Starting phenix.real_space_refine on Fri Sep 19 05:29:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_52990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_52990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_52990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_52990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb8_52990/09_2025/9qb8_52990.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 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: 1.85 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: 8.64 Time building geometry restraints manager: 2.67 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 2.720 nonbonded pdb=" CD GLU A 819 " pdb="MN MN A5000 " model vdw 2.246 2.550 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: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 aren 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 covalent geometry : bond 0.00484 (22775) covalent geometry : angle 0.73983 (30861) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.31011 ( 2) hydrogen bonds : bond 0.12691 ( 1004) hydrogen bonds : angle 5.67428 ( 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 : 1.089 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: 0.1707 time to fit residues: 53.3232 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 : 0.929 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 404 GLN A2228 GLN ** A2540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3042 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 = 0.3985 r_free = 0.3985 target = 0.130133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091574 restraints weight = 48940.231| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.77 r_work: 0.3041 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22776 Z= 0.176 Angle : 0.584 7.488 30863 Z= 0.301 Chirality : 0.043 0.159 3496 Planarity : 0.004 0.073 3983 Dihedral : 4.192 39.948 3059 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 23.69 % Favored : 73.13 % 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 aren not related in a simple way. whole: 0.40 (0.16), residues: 2791 helix: 1.75 (0.16), residues: 1059 sheet: -0.63 (0.22), residues: 544 loop : -0.60 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A3100 TYR 0.022 0.002 TYR A2121 PHE 0.013 0.002 PHE A1918 TRP 0.021 0.002 TRP A3113 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00410 (22775) covalent geometry : angle 0.58376 (30861) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.49914 ( 2) hydrogen bonds : bond 0.04257 ( 1004) hydrogen bonds : angle 4.61854 ( 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 242 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.8542 (ttm) cc_final: 0.8196 (ttm) REVERT: A 800 LYS cc_start: 0.8279 (pttm) cc_final: 0.7989 (mptt) REVERT: A 1214 ASP cc_start: 0.8432 (p0) cc_final: 0.8091 (p0) REVERT: A 1937 MET cc_start: 0.9248 (mmp) cc_final: 0.9018 (mmt) REVERT: A 2081 MET cc_start: 0.8690 (ttp) cc_final: 0.8248 (ttp) REVERT: A 2095 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 2265 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8622 (ptpp) REVERT: A 2488 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 3016 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7983 (mtt180) REVERT: A 3061 MET cc_start: 0.6366 (ptp) cc_final: 0.5974 (ptp) outliers start: 79 outliers final: 36 residues processed: 232 average time/residue: 0.1491 time to fit residues: 55.5826 Evaluate side-chains 184 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 815 THR Chi-restraints excluded: chain A residue 865 THR 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 1948 MET 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 2367 ASN 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: 0.9980 chunk 262 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS A1979 GLN A2228 GLN A2540 GLN ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.092451 restraints weight = 49007.436| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.12 r_work: 0.3089 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1275 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= 0.133 Angle : 0.526 7.438 30863 Z= 0.271 Chirality : 0.042 0.188 3496 Planarity : 0.004 0.054 3983 Dihedral : 3.973 37.222 3055 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.13 % Allowed : 22.93 % Favored : 73.94 % 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 aren not related in a simple way. whole: 0.56 (0.16), residues: 2791 helix: 1.90 (0.16), residues: 1065 sheet: -0.59 (0.22), residues: 537 loop : -0.52 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3100 TYR 0.017 0.001 TYR A2121 PHE 0.011 0.001 PHE A 582 TRP 0.016 0.001 TRP A2140 HIS 0.005 0.001 HIS A2514 Details of bonding type rmsd covalent geometry : bond 0.00306 (22775) covalent geometry : angle 0.52602 (30861) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.51186 ( 2) hydrogen bonds : bond 0.03821 ( 1004) hydrogen bonds : angle 4.34863 ( 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 236 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 158 time to evaluate : 0.697 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: 0.8509 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: A 455 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: A 631 MET cc_start: 0.8514 (ttm) cc_final: 0.8144 (ttm) REVERT: A 800 LYS cc_start: 0.8268 (pttm) cc_final: 0.7946 (mmtm) REVERT: A 1214 ASP cc_start: 0.8335 (p0) cc_final: 0.7938 (p0) REVERT: A 1937 MET cc_start: 0.9277 (mmp) cc_final: 0.9067 (mmt) REVERT: A 1957 ARG cc_start: 0.8348 (tpm170) cc_final: 0.7850 (tpm170) REVERT: A 2095 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: A 2265 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8580 (ptpp) REVERT: A 2347 ASN cc_start: 0.7623 (t0) cc_final: 0.7347 (m-40) REVERT: A 2488 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.7221 (t80) REVERT: A 2739 MET cc_start: 0.7735 (ppp) cc_final: 0.6505 (ppp) REVERT: A 3016 ARG cc_start: 0.8429 (mtt90) cc_final: 0.8148 (mtt180) REVERT: A 3061 MET cc_start: 0.6460 (ptp) cc_final: 0.6075 (ptp) outliers start: 78 outliers final: 43 residues processed: 223 average time/residue: 0.1579 time to fit residues: 55.0779 Evaluate side-chains 198 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 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 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 1325 ASN Chi-restraints excluded: chain A residue 1327 VAL 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 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 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 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 3094 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 242 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 244 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A1448 HIS A1796 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 = 0.3999 r_free = 0.3999 target = 0.130826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092694 restraints weight = 49005.889| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.12 r_work: 0.3093 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22776 Z= 0.116 Angle : 0.505 8.267 30863 Z= 0.258 Chirality : 0.041 0.188 3496 Planarity : 0.004 0.048 3983 Dihedral : 3.831 35.036 3055 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.25 % Allowed : 22.37 % 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 aren not related in a simple way. whole: 0.69 (0.16), residues: 2791 helix: 2.02 (0.16), residues: 1067 sheet: -0.48 (0.23), residues: 537 loop : -0.48 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2599 TYR 0.015 0.001 TYR A2121 PHE 0.008 0.001 PHE A2237 TRP 0.016 0.001 TRP A3113 HIS 0.004 0.001 HIS A2514 Details of bonding type rmsd covalent geometry : bond 0.00264 (22775) covalent geometry : angle 0.50526 (30861) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.53792 ( 2) hydrogen bonds : bond 0.03529 ( 1004) hydrogen bonds : angle 4.17774 ( 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 246 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 0.964 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: 0.8489 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: A 455 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: A 689 GLN cc_start: 0.8957 (tp40) cc_final: 0.8611 (tp40) REVERT: A 800 LYS cc_start: 0.8247 (pttm) cc_final: 0.7892 (mmtm) REVERT: A 1214 ASP cc_start: 0.8315 (p0) cc_final: 0.7972 (p0) REVERT: A 1904 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: A 1937 MET cc_start: 0.9319 (mmp) cc_final: 0.9090 (mmt) REVERT: A 1957 ARG cc_start: 0.8336 (tpm170) cc_final: 0.8125 (tpt90) REVERT: A 2095 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: A 2265 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8519 (ptpp) REVERT: A 2347 ASN cc_start: 0.7614 (t0) cc_final: 0.7337 (m110) REVERT: A 3061 MET cc_start: 0.6593 (ptp) cc_final: 0.6293 (ptp) outliers start: 81 outliers final: 49 residues processed: 235 average time/residue: 0.1660 time to fit residues: 62.1243 Evaluate side-chains 208 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 815 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 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 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 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 3062 MET Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3117 TRP Chi-restraints excluded: chain A residue 3201 THR 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: 20.0000 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 274 optimal weight: 40.0000 chunk 114 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 981 HIS