Starting phenix.real_space_refine on Sat Jul 4 21:00:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.map" model { file = "/net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb8_52990/07_2026/9qb8_52990.cif" } resolution = 3.4 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= -0.005 sd= 0.916 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 76 5.16 5 C 14119 2.51 5 N 3874 2.21 5 O 4269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22339 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2803, 22338 Classifications: {'peptide': 2803} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 116, 'TRANS': 2686} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 4.67, per 1000 atoms: 0.21 Number of scatterers: 22339 At special positions: 0 Unit cell: (180.686, 187.308, 113.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 76 16.00 O 4269 8.00 N 3874 7.00 C 14119 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 30 sheets defined 43.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.805A pdb=" N ASP A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 308 removed outlier: 3.596A pdb=" N HIS A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.609A pdb=" N ILE A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.581A pdb=" N PHE A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.535A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 422 through 451 removed outlier: 3.716A pdb=" N PHE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 472 through 502 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.576A pdb=" N PHE A 582 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 removed outlier: 4.061A pdb=" N ALA A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.590A pdb=" N GLU A 607 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 Processing helix chain 'A' and resid 630 through 631 No H-bonds generated for 'chain 'A' and resid 630 through 631' Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.526A pdb=" N ILE A 636 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 700 removed outlier: 4.460A pdb=" N ILE A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.798A pdb=" N GLY A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 removed outlier: 4.635A pdb=" N GLU A 777 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.880A pdb=" N CYS A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.474A pdb=" N PHE A 860 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 888 removed outlier: 5.794A pdb=" N LYS A 873 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) 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: 4.010A pdb=" N ASN A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 3.562A pdb=" N GLU A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1139 removed outlier: 3.524A 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 1167 Processing helix chain 'A' and resid 1172 through 1184 Processing helix chain 'A' and resid 1200 through 1209 removed outlier: 3.896A pdb=" N GLU A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1229 Proline residue: A1221 - end of helix Processing helix chain 'A' and resid 1237 through 1246 removed outlier: 3.523A pdb=" N LEU A1241 " --> pdb=" O PRO A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.882A pdb=" N GLY A1293 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A1311 " --> pdb=" O VAL A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1323 removed outlier: 3.519A 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 1364 through 1377 removed outlier: 4.451A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1388 removed outlier: 3.721A pdb=" N GLN A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1442 through 1460 removed outlier: 3.969A pdb=" N TYR A1446 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A1449 " --> pdb=" O PHE A1445 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG A1452 " --> pdb=" O HIS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1479 Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.950A 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 1547 removed outlier: 3.777A 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: 3.527A pdb=" N ALA A1610 " --> pdb=" O SER A1606 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A1621 " --> pdb=" O MET A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1629 Processing helix chain 'A' and resid 1634 through 1639 removed outlier: 3.564A pdb=" N ILE A1639 " --> pdb=" O ILE A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1654 removed outlier: 3.687A pdb=" N ASN A1651 " --> pdb=" O ASP A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 removed outlier: 3.665A pdb=" N ASN A1675 " --> pdb=" O ASP A1671 " (cutoff:3.500A) removed outlier: 4.028A 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 1719 through 1730 Processing helix chain 'A' and resid 1733 through 1748 Processing helix chain 'A' and resid 1768 through 1799 removed outlier: 3.703A pdb=" N GLN A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1788 " --> pdb=" O GLN A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1856 removed outlier: 3.908A pdb=" N VAL A1844 " --> pdb=" O VAL A1840 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A1846 " --> pdb=" O GLU A1842 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A1847 " --> pdb=" O VAL A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1885 Processing helix chain 'A' and resid 1898 through 1920 Processing helix chain 'A' and resid 1928 through 1944 Processing helix chain 'A' and resid 1945 through 1961 removed outlier: 3.909A pdb=" N GLY A1949 " --> pdb=" O GLY A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1982 removed outlier: 5.267A pdb=" N GLN A1979 " --> pdb=" O ASN A1975 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU A1980 " --> pdb=" O SER A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2003 removed outlier: 3.891A 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 2028 through 2038 removed outlier: 4.478A pdb=" N