Starting phenix.real_space_refine on Sun Feb 8 10:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sic_25140/02_2026/7sic_25140.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 306 5.16 5 C 28420 2.51 5 N 7560 2.21 5 O 8190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44484 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 7, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 48.04, per 1000 atoms: 1.08 Number of scatterers: 44484 At special positions: 0 Unit cell: (224.928, 112.992, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 6 15.00 Mg 2 11.99 O 8190 8.00 N 7560 7.00 C 28420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 2.1 seconds 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10668 Finding SS restraints... Secondary structure from input PDB file: 318 helices and 8 sheets defined 76.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 34 removed outlier: 3.959A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.808A pdb=" N GLU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.159A pdb=" N LYS A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.073A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.571A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 182 through 202 removed outlier: 3.999A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 223 removed outlier: 4.063A pdb=" N PHE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.582A pdb=" N ALA A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 272 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.714A pdb=" N GLY A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.972A pdb=" N SER A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 392 through 403 removed outlier: 4.143A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 424 through 427 removed outlier: 4.001A pdb=" N LEU A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 451 through 467 Processing helix chain 'A' and resid 473 through 493 removed outlier: 3.642A pdb=" N LYS A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.854A pdb=" N TRP A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.569A pdb=" N LEU A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.737A pdb=" N THR A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 712 through 732 removed outlier: 3.708A pdb=" N MET A 732 " --> pdb=" O CYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 742 removed outlier: 3.523A pdb=" N LYS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.553A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 787 removed outlier: 4.072A pdb=" N GLY A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 778 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 807 removed outlier: 3.504A pdb=" N LEU A 807 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 823 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 891 through 912 removed outlier: 4.493A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.555A pdb=" N ILE A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 962 through 971 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 983 through 995 removed outlier: 3.554A pdb=" N LEU A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 4.323A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1031 removed outlier: 3.586A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1053 Processing helix chain 'A' and resid 1070 through 1077 removed outlier: 3.611A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1080 No H-bonds generated for 'chain 'A' and resid 1078 through 1080' Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1112 through 1133 Processing helix chain 'A' and resid 1143 through 1165 Processing helix chain 'A' and resid 1168 through 1182 removed outlier: 3.961A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1202 Processing helix chain 'A' and resid 1205 through 1213 removed outlier: 3.701A pdb=" N PHE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1224 removed outlier: 3.660A pdb=" N LEU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1239 Processing helix chain 'A' and resid 1243 through 1262 removed outlier: 6.015A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1264 through 1276 Processing helix chain 'A' and resid 1278 through 1286 removed outlier: 3.697A pdb=" N CYS A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1295 removed outlier: 3.604A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1305 through 1323 removed outlier: 4.273A pdb=" N GLN A1310 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1330 removed outlier: 4.169A pdb=" N LYS A1330 " --> pdb=" O LEU A1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1327 through 1330' Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.875A pdb=" N ASN A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1349 removed outlier: 4.017A pdb=" N ILE A1343 " --> pdb=" O ASN A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1397 Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 4.147A pdb=" N ILE A1407 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1429 removed outlier: 4.212A pdb=" N GLN A1416 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1451 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1484 through 1509 Processing helix chain 'A' and resid 1511 through 1515 removed outlier: 3.630A pdb=" N GLU A1514 " --> pdb=" O ASP A1511 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN A1515 " --> pdb=" O ALA A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1511 through 1515' Processing helix chain 'A' and resid 1516 through 1525 Processing helix chain 'A' and resid 1526 through 1529 Processing helix chain 'A' and resid 1531 through 1546 removed outlier: 3.562A pdb=" N GLN A1537 " --> pdb=" O GLU A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1561 removed outlier: 4.055A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1561 " --> pdb=" O ILE A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1583 Processing helix chain 'A' and resid 1589 through 1602 removed outlier: 3.571A pdb=" N SER A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1609 Processing helix chain 'A' and resid 1610 through 1624 Processing helix chain 'A' and resid 1624 through 1635 removed outlier: 3.714A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1641 removed outlier: 3.702A pdb=" N ASP A1641 " --> pdb=" O ASN A1638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1638 through 1641' Processing helix chain 'A' and resid 1642 through 1659 Processing helix chain 'A' and resid 1663 through 1678 removed outlier: 3.708A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 removed outlier: 3.525A pdb=" N LEU A1702 " --> pdb=" O LYS A1698 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A1703 " --> pdb=" O ALA A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1726 through 1743 Processing helix chain 'A' and resid 1743 through 1754 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.867A pdb=" N ALA A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1796 Processing helix chain 'A' and resid 1801 through 1816 Processing helix chain 'A' and resid 1821 through 1826 removed outlier: 3.734A pdb=" N GLN A1825 " --> pdb=" O CYS A1821 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1821 through 1826' Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1856 through 1876 removed outlier: 3.644A pdb=" N LEU A1874 " --> pdb=" O PHE A1870 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS A1876 " --> pdb=" O SER A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 3.655A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1931 Processing helix chain 'A' and resid 1937 through 1948 removed outlier: 3.513A pdb=" N VAL A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1974 Processing helix chain 'A' and resid 1985 through 1997 Processing helix chain 'A' and resid 2000 through 2013 Processing helix chain 'A' and resid 2015 through 2020 Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 Processing helix chain 'A' and resid 2056 through 2071 Processing helix chain 'A' and resid 2073 through 2088 Processing helix chain 'A' and resid 2092 through 2106 Processing helix chain 'A' and resid 2123 through 2137 Processing helix chain 'A' and resid 2139 through 2160 Processing helix chain 'A' and resid 2165 through 2168 Processing helix chain 'A' and resid 2169 through 2191 removed outlier: 3.613A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2212 Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2243 through 2265 removed outlier: 4.316A pdb=" N ILE A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.624A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 4.022A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2323 Processing helix chain 'A' and resid 2327 through 2349 removed outlier: 4.119A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2360 Processing helix chain 'A' and resid 2360 through 2371 removed outlier: 3.851A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2406 removed outlier: 3.631A pdb=" N ARG A2380 " --> pdb=" O SER A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2422 removed outlier: 3.595A pdb=" N LEU A2417 " --> pdb=" O LYS A2413 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A2422 " --> pdb=" O LYS A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2476 removed outlier: 4.124A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2482 No H-bonds generated for 'chain 'A' and resid 2480 through 2482' Processing helix chain 'A' and resid 2483 through 2493 Processing helix chain 'A' and resid 2497 through 2507 Processing helix chain 'A' and resid 2508 through 2511 Processing helix chain 'A' and resid 2512 through 2518 Proline residue: A2518 - end of helix Processing helix chain 'A' and resid 2519 through 2525 Processing helix chain 'A' and resid 2536 through 2552 Processing helix chain 'A' and resid 2552 through 2565 removed outlier: 3.606A pdb=" N THR A2556 " --> pdb=" O HIS A2552 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2573 removed outlier: 3.947A pdb=" N PHE A2571 " --> pdb=" O ASN A2567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2613 removed outlier: 3.964A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2633 removed outlier: 3.749A pdb=" N VAL A2617 " --> pdb=" O ARG A2613 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2641 removed outlier: 3.655A pdb=" N LYS A2639 " --> pdb=" O THR A2636 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2656 removed outlier: 4.117A pdb=" N LYS A2655 " --> pdb=" O GLN A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2741 Processing helix chain 'A' and resid 2742 through 2748 removed outlier: 3.616A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2782 removed outlier: 3.774A pdb=" N ASN A2782 " --> pdb=" O GLU A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2792 