_final: 0.7982 (p) REVERT: A 3038 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7117 (pp) REVERT: A 3062 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7043 (tpp) REVERT: A 3144 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.5472 (t80) outliers start: 98 outliers final: 51 residues processed: 293 average time/residue: 0.6913 time to fit residues: 232.4310 Evaluate side-chains 284 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 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 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 1428 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1621 THR 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 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN Chi-restraints excluded: chain A residue 1912 GLN 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 2262 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 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 2738 GLU Chi-restraints excluded: chain A residue 2758 ASN 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 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 3038 ILE Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3144 PHE Chi-restraints excluded: chain A residue 3145 SER 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 226 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 188 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A1912 GLN ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3622 r_free = 0.3622 target = 0.138630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104926 restraints weight = 31854.716| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.12 r_work: 0.2945 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1089 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= 0.141 Angle : 0.477 6.472 30796 Z= 0.249 Chirality : 0.042 0.146 3490 Planarity : 0.004 0.066 3971 Dihedral : 4.369 59.827 3058 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.82 % Allowed : 23.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.16), residues: 2783 helix: 2.25 (0.16), residues: 1067 sheet: 0.13 (0.22), residues: 585 loop : -0.46 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2744 TYR 0.012 0.001 TYR A2121 PHE 0.012 0.001 PHE A 359 TRP 0.012 0.001 TRP A2746 HIS 0.010 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00334 (22727) covalent geometry : angle 0.47626 (30794) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.96236 ( 2) hydrogen bonds : bond 0.03652 ( 1024) hydrogen bonds : angle 4.12279 ( 2856) *********************** 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 315 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 220 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7430 (m-40) cc_final: 0.7062 (m110) REVERT: A 471 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9056 (mp) REVERT: A 570 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 574 MET cc_start: 0.8170 (mmp) cc_final: 0.7847 (mmp) REVERT: A 948 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7796 (m-70) REVERT: A 1156 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8289 (mmmm) REVERT: A 1407 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8190 (p90) REVERT: A 1826 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7088 (mm-40) REVERT: A 2175 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.7942 (m100) REVERT: A 2221 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7663 (mm) REVERT: A 2455 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: A 2525 ARG cc_start: 0.7956 (ttt90) cc_final: 0.7411 (ttt90) REVERT: A 2554 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: A 2660 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7485 (mt0) REVERT: A 2692 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.4943 (pm20) REVERT: A 2769 ARG cc_start: 0.8975 (mpp80) cc_final: 0.8744 (mpp80) REVERT: A 2987 ASN cc_start: 0.7124 (p0) cc_final: 0.6497 (m110) REVERT: A 3035 THR cc_start: 0.8267 (p) cc_final: 0.7977 (p) REVERT: A 3038 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7140 (pp) REVERT: A 3062 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7032 (tpp) REVERT: A 3144 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.5356 (t80) REVERT: A 3203 LYS cc_start: 0.6834 (mttm) cc_final: 0.6216 (mtpt) outliers start: 95 outliers final: 51 residues processed: 282 average time/residue: 0.6830 time to fit residues: 220.3829 Evaluate side-chains 284 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 471 LEU Chi-restraints excluded: chain A residue 495 LEU 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 886 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 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 1539 GLN Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1621 THR 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 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 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2175 TRP Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 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 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 2758 ASN Chi-restraints excluded: chain A residue 2784 MET 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 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 3145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 148 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS A2500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105075 restraints weight = 31544.128| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.17 r_work: 0.2956 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1097 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= 0.109 Angle : 0.459 6.693 30796 Z= 0.240 Chirality : 0.041 0.155 3490 Planarity : 0.004 0.070 3971 Dihedral : 4.311 59.832 3058 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.22 % Allowed : 23.