ILE A2032 " --> pdb=" O GLY A2028 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A2038 " --> pdb=" O ARG A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2059 removed outlier: 4.285A 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 2413 removed outlier: 4.448A pdb=" N ASN A2411 " --> pdb=" O ALA A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2452 Processing helix chain 'A' and resid 2458 through 2470 removed outlier: 3.526A pdb=" N GLY A2470 " --> pdb=" O LEU A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2609 through 2617 Processing helix chain 'A' and resid 2742 through 2748 removed outlier: 3.963A pdb=" N TRP A2746 " --> pdb=" O SER A2742 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN A2748 " --> pdb=" O ARG A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2787 removed outlier: 3.841A pdb=" N GLN A2787 " --> pdb=" O LEU A2783 " (cutoff:3.500A) Processing helix chain 'A' and resid 2823 through 2828 removed outlier: 3.747A pdb=" N THR A2827 " --> pdb=" O VAL A2824 " (cutoff:3.500A) removed outlier: 3.960A 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 2853 through 2856 Processing helix chain 'A' and resid 2868 through 2884 Processing helix chain 'A' and resid 2979 through 2983 removed outlier: 4.137A pdb=" N TRP A2983 " --> pdb=" O ARG A2980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3056 through 3070 Processing helix chain 'A' and resid 3072 through 3086 removed outlier: 3.584A pdb=" N ARG A3076 " --> pdb=" O ALA A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3102 removed outlier: 3.765A pdb=" N LEU A3099 " --> pdb=" O THR A3095 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A3100 " --> pdb=" O PRO A3096 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS A3101 " --> pdb=" O GLU A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3190 through 3195 removed outlier: 3.582A pdb=" N TYR A3193 " --> pdb=" O GLU A3190 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU A3194 " --> pdb=" O ARG A3191 " (cutoff:3.500A) 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: 5.942A pdb=" N TYR A 345 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS A 509 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A 347 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 316 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TRP A 348 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 318 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 319 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.685A 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 779 through 780 Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 936 Processing sheet with id=AA6, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 3.810A pdb=" N GLY A1188 " --> pdb=" O SER A1282 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A1269 " --> pdb=" O THR A1276 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLN A1278 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N GLY A1267 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA8, first strand: chain 'A' and resid 1464 through 1466 removed outlier: 4.271A pdb=" N ASN A1464 " --> pdb=" O ASP A1603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1679 through 1682 Processing sheet with id=AB1, first strand: chain 'A' and resid 1697 through 1699 Processing sheet with id=AB2, first strand: chain 'A' and resid 1810 through 1817 removed outlier: 6.433A pdb=" N ARG A1822 " --> pdb=" O ALA A1816 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.623A pdb=" N LEU A2070 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A2210 " --> pdb=" O ALA A2247 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN A2249 " --> pdb=" O THR A2210 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A2212 " --> pdb=" O GLN A2249 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A2246 " --> pdb=" O THR A2268 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER A2270 " --> pdb=" O LEU A2246 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A2248 " --> pdb=" O SER A2270 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A2269 " --> pdb=" O VAL A2314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2091 through 2096 removed outlier: 4.746A pdb=" N GLU A2095 " --> pdb=" O LYS A2080 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS A2080 " --> pdb=" O GLU A2095 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY A2079 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR A2202 " --> pdb=" O GLY A2079 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A2081 " --> pdb=" O THR A2202 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE A2204 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A2083 " --> pdb=" O ILE A2204 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY A2254 " --> pdb=" O THR A2304 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR A2306 " --> pdb=" O GLY A2254 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A2256 " --> pdb=" O THR A2306 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS A2308 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A2258 " --> pdb=" O LYS A2308 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A2291 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A2304 " --> pdb=" O GLN A2289 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN A2289 " --> pdb=" O THR A2304 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2098 through 2100 removed outlier: 6.705A pdb=" N PHE A2098 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN A2162 " --> pdb=" O LEU A2197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2168 through 2172 Processing sheet with id=AB7, first strand: chain 'A' and resid 2281 through 2283 removed outlier: 5.996A pdb=" N ASP A2321 " --> pdb=" O THR A2340 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A2342 " --> pdb=" O ASP A2321 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A2323 " --> pdb=" O ILE A2342 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY A2339 " --> pdb=" O THR A2361 