Processing helix chain 'A' and resid 2797 through 2808 Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2832 through 2839 removed outlier: 3.838A pdb=" N MET A2836 " --> pdb=" O ARG A2832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A2838 " --> pdb=" O PHE A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2867 Processing helix chain 'A' and resid 2872 through 2874 No H-bonds generated for 'chain 'A' and resid 2872 through 2874' Processing helix chain 'A' and resid 2895 through 2900 Processing helix chain 'A' and resid 2911 through 2917 Processing helix chain 'A' and resid 2925 through 2941 Processing helix chain 'A' and resid 2941 through 2954 removed outlier: 3.531A pdb=" N TYR A2954 " --> pdb=" O GLU A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2963 through 2971 Processing helix chain 'A' and resid 3002 through 3019 Processing helix chain 'A' and resid 3027 through 3041 Processing helix chain 'A' and resid 3041 through 3047 removed outlier: 3.731A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3048 through 3053 removed outlier: 6.087A pdb=" N GLY A3051 " --> pdb=" O LEU A3048 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 19 through 34 removed outlier: 3.959A pdb=" N LYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.808A pdb=" N GLU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 109 removed outlier: 4.160A pdb=" N LYS B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.073A pdb=" N LEU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.571A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 182 through 202 removed outlier: 3.999A pdb=" N LEU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 202 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.063A pdb=" N PHE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.582A pdb=" N ALA B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 269 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 272 through 291 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.714A pdb=" N GLY B 301 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 324 removed outlier: 3.972A pdb=" N SER B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 Processing helix chain 'B' and resid 392 through 403 removed outlier: 4.143A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 Processing helix chain 'B' and resid 424 through 427 removed outlier: 4.001A pdb=" N LEU B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 451 through 467 Processing helix chain 'B' and resid 473 through 493 removed outlier: 3.642A pdb=" N LYS B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.854A pdb=" N TRP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.569A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 596 through 601 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.737A pdb=" N THR B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 645 through 656 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 712 through 732 removed outlier: 3.708A pdb=" N MET B 732 " --> pdb=" O CYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 742 removed outlier: 3.523A pdb=" N LYS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 766 removed outlier: 3.553A pdb=" N GLU B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 759 " --> pdb=" O CYS B 755 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 787 removed outlier: 4.072A pdb=" N GLY B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 787 " --> pdb=" O CYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 807 removed outlier: 3.504A pdb=" N LEU B 807 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 823 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 891 through 912 removed outlier: 4.493A pdb=" N GLN B 912 " --> pdb=" O VAL B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 931 removed outlier: 3.555A pdb=" N ILE B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 962 through 971 Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 983 through 995 removed outlier: 3.554A pdb=" N LEU B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 removed outlier: 4.323A pdb=" N GLN B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1031 removed outlier: 3.586A pdb=" N VAL B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1053 Processing helix chain 'B' and resid 1070 through 1077 removed outlier: 3.611A pdb=" N THR B1075 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B1076 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1082 through 1093 Processing helix chain 'B' and resid 1094 through 1097 Processing helix chain 'B' and resid 1112 through 1133 Processing helix chain 'B' and resid 1143 through 1165 Processing helix chain 'B' and resid 1168 through 1182 removed outlier: 3.961A pdb=" N LYS B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1202 Processing helix chain 'B' and resid 1205 through 1213 removed outlier: 3.701A pdb=" N PHE B1209 " --> pdb=" O ARG B1205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS B1213 " --> pdb=" O PHE B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1224 removed outlier: 3.660A pdb=" N LEU B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1239 Processing helix chain 'B' and resid 1243 through 1262 removed outlier: 6.016A pdb=" N LYS B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B1254 " --> pdb=" O SER B1250 " (cutoff:3.500A) Proline residue: B1257 - end of helix Processing