A1638 HIS 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 = 0.3967 r_free = 0.3967 target = 0.128704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.089663 restraints weight = 48885.840| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.43 r_work: 0.3059 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22776 Z= 0.187 Angle : 0.545 11.882 30863 Z= 0.280 Chirality : 0.043 0.161 3496 Planarity : 0.004 0.058 3983 Dihedral : 3.868 20.777 3053 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.21 % Allowed : 22.09 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2791 helix: 2.00 (0.16), residues: 1063 sheet: -0.56 (0.22), residues: 547 loop : -0.44 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3100 TYR 0.024 0.001 TYR A2121 PHE 0.013 0.001 PHE A1918 TRP 0.028 0.002 TRP A3081 HIS 0.004 0.001 HIS A2514 Details of bonding type rmsd covalent geometry : bond 0.00436 (22775) covalent geometry : angle 0.54495 (30861) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.53067 ( 2) hydrogen bonds : bond 0.03984 ( 1004) hydrogen bonds : angle 4.27272 ( 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 241 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 161 time to evaluate : 0.897 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: 0.8522 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: A 455 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: A 689 GLN cc_start: 0.8978 (tp40) cc_final: 0.8774 (tp40) REVERT: A 1214 ASP cc_start: 0.8327 (p0) cc_final: 0.7963 (p0) REVERT: A 1957 ARG cc_start: 0.8408 (tpm170) cc_final: 0.7942 (tpm170) REVERT: A 2095 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 2265 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8474 (ptpp) REVERT: A 2303 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7872 (mtt) REVERT: A 3016 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8344 (mtt-85) REVERT: A 3061 MET cc_start: 0.6915 (ptp) cc_final: 0.6448 (ptp) outliers start: 80 outliers final: 52 residues processed: 224 average time/residue: 0.1642 time to fit residues: 58.0840 Evaluate side-chains 211 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 705 ILE Chi-restraints excluded: chain A residue 754 ILE 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 1535 ILE 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 1664 ARG 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 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP 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 2263 VAL 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 2615 ARG 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 3119 LYS 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: 4.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 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 = 0.3972 r_free = 0.3972 target = 0.129085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091019 restraints weight = 48847.052| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.13 r_work: 0.3062 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22776 Z= 0.151 Angle : 0.525 8.976 30863 Z= 0.268 Chirality : 0.042 0.210 3496 Planarity : 0.004 0.050 3983 Dihedral : 3.799 20.748 3053 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.85 % Allowed : 22.41 % Favored : 74.74 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2791 helix: 2.07 (0.16), residues: 1061 sheet: -0.48 (0.23), residues: 537 loop : -0.48 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3100 TYR 0.018 0.001 TYR A2121 PHE 0.012 0.001 PHE A2237 TRP 0.017 0.001 TRP A2140 HIS 0.012 0.001 HIS A2514 Details of bonding type rmsd covalent geometry : bond 0.00355 (22775) covalent geometry : angle 0.52542 (30861) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.56061 ( 2) hydrogen bonds : bond 0.03707 ( 1004) hydrogen bonds : angle 4.19731 ( 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 227 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 0.947 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: 0.8572 (OUTLIER) cc_final: 0.8312 (mm-30) REVERT: A 455 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: A 689 GLN cc_start: 0.8973 (tp40) cc_final: 0.8758 (tp40) REVERT: A 994 MET cc_start: 0.5429 (pmm) cc_final: 0.4663 (mmt) REVERT: A 1214 ASP cc_start: 0.8329 (p0) cc_final: 0.7999 (p0) REVERT: A 1266 MET cc_start: 0.9005 (mmm) cc_final: 0.8770 (mmt) REVERT: A 1319 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 1957 ARG cc_start: 0.8401 (tpm170) cc_final: 0.8126 (tpm170) REVERT: A 2095 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 2265 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8562 (ptpp) REVERT: A 2303 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: A 2993 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: A 3016 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8236 (mtt-85) REVERT: A 