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR A2363 " --> pdb=" O GLY A2339 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A2341 " --> pdb=" O THR A2363 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A2403 " --> pdb=" O LEU A2360 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU A2362 " --> pdb=" O GLN A2403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2330 through 2333 removed outlier: 6.562A pdb=" N GLY A2346 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLU A2372 " --> pdb=" O GLY A2346 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A2348 " --> pdb=" O GLU A2372 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE A2374 " --> pdb=" O ASN A2348 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A2350 " --> pdb=" O PHE A2374 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ARG A2418 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS A2371 " --> pdb=" O ARG A2418 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N HIS A2420 " --> pdb=" O HIS A2371 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A2373 " --> pdb=" O HIS A2420 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE A2417 " --> pdb=" O ALA A2429 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A2426 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A2435 " --> pdb=" O ARG A2432 " (cutoff:3.500A) removed outlier: 12.655A pdb=" N THR A2474 " --> pdb=" O GLY A2435 " (cutoff:3.500A) removed outlier: 12.192A pdb=" N GLN A2437 " --> pdb=" O THR A2474 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N GLU A2476 " --> pdb=" O GLN A2437 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N ALA A2439 " --> pdb=" O GLU A2476 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG A2478 " --> pdb=" O ALA A2439 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER A2441 " --> pdb=" O ARG A2478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A2477 " --> pdb=" O TYR A2488 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A2488 " --> pdb=" O VAL A2477 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A2485 " --> pdb=" O GLN A2498 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A2495 " --> pdb=" O ALA A2517 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A2519 " --> pdb=" O LEU A2495 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR A2497 " --> pdb=" O THR A2519 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR A2516 " --> pdb=" O GLN A2540 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE A2542 " --> pdb=" O THR A2516 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A2518 " --> pdb=" O ILE A2542 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A2565 " --> pdb=" O GLY A2625 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A2625 " --> pdb=" O GLY A2565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2383 through 2384 removed outlier: 4.647A pdb=" N ILE A2393 " --> pdb=" O LYS A2384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2525 through 2527 removed outlier: 7.300A pdb=" N ILE A2553 " --> pdb=" O ALA A2601 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2637 through 2640 removed outlier: 6.349A pdb=" N ARG A2637 " --> pdb=" O CYS A2663 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU A2665 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU A2639 " --> pdb=" O GLU A2665 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR A2711 " --> pdb=" O ALA A2686 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA A2686 " --> pdb=" O TYR A2711 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A2713 " --> pdb=" O LYS A2684 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 4.065A pdb=" N ASN A2645 " --> pdb=" O VAL A2726 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A2726 " --> pdb=" O ASN A2645 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A2720 " --> pdb=" O LEU A2651 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A2651 " --> pdb=" O VAL A2720 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 4.065A pdb=" N ASN A2645 " --> pdb=" O VAL A2726 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A2726 " --> pdb=" O ASN A2645 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG A2723 " --> pdb=" O LEU A2678 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A2678 " --> pdb=" O ARG A2723 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A2725 " --> pdb=" O GLY A2676 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY A2676 " --> pdb=" O LYS A2725 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A2727 " --> pdb=" O VAL A2674 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A2674 " --> pdb=" O HIS A2727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2731 through 2733 removed outlier: 5.947A pdb=" N LEU A2731 " --> pdb=" O ILE A2753 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A2752 " --> pdb=" O ARG A2814 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A2816 " --> pdb=" O ILE A2752 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A2754 " --> pdb=" O THR A2816 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2858 through 2861 Processing sheet with id=AC7, first strand: chain 'A' and resid 2910 through 2912 removed outlier: 6.843A pdb=" N THR A2911 " --> pdb=" O SER A2975 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2935 through 2938 removed outlier: 6.241A pdb=" N LEU A2988 " --> pdb=" O VAL A3008 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A3008 " --> pdb=" O LEU A2988 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2947 through 2950 Processing sheet with id=AD1, first strand: chain 'A' and resid 3104 through 3110 removed outlier: 6.457A pdb=" N GLN A3152 " --> pdb=" O ILE A3198 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A3200 " --> pdb=" O GLN A3152 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR A3154 " --> pdb=" O VAL A3200 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A3202 " --> pdb=" O TYR A3154 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG A3156 " --> pdb=" O LEU A3202 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR A3199 " --> pdb=" O VAL A3188 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL A3188 " --> pdb=" O TYR A3199 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A3201 " --> pdb=" O THR A3186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3123 through 3125 Processing sheet with id=AD3, first strand: chain 'A' and resid 3132 through 3134 removed outlier: 3.608A pdb=" N ASP A3164 " --> pdb=" O THR A3176 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2808 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: 8.43 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3816 1.32 - 1.44: 5853 1.44 - 1.57: 12968 1.57 - 1.69: 0 1.69 - 1.82: 138 Bond restraints: 22775 Sorted by residual: bond pdb=" N TYR A 536 " pdb=" CA TYR A 536 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.22e+01 bond pdb=" C PRO A 537 " pdb=" O PRO A 537 " ideal model delta sigma weight residual 1.238 1.196 0.042 1.37e-02 5.33e+03 9.28e+00 bond pdb=" N MET A 631 " pdb=" CA MET A 631 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.41e-02 5.03e+03 9.01e+00 bond pdb=" N VAL A 814 " pdb=" CA VAL A 814 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.94e+00 bond pdb=" N VAL A 830 " pdb=" CA VAL A 830 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.55e+00 ... (remaining 22770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 30178 2.21 - 4.42: 585 4.42 - 6.63: 74 6.63 - 8.84: 18 8.84 - 11.05: 6 Bond angle restraints: 30861 Sorted by residual: angle pdb=" C PHE A 835 " pdb=" CA PHE A 835 " pdb=" CB PHE A 835 " ideal model delta sigma weight residual 110.77 102.74 8.03 1.67e+00 3.59e-01 2.31e+01 angle pdb=" CA ASN A 535 " pdb=" C ASN A 535 " pdb=" O ASN A 535 " ideal model delta sigma weight residual 122.13 117.30 4.83 1.13e+00 7.83e-01 1.83e+01 angle pdb=" C TYR A 536 " pdb=" CA TYR A 536 " pdb=" CB TYR A 536 " ideal model delta sigma weight residual 113.49 105.73 7.76 1.82e+00 3.02e-01 1.82e+01 angle pdb=" N GLU A2596 " pdb=" CA GLU A2596 " pdb=" C GLU A2596 " ideal model delta sigma weight residual 113.38 108.69 4.69 1.17e+00 7.31e-01 1.61e+01 angle pdb=" CA ARG A3209 " pdb=" CB ARG A3209 " pdb=" CG ARG A3209 " ideal model delta sigma weight residual 114.10 122.01 -7.91 2.00e+00 2.50e-01 1.56e+01 ... (remaining 30856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11798 17.92 - 35.85: 1555 35.85 - 53.77: 362 53.77 - 71.70: 86 71.70 - 89.62: 24 Dihedral angle restraints: 13825 sinusoidal: 5660 harmonic: 8165 Sorted by residual: dihedral pdb=" CA MET A2967 " pdb=" C MET A2967 " pdb=" N VAL A2968 " pdb=" CA VAL A2968 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA TRP A2140 " pdb=" C TRP A2140 " pdb=" N PRO A2141 " pdb=" CA PRO A2141 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A1577 " pdb=" C SER A1577 " pdb=" N THR A1578 " pdb=" CA THR A1578 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 13822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2613 0.048 - 0.097: 679 0.097 - 0.145: 186 0.145 - 0.193: 14 0.193 - 0.242: 4 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CA ILE A 824 " pdb=" N ILE A 824 " pdb=" C ILE A 824 " pdb=" CB ILE A 824 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL A 321 " pdb=" N VAL A 321 " pdb=" C VAL A 321 " pdb=" CB VAL A 321 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A3005 " pdb=" CA ILE A3005 " pdb=" CG1 ILE A3005 " pdb=" CG2 ILE A3005 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 3493 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 716 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 717 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 823 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C CYS A 823 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS A 823 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 824 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 630 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C LYS A 630 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 630 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 631 " -0.014 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3561 2.76 - 3.30: 22412 3.30 - 3.83: 36941 3.83 - 4.37: 43353 4.37 - 4.90: 74420 Nonbonded interactions: 180687 Sorted by model distance: nonbonded pdb=" CG GLU A 819 " pdb="MN MN A5000 " model vdw 2.227 3.460 nonbonded pdb=" CD GLU A 819 " pdb="MN MN A5000 " model vdw 2.246 3.290 nonbonded pdb=" N ASN A 535 " pdb=" OD1 ASN A 535 " model vdw 2.396 3.120 nonbonded pdb=" OG1 THR A 638 " pdb=" N LYS A 639 " model vdw 2.463 3.120 nonbonded pdb=" O LEU A1699 " pdb=" OD1 ASP A1700 " model vdw 2.477 3.040 ... (remaining 180682 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: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.980 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22776 Z= 0.240 Angle : 0.740 11.052 30863 Z= 0.402 Chirality : 0.047 0.242 3496 Planarity : 0.005 0.112 3983 Dihedral : 17.108 89.622 8560 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 0.44 % Allowed : 28.71 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2791 helix: 1.45 (0.16), residues: 1057 sheet: -0.64 (0.22), residues: 549 loop : -0.69 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3100 TYR 0.021 0.002 TYR A 536 PHE 0.017 0.002 PHE A 778 TRP 0.035 0.002 TRP A3113 HIS 0.005 0.001 HIS A2514 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (22775) covalent geometry : angle 0.73983 / 0.40 (30861) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.31011 / 0.16 ( 2) hydrogen bonds : bond 0.12691 / 8.40 ( 1004) hydrogen bonds : angle 5.67428 / 4.11 ( 2808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 PHE cc_start: 0.7505 (m-80) cc_final: 0.7214 (m-80) REVERT: A 1214 ASP cc_start: 0.8343 (p0) cc_final: 0.8053 (p0) REVERT: A 1937 MET cc_start: 0.9298 (mmp) cc_final: 0.9024 (mmt) REVERT: A 3061 MET cc_start: 0.6376 (ptp) cc_final: 0.5992 (ptp) REVERT: A 3119 LYS cc_start: 0.8858 (ptpp) cc_final: 0.8657 (ptpp) outliers start: 11 outliers final: 4 residues processed: 