helix chain 'B' and resid 1264 through 1276 Processing helix chain 'B' and resid 1278 through 1286 removed outlier: 3.697A pdb=" N CYS B1286 " --> pdb=" O LEU B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1286 through 1295 removed outlier: 3.604A pdb=" N ASN B1293 " --> pdb=" O LYS B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1298 No H-bonds generated for 'chain 'B' and resid 1296 through 1298' Processing helix chain 'B' and resid 1305 through 1323 removed outlier: 4.273A pdb=" N GLN B1310 " --> pdb=" O SER B1306 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B1311 " --> pdb=" O GLY B1307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B1312 " --> pdb=" O MET B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1327 through 1330 removed outlier: 4.169A pdb=" N LYS B1330 " --> pdb=" O LEU B1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1327 through 1330' Processing helix chain 'B' and resid 1331 through 1339 removed outlier: 3.875A pdb=" N ASN B1339 " --> pdb=" O LEU B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1349 removed outlier: 4.017A pdb=" N ILE B1343 " --> pdb=" O ASN B1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1397 Processing helix chain 'B' and resid 1403 through 1409 removed outlier: 4.147A pdb=" N ILE B1407 " --> pdb=" O SER B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1412 through 1429 removed outlier: 4.212A pdb=" N GLN B1416 " --> pdb=" O PRO B1412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1451 Processing helix chain 'B' and resid 1460 through 1478 Processing helix chain 'B' and resid 1484 through 1509 Processing helix chain 'B' and resid 1511 through 1515 removed outlier: 3.630A pdb=" N GLU B1514 " --> pdb=" O ASP B1511 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B1515 " --> pdb=" O ALA B1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1511 through 1515' Processing helix chain 'B' and resid 1516 through 1525 Processing helix chain 'B' and resid 1526 through 1529 Processing helix chain 'B' and resid 1531 through 1546 removed outlier: 3.562A pdb=" N GLN B1537 " --> pdb=" O GLU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1561 removed outlier: 4.055A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B1561 " --> pdb=" O ILE B1557 " (cutoff:3.500A) Processing helix chain 'B' and resid 1571 through 1583 Processing helix chain 'B' and resid 1589 through 1602 removed outlier: 3.571A pdb=" N SER B1601 " --> pdb=" O PHE B1597 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B1602 " --> pdb=" O LEU B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1609 Processing helix chain 'B' and resid 1610 through 1624 Processing helix chain 'B' and resid 1624 through 1635 removed outlier: 3.714A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1641 removed outlier: 3.702A pdb=" N ASP B1641 " --> pdb=" O ASN B1638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1638 through 1641' Processing helix chain 'B' and resid 1642 through 1659 Processing helix chain 'B' and resid 1663 through 1678 removed outlier: 3.708A pdb=" N VAL B1667 " --> pdb=" O GLY B1663 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1703 removed outlier: 3.525A pdb=" N LEU B1702 " --> pdb=" O LYS B1698 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B1703 " --> pdb=" O ALA B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1722 Processing helix chain 'B' and resid 1726 through 1743 Processing helix chain 'B' and resid 1743 through 1754 Processing helix chain 'B' and resid 1758 through 1764 removed outlier: 3.867A pdb=" N ALA B1762 " --> pdb=" O ASP B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1791 through 1796 Processing helix chain 'B' and resid 1801 through 1816 Processing helix chain 'B' and resid 1821 through 1826 removed outlier: 3.734A pdb=" N GLN B1825 " --> pdb=" O CYS B1821 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1821 through 1826' Processing helix chain 'B' and resid 1827 through 1832 Processing helix chain 'B' and resid 1834 through 1852 Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1856 through 1876 removed outlier: 3.644A pdb=" N LEU B1874 " --> pdb=" O PHE B1870 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS B1876 " --> pdb=" O SER B1872 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1918 removed outlier: 3.655A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1931 Processing helix chain 'B' and resid 1937 through 1948 removed outlier: 3.513A pdb=" N VAL B1941 " --> pdb=" O ASN B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1974 Processing helix chain 'B' and resid 1985 through 1997 Processing helix chain 'B' and resid 2000 through 2013 Processing helix chain 'B' and resid 2015 through 2020 Processing helix chain 'B' and resid 2028 through 2039 Processing helix chain 'B' and resid 2041 through 2052 Processing helix chain 'B' and resid 2056 through 2071 Processing helix chain 'B' and resid 2073 through 2088 Processing helix chain 'B' and resid 2092 through 2106 Processing helix chain 'B' and resid 2123 through 2137 Processing helix chain 'B' and resid 2139 through 2160 Processing helix chain 'B' and resid 2165 through 2168 Processing helix chain 'B' and resid 2169 through 2191 removed outlier: 3.613A pdb=" N GLU B2187 " --> pdb=" O GLU B2183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B2188 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2212 Processing