3061 MET cc_start: 0.6974 (ptp) cc_final: 0.6504 (ptp) outliers start: 71 outliers final: 52 residues processed: 214 average time/residue: 0.1567 time to fit residues: 53.7557 Evaluate side-chains 211 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 705 ILE Chi-restraints excluded: chain A residue 754 ILE 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 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 1793 LEU 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 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 2263 VAL 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 3062 MET 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: 5.9990 chunk 222 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 148 optimal weight: 0.0970 chunk 256 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 191 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 551 HIS ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1912 GLN A2500 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 = 0.3991 r_free = 0.3991 target = 0.130452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092454 restraints weight = 48918.824| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.15 r_work: 0.3092 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22776 Z= 0.109 Angle : 0.511 9.881 30863 Z= 0.258 Chirality : 0.041 0.193 3496 Planarity : 0.004 0.050 3983 Dihedral : 3.658 20.637 3053 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.65 % Allowed : 22.69 % Favored : 74.66 % 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 aren not related in a simple way. whole: 0.85 (0.17), residues: 2791 helix: 2.20 (0.16), residues: 1067 sheet: -0.40 (0.23), residues: 536 loop : -0.45 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3100 TYR 0.014 0.001 TYR A2121 PHE 0.009 0.001 PHE A2237 TRP 0.016 0.001 TRP A2140 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00250 (22775) covalent geometry : angle 0.51107 (30861) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.51665 ( 2) hydrogen bonds : bond 0.03343 ( 1004) hydrogen bonds : angle 4.08147 ( 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 230 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 0.860 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: 0.8540 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: A 455 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: A 689 GLN cc_start: 0.8907 (tp40) cc_final: 0.8688 (tp40) REVERT: A 994 MET cc_start: 0.5388 (pmm) cc_final: 0.4742 (mmt) REVERT: A 1214 ASP cc_start: 0.8359 (p0) cc_final: 0.8032 (p0) REVERT: A 1319 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 1957 ARG cc_start: 0.8319 (tpm170) cc_final: 0.7917 (tpm170) REVERT: A 1986 TYR cc_start: 0.6612 (t80) cc_final: 0.6408 (t80) REVERT: A 1999 ASP cc_start: 0.8316 (t0) cc_final: 0.8043 (m-30) REVERT: A 2081 MET cc_start: 0.8546 (ttp) cc_final: 0.7830 (ttp) REVERT: A 2095 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: A 2265 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8630 (ptpp) REVERT: A 2303 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: A 2941 MET cc_start: 0.5577 (tpp) cc_final: 0.5105 (tpp) REVERT: A 2993 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: A 3016 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8115 (mtm-85) REVERT: A 3061 MET cc_start: 0.6880 (ptp) cc_final: 0.6448 (ptp) REVERT: A 3100 ARG cc_start: 0.5656 (mtm-85) cc_final: 0.5454 (mtm-85) outliers start: 66 outliers final: 45 residues processed: 222 average time/residue: 0.1548 time to fit residues: 54.5503 Evaluate side-chains 205 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 570 PHE 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 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 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 1764 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 1931 SER 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 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 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: 0.9980 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS A1981 GLN A1982 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 = 0.3983 r_free = 0.3983 target = 0.129860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091811 restraints weight = 48775.458| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.16 r_work: 0.3086 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2171 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= 0.133 Angle : 0.528 10.415 30863 Z= 0.266 Chirality : 0.042 0.300 3496 Planarity : 0.004 0.049 3983 Dihedral : 3.668 20.642 3053 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 22.77 % Favored : 74.78 % 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 aren not related in a simple way. whole: 0.88 (0.17), residues: 2791 helix: 2.24 (0.16), residues: 1060 sheet: -0.36 (0.23), residues: 536 loop : -0.45 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2723 TYR 0.016 0.001 TYR A2121 PHE 0.010 0.001 PHE A2237 TRP 0.016 0.001 TRP A2140 HIS 0.005 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00308 (22775) covalent geometry : angle 0.52808 (30861) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.52931 ( 2) hydrogen bonds : bond 0.03455 ( 1004) hydrogen bonds : angle 4.06996 ( 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 216 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 0.825 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: 0.8521 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: A 689 GLN cc_start: 0.8903 (tp40) cc_final: 0.8677 (tp40) REVERT: A 994 MET cc_start: 0.5382 (pmm) cc_final: 0.4732 (mmt) REVERT: A 1214 ASP cc_start: 0.8368 (p0) cc_final: 0.8033 (p0) REVERT: A 1319 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 1957 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7942 (tpm170) REVERT: A 1999 ASP cc_start: 0.8304 (t0) cc_final: 0.8048 (m-30) REVERT: A 2081 MET cc_start: 0.8548 (ttp) cc_final: 0.7860 (ttp) REVERT: A 2095 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: A 2265 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8667 (ptpp) REVERT: A 2303 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7816 (mtt) REVERT: A 2941 MET cc_start: 0.5560 (tpp) cc_final: 0.5167 (tpp) REVERT: A 3016 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8044 (mtm-85) REVERT: A 3061 MET cc_start: 0.6797 (ptp) cc_final: 0.6404 (ptp) outliers start: 61 outliers final: 47 residues processed: 208 average time/residue: 0.1439 time to fit residues: 47.7328 Evaluate side-chains 203 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 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 1764 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 1931 SER 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 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 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 3123 ILE Chi-restraints excluded: chain A residue 3124 LEU Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 229 optimal weight: 0.4980 chunk 270 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 232 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 HIS A1981 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 = 0.3996 r_free = 0.3996 target = 0.130807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092491 restraints weight = 49155.856| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.50 r_work: 0.3099 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22776 Z= 0.103 Angle : 0.523 10.990 30863 Z= 0.263 Chirality : 0.042 0.274 3496 Planarity : 0.004 0.063 3983 Dihedral : 3.607 20.431 3053 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.21 % Allowed : 22.93 % Favored : 74.86 % 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 aren not related in a simple way. whole: 0.96 (0.17), residues: 2791 helix: 2.33 (0.16), residues: 1063 sheet: -0.28 (0.23), residues: 532 loop : -0.44 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A3100 TYR 0.018 0.001 TYR A1986 PHE 0.009 0.001 PHE A 582 TRP 0.016 0.001 TRP A2046 HIS 0.005 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00232 (22775) covalent geometry : angle 0.52280 (30861) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.50887 ( 2) hydrogen bonds : bond 0.03215 ( 1004) hydrogen bonds : angle 3.98852 ( 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 214 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.932 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 689 GLN cc_start: 0.8892 (tp40) cc_final: 0.8683 (tp40) REVERT: A 994 MET cc_start: 0.5490 (pmm) cc_final: 0.4705 (tpt) REVERT: A 1214 ASP cc_start: 0.8380 (p0) cc_final: 0.8061 (p0) REVERT: A 1319 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 1957 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7916 (tpm170) REVERT: A 1986 TYR cc_start: 0.6640 (t80) cc_final: 0.6424 (t80) REVERT: A 1999 ASP cc_start: 0.8305 (t0) cc_final: 0.8048 (m-30) REVERT: A 2081 MET cc_start: 0.8522 (ttp) cc_final: 0.7795 (ttp) REVERT: A 2095 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: A 2265 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8617 (ptpp) REVERT: A 2614 LEU cc_start: 0.8823 (tp) cc_final: 0.8612 (tp) REVERT: A 2941 MET cc_start: 0.5849 (tpp) cc_final: 0.5402 (tpp) REVERT: A 3016 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8045 (mtm-85) outliers start: 55 outliers final: 47 residues processed: 204 average time/residue: 0.1707 time to fit residues: 55.0567 Evaluate side-chains 205 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 414 LEU 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 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 1340 LEU Chi-restraints excluded: chain A residue 1434 HIS 