197 average time/residue: 0.1588 time to fit residues: 49.7807 Evaluate side-chains 156 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 2613 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 404 GLN A2228 GLN ** A2371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 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 = 0.3986 r_free = 0.3986 target = 0.130147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091618 restraints weight = 48948.390| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.79 r_work: 0.3054 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22776 Z= 0.178 Angle : 0.588 7.373 30863 Z= 0.304 Chirality : 0.043 0.159 3496 Planarity : 0.004 0.075 3983 Dihedral : 4.190 40.201 3059 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 23.90 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2791 helix: 1.74 (0.16), residues: 1059 sheet: -0.62 (0.22), residues: 544 loop : -0.60 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A3100 TYR 0.021 0.002 TYR A 536 PHE 0.013 0.001 PHE A1918 TRP 0.020 0.002 TRP A3113 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (22775) covalent geometry : angle 0.58833 / 0.30 (30861) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.38248 / 0.20 ( 2) hydrogen bonds : bond 0.04364 / 2.92 ( 1004) hydrogen bonds : angle 4.65939 / 3.36 ( 2808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.8550 (ttm) cc_final: 0.8199 (ttm) REVERT: A 800 LYS cc_start: 0.8111 (pttm) cc_final: 0.7887 (mmtm) REVERT: A 1214 ASP cc_start: 0.8421 (p0) cc_final: 0.8080 (p0) REVERT: A 1937 MET cc_start: 0.9261 (mmp) cc_final: 0.8994 (mmt) REVERT: A 2081 MET cc_start: 0.8727 (ttp) cc_final: 0.8315 (ttp) REVERT: A 2095 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: A 2265 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8622 (ptpp) REVERT: A 2488 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 3016 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7949 (mtt180) REVERT: A 3061 MET cc_start: 0.6328 (ptp) cc_final: 0.5948 (ptp) outliers start: 79 outliers final: 36 residues processed: 230 average time/residue: 0.1523 time to fit residues: 55.7908 Evaluate side-chains 186 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2488 TYR Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3015 VAL Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 101 optimal weight: 0.5980 chunk 262 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 HIS A1979 GLN A2228 GLN A2540 GLN ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093304 restraints weight = 49040.578| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.16 r_work: 0.3112 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22776 Z= 0.114 Angle : 0.520 7.912 30863 Z= 0.267 Chirality : 0.042 0.192 3496 Planarity : 0.004 0.052 3983 Dihedral : 3.929 37.000 3055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.49 % Allowed : 23.41 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2791 helix: 1.92 (0.16), residues: 1066 sheet: -0.50 (0.22), residues: 549 loop : -0.51 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3100 TYR 0.018 0.001 TYR A2581 PHE 0.011 0.001 PHE A 984 TRP 0.014 0.001 TRP A2140 HIS 0.007 0.001 HIS A2513 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (22775) covalent geometry : angle 0.51959 / 0.27 (30861) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.52276 / 0.28 ( 2) hydrogen bonds : bond 0.03691 / 2.45 ( 1004) hydrogen bonds : angle 4.31934 / 3.11 ( 2808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: A 631 MET cc_start: 0.8538 (ttm) cc_final: 0.8221 (ttm) REVERT: A 689 GLN cc_start: 0.8980 (tp40) cc_final: 0.8668 (tp40) REVERT: A 800 LYS cc_start: 0.8148 (pttm) cc_final: 0.7877 (mmtm) REVERT: A 1214 ASP cc_start: 0.8326 (p0) cc_final: 0.7938 (p0) REVERT: A 1937 MET cc_start: 0.9280 (mmp) cc_final: 0.9021 (mmt) REVERT: A 1957 ARG cc_start: 0.8308 (tpm170) cc_final: 0.7816 (tpm170) REVERT: A 2095 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 2265 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8562 (ptpp) REVERT: A 2347 ASN cc_start: 0.7605 (t0) cc_final: 0.7313 (m-40) REVERT: A 2739 MET cc_start: 0.7701 (ppp) cc_final: 0.6605 (ppp) REVERT: A 3016 ARG cc_start: 0.8365 (mtt90) cc_final: 0.8100 (mtt180) REVERT: A 3061 MET cc_start: 0.6321 (ptp) cc_final: 0.5977 (ptp) outliers start: 62 outliers final: 34 residues processed: 216 average time/residue: 0.1331 time to fit residues: 45.9743 Evaluate side-chains 188 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2514 HIS Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 242 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 244 optimal weight: 40.0000 chunk 169 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 656 HIS A 981 HIS A1824 ASN ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.129749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091705 restraints weight = 48842.415| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.29 r_work: 0.3078 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.151 Angle : 0.522 8.187 30863 Z= 0.268 Chirality : 0.042 0.171 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.828 20.605 3053 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 22.69 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2791 helix: 1.99 (0.16), residues: 1061 sheet: -0.50 (0.23), residues: 526 loop : -0.48 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2599 TYR 0.021 0.001 TYR A2121 PHE 0.011 0.001 PHE A1918 TRP 0.018 0.001 TRP A3113 HIS 0.004 0.001 HIS A2514 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (22775) covalent geometry : angle 0.52193 / 0.27 (30861) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.56522 / 0.30 ( 2) hydrogen bonds : bond 0.03757 / 2.51 ( 1004) hydrogen bonds : angle 4.23883 / 3.05 ( 2808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 160 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: A 455 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: A 631 MET cc_start: 0.8424 (ttm) cc_final: 