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2783 helix: 2.33 (0.16), residues: 1062 sheet: 0.16 (0.22), residues: 585 loop : -0.46 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2744 TYR 0.014 0.001 TYR A 306 PHE 0.011 0.001 PHE A 359 TRP 0.011 0.001 TRP A2746 HIS 0.011 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00250 (22727) covalent geometry : angle 0.45830 (30794) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.85641 ( 2) hydrogen bonds : bond 0.03387 ( 1024) hydrogen bonds : angle 4.04655 ( 2856) *********************** 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 304 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 224 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7591 (m-40) cc_final: 0.7340 (m110) REVERT: A 471 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9065 (mp) REVERT: A 570 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8463 (t80) REVERT: A 574 MET cc_start: 0.8154 (mmp) cc_final: 0.7822 (mmp) REVERT: A 941 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 1407 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8173 (p90) REVERT: A 1826 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7120 (mm-40) REVERT: A 1863 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7303 (ppp) REVERT: A 2221 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7564 (mm) REVERT: A 2455 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: A 2525 ARG cc_start: 0.7898 (ttt90) cc_final: 0.7343 (ttt90) REVERT: A 2554 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: A 2660 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7561 (mt0) REVERT: A 2675 GLU cc_start: 0.6707 (mp0) cc_final: 0.6109 (mp0) REVERT: A 2692 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.4851 (pm20) REVERT: A 2744 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7758 (mtp-110) REVERT: A 2987 ASN cc_start: 0.6997 (p0) cc_final: 0.6196 (m110) REVERT: A 3038 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7043 (pp) REVERT: A 3062 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6980 (tpp) REVERT: A 3144 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.5251 (t80) REVERT: A 3203 LYS cc_start: 0.6943 (mttm) cc_final: 0.6273 (mtpt) outliers start: 80 outliers final: 49 residues processed: 275 average time/residue: 0.6536 time to fit residues: 207.5920 Evaluate side-chains 278 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 886 ILE Chi-restraints excluded: chain A residue 941 ILE 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 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 1539 GLN Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1621 THR 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 1808 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1826 GLN 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 2213 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 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 2738 GLU Chi-restraints excluded: chain A residue 2758 ASN 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 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 3038 ILE 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 60 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 212 optimal weight: 5.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1548 ASN ** A1883 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104132 restraints weight = 31856.365| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.19 r_work: 0.2929 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22728 Z= 0.141 Angle : 0.481 6.710 30796 Z= 0.251 Chirality : 0.042 0.202 3490 Planarity : 0.004 0.074 3971 Dihedral : 4.366 59.101 3058 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.30 % Allowed : 23.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.16), residues: 2783 helix: 2.27 (0.16), residues: 1062 sheet: 0.13 (0.22), residues: 588 loop : -0.49 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2744 TYR 0.018 0.001 TYR A 306 PHE 0.013 0.001 PHE A2282 TRP 0.013 0.001 TRP A2687 HIS 0.012 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00333 (22727) covalent geometry : angle 0.48104 (30794) SS BOND : bond 0.00074 ( 1) SS BOND : angle 1.92792 ( 2) hydrogen bonds : bond 0.03662 ( 1024) hydrogen bonds : angle 4.10169 ( 2856) *********************** 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 301 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 219 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 570 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8455 (t80) REVERT: A 574 MET cc_start: 0.8169 (mmp) cc_final: 0.7822 (mmp) REVERT: A 941 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 948 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7744 (m-70) REVERT: A 1407 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8183 (p90) REVERT: A 1826 GLN cc_start: 0.7504 (mm110) cc_final: 0.7165 (mm-40) REVERT: A 2175 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7938 (m100) REVERT: A 2221 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7659 (mm) REVERT: A 2455 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: A 2525 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7356 (ttt90) REVERT: A 2554 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: A 2660 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7578 (mt0) REVERT: A 2692 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.4791 (pm20) REVERT: A 2987 ASN cc_start: 0.7136 (p0) cc_final: 0.6637 (m110) REVERT: A 3035 THR cc_start: 0.8252 (p) cc_final: 0.7969 (p) REVERT: A 3038 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 3062 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6996 (tpp) REVERT: A 3144 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.5340 (t80) REVERT: A 3203 LYS cc_start: 0.7041 (mttm) cc_final: 0.6324 (mtpt) outliers start: 82 outliers final: 52 residues processed: 275 average time/residue: 0.5605 time to fit residues: 177.5109 Evaluate side-chains 282 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 495 LEU 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 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 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 1539 GLN Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1621 THR 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 1808 LEU Chi-restraints excluded: chain A residue 1825 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 2175 TRP Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 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 2738 GLU Chi-restraints excluded: chain A residue 2758 ASN 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 2972 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 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 3145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 266 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 235 optimal weight: 0.0060 chunk 138 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A1356 HIS ** 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 = 0.3638 r_free = 0.3638 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106161 restraints weight = 31753.571| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.10 r_work: 0.2975 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22728 Z= 0.107 Angle : 0.465 8.463 30796 Z= 0.243 Chirality : 0.041 0.189 3490 Planarity : 0.004 0.075 3971 Dihedral : 4.212 58.886 3056 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.98 % Allowed : 23.94 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 2783 helix: 2.33 (0.16), residues: 1063 sheet: 0.16 (0.22), residues: 588 loop : -0.47 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A2744 TYR 0.018 0.001 TYR A 306 PHE 0.011 0.001 PHE A 359 TRP 0.011 0.001 TRP A2687 HIS 0.013 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00244 (22727) covalent geometry : angle 0.46509 (30794) SS BOND : bond 0.00077 ( 1) SS BOND : angle 1.83421 ( 2) hydrogen bonds : bond 0.03348 ( 1024) hydrogen bonds : angle 4.03559 ( 2856) ********************** 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 302 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 570 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8438 (t80) REVERT: A 941 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8934 (tp) REVERT: A 1407 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8168 (p90) REVERT: A 1826 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7050 (mm-40) REVERT: A 2221 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7560 (mm) REVERT: A 2455 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 2525 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7263 (ttt90) REVERT: A 2554 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: A 2638 LEU cc_start: 0.8548 (tp) cc_final: 0.8229 (tm) REVERT: A 2660 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7600 (mt0) REVERT: A 2675 GLU cc_start: 0.6733 (mp0) cc_final: 0.6137 (mp0) REVERT: A 2677 GLU cc_start: 0.7639 (tt0) cc_final: 0.7422 (tt0) REVERT: A 2692 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.4843 (pm20) REVERT: A 2744 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7573 (mtp-110) REVERT: A 2987 ASN cc_start: 0.7039 (p0) cc_final: 0.6358 (m110) REVERT: A 3038 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7062 (pp) REVERT: A 3062 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6976 (tpp) REVERT: A 3144 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5262 (t80) REVERT: A 3203 LYS cc_start: 0.7100 (mttm) cc_final: 0.6374 (mtpt) outliers start: 74 outliers final: 45 residues processed: 277 average time/residue: 0.5620 time to fit residues: 179.7851 Evaluate side-chains 275 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 957 MET Chi-restraints excluded: chain A residue 1120 PHE 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 1583 LEU Chi-restraints excluded: chain A residue 1621 THR 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 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 2143 THR Chi-restraints excluded: chain A residue 2167 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2358 THR 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 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 2758 ASN 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 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 3145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 206 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 230 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105795 restraints weight = 31783.045| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.20 r_work: 0.2971 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22728 Z= 0.105 Angle : 0.466 6.656 30796 Z= 0.243 Chirality : 0.041 0.186 3490 Planarity : 0.004 0.075 3971 Dihedral : 4.186 59.142 3056 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.90 % Allowed : 24.14 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 2783 helix: 2.35 (0.16), residues: 1061 sheet: 0.18 (0.22), residues: 588 loop : -0.47 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A2744 TYR 0.022 0.001 TYR A 306 PHE 0.011 0.001 PHE A 359 TRP 0.012 0.001 TRP A2746 HIS 0.013 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00240 (22727) covalent geometry : angle 0.46566 (30794) SS BOND : bond 0.00078 ( 1) SS BOND : angle 1.79066 ( 2) hydrogen bonds : bond 0.03318 ( 1024) hydrogen bonds : angle 4.01894 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7645.56 seconds wall clock time: 131 minutes 0.53 seconds (7860.53 seconds total)