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 1764 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 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 2818 ARG Chi-restraints excluded: chain A residue 2880 LYS Chi-restraints excluded: chain A residue 3005 ILE 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 3123 ILE Chi-restraints excluded: chain A residue 3124 LEU Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 178 optimal weight: 0.0370 chunk 211 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.130858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092759 restraints weight = 48944.283| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.48 r_work: 0.3102 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2324 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= 0.105 Angle : 0.527 10.607 30863 Z= 0.264 Chirality : 0.041 0.267 3496 Planarity : 0.004 0.049 3983 Dihedral : 3.566 20.437 3053 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.25 % Allowed : 22.65 % Favored : 75.10 % 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 aren not related in a simple way. whole: 1.02 (0.17), residues: 2791 helix: 2.38 (0.16), residues: 1064 sheet: -0.22 (0.23), residues: 532 loop : -0.44 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2653 TYR 0.015 0.001 TYR A1986 PHE 0.011 0.001 PHE A 582 TRP 0.016 0.001 TRP A2046 HIS 0.004 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00239 (22775) covalent geometry : angle 0.52657 (30861) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.49386 ( 2) hydrogen bonds : bond 0.03168 ( 1004) hydrogen bonds : angle 3.95151 ( 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 214 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 689 GLN cc_start: 0.8893 (tp40) cc_final: 0.8681 (tp40) REVERT: A 994 MET cc_start: 0.5484 (pmm) cc_final: 0.4709 (tpt) REVERT: A 1214 ASP cc_start: 0.8398 (p0) cc_final: 0.8074 (p0) REVERT: A 1319 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 1957 ARG cc_start: 0.8333 (tpm170) cc_final: 0.7900 (tpm170) REVERT: A 1986 TYR cc_start: 0.6615 (t80) cc_final: 0.6385 (t80) REVERT: A 1999 ASP cc_start: 0.8316 (t0) cc_final: 0.8050 (m-30) REVERT: A 2081 MET cc_start: 0.8505 (ttp) cc_final: 0.7757 (ttp) REVERT: A 2095 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: A 2265 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8633 (ptpp) REVERT: A 2303 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7775 (mtt) REVERT: A 2614 LEU cc_start: 0.8803 (tp) cc_final: 0.8596 (tp) REVERT: A 2653 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7754 (ttp80) REVERT: A 2941 MET cc_start: 0.5952 (tpp) cc_final: 0.5529 (tpp) REVERT: A 3016 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8007 (mtm-85) outliers start: 56 outliers final: 47 residues processed: 203 average time/residue: 0.1671 time to fit residues: 54.0814 Evaluate side-chains 205 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU 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 865 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 941 ILE 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 1340 LEU Chi-restraints excluded: chain A residue 1434 HIS 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 1862 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1931 SER 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 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 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 3015 VAL 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 3124 LEU Chi-restraints excluded: chain A residue 3201 THR Chi-restraints excluded: chain A residue 3202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 57 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091414 restraints weight = 48868.245| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.27 r_work: 0.3069 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22776 Z= 0.150 Angle : 0.544 11.525 30863 Z= 0.273 Chirality : 0.042 0.255 3496 Planarity : 0.004 0.049 3983 Dihedral : 3.650 20.815 3053 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 22.73 % Favored : 75.14 % 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 aren not related in a simple way. whole: 0.97 (0.17), residues: 2791 helix: 2.33 (0.16), residues: 1059 sheet: -0.29 (0.23), residues: 543 loop : -0.41 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2723 TYR 0.017 0.001 TYR A2121 PHE 0.013 0.001 PHE A 984 TRP 0.017 0.001 TRP A3113 HIS 0.008 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00352 (22775) covalent geometry : angle 0.54393 (30861) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.55832 ( 2) hydrogen bonds : bond 0.03506 ( 1004) hydrogen bonds : angle 4.03973 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.50 seconds wall clock time: 100 minutes 44.62 seconds (6044.62 seconds total)