0.8080 (ttm) REVERT: A 689 GLN cc_start: 0.8963 (tp40) cc_final: 0.8586 (tp40) REVERT: A 800 LYS cc_start: 0.8115 (pttm) cc_final: 0.7882 (mmtm) REVERT: A 1214 ASP cc_start: 0.8290 (p0) cc_final: 0.7937 (p0) REVERT: A 1904 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 1937 MET cc_start: 0.9327 (mmp) cc_final: 0.9100 (mmt) REVERT: A 1957 ARG cc_start: 0.8359 (tpm170) cc_final: 0.8097 (tpm170) REVERT: A 2095 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: A 2265 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8420 (ptpp) REVERT: A 2347 ASN cc_start: 0.7590 (t0) cc_final: 0.7362 (m-40) REVERT: A 2614 LEU cc_start: 0.8974 (tp) cc_final: 0.8773 (tp) REVERT: A 3061 MET cc_start: 0.6721 (ptp) cc_final: 0.6377 (ptp) outliers start: 83 outliers final: 49 residues processed: 230 average time/residue: 0.1586 time to fit residues: 57.6951 Evaluate side-chains 204 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1904 GLU Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2263 VAL Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 262 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 222 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 chunk 114 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A1638 HIS A1796 HIS ** A2603 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 = 0.3983 r_free = 0.3983 target = 0.129783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091679 restraints weight = 48782.075| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.12 r_work: 0.3083 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22776 Z= 0.140 Angle : 0.515 10.654 30863 Z= 0.263 Chirality : 0.042 0.187 3496 Planarity : 0.004 0.054 3983 Dihedral : 3.761 20.458 3053 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 22.77 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2791 helix: 2.08 (0.16), residues: 1061 sheet: -0.46 (0.23), residues: 537 loop : -0.46 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2980 TYR 0.018 0.001 TYR A2121 PHE 0.010 0.001 PHE A1918 TRP 0.029 0.001 TRP A3081 HIS 0.016 0.001 HIS A2514 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (22775) covalent geometry : angle 0.51455 / 0.26 (30861) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.49998 / 0.26 ( 2) hydrogen bonds : bond 0.03627 / 2.42 ( 1004) hydrogen bonds : angle 4.17472 / 3.01 ( 2808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 161 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8272 (mm-30) REVERT: A 455 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: A 689 GLN cc_start: 0.8940 (tp40) cc_final: 0.8719 (tp40) REVERT: A 800 LYS cc_start: 0.8161 (pttm) cc_final: 0.7930 (mptt) REVERT: A 1214 ASP cc_start: 0.8347 (p0) cc_final: 0.7980 (p0) REVERT: A 1904 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 1937 MET cc_start: 0.9342 (mmp) cc_final: 0.9141 (mmt) REVERT: A 1957 ARG cc_start: 0.8372 (tpm170) cc_final: 0.7914 (tpm170) REVERT: A 2095 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 2265 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8558 (ptpp) REVERT: A 2303 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7763 (mtt) REVERT: A 3061 MET cc_start: 0.6730 (ptp) cc_final: 0.6270 (ptp) outliers start: 76 outliers final: 50 residues processed: 223 average time/residue: 0.1512 time to fit residues: 53.9457 Evaluate side-chains 210 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1904 GLU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3062 MET Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS A1796 HIS ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.130819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092998 restraints weight = 48905.530| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.33 r_work: 0.3109 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22776 Z= 0.107 Angle : 0.509 9.447 30863 Z= 0.257 Chirality : 0.041 0.173 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.655 20.482 3053 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.53 % Allowed : 22.77 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2791 helix: 2.17 (0.16), residues: 1067 sheet: -0.37 (0.23), residues: 536 loop : -0.45 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2980 TYR 0.014 0.001 TYR A2121 PHE 0.011 0.001 PHE A3032 TRP 0.037 0.001 TRP A3081 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22775) covalent geometry : angle 0.50881 / 0.26 (30861) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.49210 / 0.26 ( 2) hydrogen bonds : bond 0.03325 / 2.22 ( 1004) hydrogen bonds : angle 4.05950 / 2.93 ( 2808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: A 643 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7868 (mmm-85) REVERT: A 689 GLN cc_start: 0.8872 (tp40) cc_final: 0.8642 (tp40) REVERT: A 994 MET cc_start: 0.5367 (pmm) cc_final: 0.4699 (mmt) REVERT: A 1214 ASP cc_start: 0.8377 (p0) cc_final: 0.8048 (p0) REVERT: A 1319 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 1904 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: A 1957 ARG cc_start: 0.8297 (tpm170) cc_final: 0.7894 (tpm170) REVERT: A 2095 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: A 2265 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8603 (ptpp) REVERT: A 3016 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7972 (ttm110) REVERT: A 3061 MET cc_start: 0.6801 (ptp) cc_final: 0.6357 (ptp) outliers start: 63 outliers final: 44 residues processed: 219 average time/residue: 0.1472 time to fit residues: 51.2557 Evaluate side-chains 208 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1904 GLU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2584 GLN Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 2968 VAL Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3119 LYS Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 3 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 148 optimal weight: 0.0980 chunk 256 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 601 ASN A 981 HIS ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093668 restraints weight = 48903.409| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.15 r_work: 0.3122 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22776 Z= 0.099 Angle : 0.501 10.103 30863 Z= 0.253 Chirality : 0.041 0.174 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.554 20.365 3053 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.25 % Allowed : 23.37 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2791 helix: 2.29 (0.16), residues: 1065 sheet: -0.33 (0.23), residues: 540 loop : -0.45 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2723 TYR 0.012 0.001 TYR A2121 PHE 0.014 0.001 PHE A 582 TRP 0.024 0.001 TRP A3081 HIS 0.005 0.001 HIS A 981 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (22775) covalent geometry : angle 0.50148 / 0.25 (30861) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 0.46962 / 0.25 ( 2) hydrogen bonds : bond 0.03169 / 2.11 ( 1004) hydrogen bonds : angle 3.97018 / 2.87 ( 2808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: A 631 MET cc_start: 0.8108 (ttm) cc_final: 0.7868 (ttm) REVERT: A 643 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7869 (mmm-85) REVERT: A 689 GLN cc_start: 0.8838 (tp40) cc_final: 0.8592 (tp40) REVERT: A 994 MET cc_start: 0.5318 (pmm) cc_final: 0.4687 (mmt) REVERT: A 1214 ASP cc_start: 0.8391 (p0) cc_final: 0.8078 (p0) REVERT: A 1319 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 1957 ARG cc_start: 0.8267 (tpm170) cc_final: 0.7879 (tpm170) REVERT: A 1999 ASP cc_start: 0.8293 (t0) cc_final: 0.8038 (m-30) REVERT: A 2081 MET cc_start: 0.8476 (ttp) cc_final: 0.7713 (ttp) REVERT: A 2095 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: A 2265 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8581 (ptpp) REVERT: A 2303 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7758 (mtt) REVERT: A 2941 MET cc_start: 0.5636 (tpp) cc_final: 0.5188 (tpp) REVERT: A 3016 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7939 (ttm110) REVERT: A 3061 MET cc_start: 0.6841 (ptp) cc_final: 0.6431 (ptp) REVERT: A 3062 MET cc_start: 0.5880 (mmm) cc_final: 0.5615 (mmm) outliers start: 56 outliers final: 42 residues processed: 217 average time/residue: 0.1546 time to fit residues: 52.7629 Evaluate side-chains 205 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 210 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 102 optimal weight: 0.0050 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS A1982 GLN ** A2603 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 = 0.3989 r_free = 0.3989 target = 0.130230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092175 restraints weight = 48818.347| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.16 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22776 Z= 0.132 Angle : 0.524 11.447 30863 Z= 0.264 Chirality : 0.042 0.281 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.598 20.481 3053 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.61 % Allowed : 22.97 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2791 helix: 2.31 (0.16), residues: 1058 sheet: -0.29 (0.23), residues: 546 loop : -0.44 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2723 TYR 0.018 0.001 TYR A2121 PHE 0.011 0.001 PHE A 582 TRP 0.018 0.001 TRP A3081 HIS 0.004 0.001 HIS A1129 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22775) covalent geometry : angle 0.52401 / 0.26 (30861) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.54257 / 0.29 ( 2) hydrogen bonds : bond 0.03399 / 2.29 ( 1004) hydrogen bonds : angle 4.00757 / 2.89 ( 2808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: A 643 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7890 (mmm-85) REVERT: A 689 GLN cc_start: 0.8886 (tp40) cc_final: 0.8633 (tp40) REVERT: A 994 MET cc_start: 0.5307 (pmm) cc_final: 0.4692 (mmt) REVERT: A 1214 ASP cc_start: 0.8365 (p0) cc_final: 0.8045 (p0) REVERT: A 1319 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8380 (tt) REVERT: A 1912 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: A 1957 ARG cc_start: 0.8344 (tpm170) cc_final: 0.7916 (tpm170) REVERT: A 1999 ASP cc_start: 0.8352 (t0) cc_final: 0.8077 (m-30) REVERT: A 2095 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 2265 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8592 (ptpp) REVERT: A 2303 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7790 (mtt) REVERT: A 2941 MET cc_start: 0.5297 (tpp) cc_final: 0.4900 (tpp) REVERT: A 2993 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5499 (mp0) REVERT: A 3016 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7898 (ttm110) REVERT: A 3061 MET cc_start: 0.6854 (ptp) cc_final: 0.6433 (ptp) REVERT: A 3062 MET cc_start: 0.6078 (mmm) cc_final: 0.5823 (mmm) REVERT: A 3100 ARG cc_start: 0.5430 (mtm-85) cc_final: 0.5181 (mtm-85) outliers start: 65 outliers final: 49 residues processed: 210 average time/residue: 0.1488 time to fit residues: 49.6255 Evaluate side-chains 210 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1434 HIS Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 2993 GLU Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3119 LYS Chi-restraints excluded: chain A residue 3201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 229 optimal weight: 6.9990 chunk 270 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 218 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A1124 HIS A1129 HIS A1981 GLN ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.129576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091616 restraints weight = 49242.245| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.20 r_work: 0.3062 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22776 Z= 0.149 Angle : 0.534 11.169 30863 Z= 0.269 Chirality : 0.042 0.269 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.651 20.649 3053 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.45 % Allowed : 23.05 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2791 helix: 2.28 (0.16), residues: 1058 sheet: -0.29 (0.23), residues: 545 loop : -0.44 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2653 TYR 0.022 0.001 TYR A1986 PHE 0.012 0.001 PHE A 582 TRP 0.018 0.001 TRP A3081 HIS 0.005 0.001 HIS A1129 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (22775) covalent geometry : angle 0.53430 / 0.27 (30861) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.73052 / 0.39 ( 2) hydrogen bonds : bond 0.03507 / 2.36 ( 1004) hydrogen bonds : angle 4.05155 / 2.92 ( 2808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: A 643 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7908 (mmm-85) REVERT: A 689 GLN cc_start: 0.8925 (tp40) cc_final: 0.8657 (tp40) REVERT: A 994 MET cc_start: 0.5424 (pmm) cc_final: 0.4704 (mmt) REVERT: A 1214 ASP cc_start: 0.8358 (p0) cc_final: 0.8028 (p0) REVERT: A 1319 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 1957 ARG cc_start: 0.8392 (tpm170) cc_final: 0.7965 (tpm170) REVERT: A 1999 ASP cc_start: 0.8396 (t0) cc_final: 0.8091 (m-30) REVERT: A 2095 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: A 2265 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8585 (ptpp) REVERT: A 2303 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: A 2941 MET cc_start: 0.5865 (tpp) cc_final: 0.5358 (tpp) REVERT: A 2993 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5529 (mp0) REVERT: A 3016 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7954 (ttm110) REVERT: A 3100 ARG cc_start: 0.5783 (mtm-85) cc_final: 0.5493 (mtm-85) outliers start: 61 outliers final: 49 residues processed: 205 average time/residue: 0.1568 time to fit residues: 51.5124 Evaluate side-chains 207 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1434 HIS Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 2993 GLU Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3119 LYS Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 178 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.2980 chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A1796 HIS A1912 GLN A1981 GLN ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.130293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091688 restraints weight = 49166.737| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.45 r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22776 Z= 0.120 Angle : 0.526 11.447 30863 Z= 0.264 Chirality : 0.042 0.306 3496 Planarity : 0.004 0.049 3983 Dihedral : 3.609 20.416 3053 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.37 % Allowed : 23.13 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2791 helix: 2.32 (0.16), residues: 1065 sheet: -0.20 (0.23), residues: 537 loop : -0.48 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2723 TYR 0.016 0.001 TYR A2121 PHE 0.011 0.001 PHE A 582 TRP 0.020 0.001 TRP A3081 HIS 0.004 0.001 HIS A2412 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22775) covalent geometry : angle 0.52553 / 0.26 (30861) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.74296 / 0.39 ( 2) hydrogen bonds : bond 0.03315 / 2.22 ( 1004) hydrogen bonds : angle 3.99163 / 2.89 ( 2808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: A 689 GLN cc_start: 0.8856 (tp40) cc_final: 0.8614 (tp40) REVERT: A 994 MET cc_start: 0.5479 (pmm) cc_final: 0.4674 (mmt) REVERT: A 1214 ASP cc_start: 0.8355 (p0) cc_final: 0.8017 (p0) REVERT: A 1319 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 1957 ARG cc_start: 0.8345 (tpm170) cc_final: 0.7938 (tpm170) REVERT: A 1999 ASP cc_start: 0.8290 (t0) cc_final: 0.8041 (m-30) REVERT: A 2095 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: A 2265 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8535 (ptpp) REVERT: A 2303 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7834 (mtt) REVERT: A 2941 MET cc_start: 0.6445 (tpp) cc_final: 0.5903 (tpp) REVERT: A 2993 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: A 3016 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8003 (ttm110) outliers start: 59 outliers final: 48 residues processed: 204 average time/residue: 0.1623 time to fit residues: 52.6301 Evaluate side-chains 207 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1434 HIS Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1963 VAL Chi-restraints excluded: chain A residue 1981 GLN Chi-restraints excluded: chain A residue 2019 THR Chi-restraints excluded: chain A residue 2095 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2265 LYS Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2725 LYS Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 2993 GLU Chi-restraints excluded: chain A residue 3005 ILE Chi-restraints excluded: chain A residue 3033 SER Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3119 LYS Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 57 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A1981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.130266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092240 restraints weight = 49114.346| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.15 r_work: 0.3091 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 22776 Z= 0.181 Angle : 0.734 59.149 30863 Z= 0.401 Chirality : 0.044 0.586 3496 Planarity : 0.004 0.090 3983 Dihedral : 3.619 20.408 3053 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.21 % Allowed : 23.33 % Favored : 74.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2791 helix: 2.31 (0.16), residues: 1065 sheet: -0.20 (0.23), residues: 537 loop : -0.48 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.000 ARG A 643 TYR 0.015 0.001 TYR A2121 PHE 0.010 0.001 PHE A2237 TRP 0.018 0.001 TRP A3081 HIS 0.003 0.001 HIS A1601 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (22775) covalent geometry : angle 0.73435 / 0.40 (30861) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 0.74155 / 0.39 ( 2) hydrogen bonds : bond 0.03369 / 2.26 ( 1004) hydrogen bonds : angle 3.99587 / 2.89 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5668.24 seconds wall clock time: 98 minutes 0.87 seconds (5880.87 seconds total)