helix chain 'B' and resid 2216 through 2237 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2243 through 2265 removed outlier: 4.316A pdb=" N ILE B2247 " --> pdb=" O GLN B2243 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2282 removed outlier: 3.624A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2289 through 2302 removed outlier: 4.022A pdb=" N LEU B2293 " --> pdb=" O SER B2289 " (cutoff:3.500A) Processing helix chain 'B' and resid 2304 through 2323 Processing helix chain 'B' and resid 2327 through 2349 removed outlier: 4.119A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2360 Processing helix chain 'B' and resid 2360 through 2371 removed outlier: 3.852A pdb=" N TYR B2371 " --> pdb=" O VAL B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2406 removed outlier: 3.631A pdb=" N ARG B2380 " --> pdb=" O SER B2376 " (cutoff:3.500A) Processing helix chain 'B' and resid 2407 through 2422 removed outlier: 3.594A pdb=" N LEU B2417 " --> pdb=" O LYS B2413 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B2422 " --> pdb=" O LYS B2418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2437 through 2476 removed outlier: 4.123A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2482 No H-bonds generated for 'chain 'B' and resid 2480 through 2482' Processing helix chain 'B' and resid 2483 through 2493 Processing helix chain 'B' and resid 2497 through 2507 Processing helix chain 'B' and resid 2508 through 2511 Processing helix chain 'B' and resid 2512 through 2518 Proline residue: B2518 - end of helix Processing helix chain 'B' and resid 2519 through 2525 Processing helix chain 'B' and resid 2536 through 2552 Processing helix chain 'B' and resid 2552 through 2565 removed outlier: 3.606A pdb=" N THR B2556 " --> pdb=" O HIS B2552 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2567 through 2573 removed outlier: 3.947A pdb=" N PHE B2571 " --> pdb=" O ASN B2567 " (cutoff:3.500A) Processing helix chain 'B' and resid 2592 through 2613 removed outlier: 3.964A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2613 through 2633 removed outlier: 3.749A pdb=" N VAL B2617 " --> pdb=" O ARG B2613 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2641 removed outlier: 3.655A pdb=" N LYS B2639 " --> pdb=" O THR B2636 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2656 removed outlier: 4.117A pdb=" N LYS B2655 " --> pdb=" O GLN B2651 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2741 Processing helix chain 'B' and resid 2742 through 2748 removed outlier: 3.616A pdb=" N ARG B2748 " --> pdb=" O GLU B2744 " (cutoff:3.500A) Processing helix chain 'B' and resid 2776 through 2782 removed outlier: 3.774A pdb=" N ASN B2782 " --> pdb=" O GLU B2778 " (cutoff:3.500A) Processing helix chain 'B' and resid 2786 through 2792 Processing helix chain 'B' and resid 2797 through 2808 Processing helix chain 'B' and resid 2812 through 2826 Processing helix chain 'B' and resid 2832 through 2839 removed outlier: 3.838A pdb=" N MET B2836 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B2838 " --> pdb=" O PHE B2834 " (cutoff:3.500A) Processing helix chain 'B' and resid 2841 through 2867 Processing helix chain 'B' and resid 2872 through 2874 No H-bonds generated for 'chain 'B' and resid 2872 through 2874' Processing helix chain 'B' and resid 2895 through 2900 Processing helix chain 'B' and resid 2911 through 2917 Processing helix chain 'B' and resid 2925 through 2941 Processing helix chain 'B' and resid 2941 through 2954 removed outlier: 3.531A pdb=" N TYR B2954 " --> pdb=" O GLU B2950 " (cutoff:3.500A) Processing helix chain 'B' and resid 2963 through 2971 Processing helix chain 'B' and resid 3002 through 3019 Processing helix chain 'B' and resid 3027 through 3041 Processing helix chain 'B' and resid 3041 through 3047 removed outlier: 3.731A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3048 through 3053 removed outlier: 6.087A pdb=" N GLY B3051 " --> pdb=" O LEU B3048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id=AA2, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.093A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP A2703 " --> pdb=" O PHE A2686 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A2686 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A2705 " --> pdb=" O GLN A2684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.093A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1063 Processing sheet with id=AA6, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.093A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP B2703 " --> pdb=" O PHE B2686 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE B2686 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B2705 " --> pdb=" O GLN B2684 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.093A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2773 through 2775 2847 hydrogen bonds defined for protein. 8379 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: 12.08 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13991 1.34 - 1.46: 6421 1.46 - 1.58: 24444 1.58 - 1.70: 8 1.70 - 1.82: 450 Bond restraints: 45314 Sorted by residual: bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O5' ANP B3101 " pdb=" PA ANP B3101 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 45309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 61035 3.64 - 7.29: 171 7.29 - 10.93: 26 10.93 - 14.57: 0 14.57 - 18.22: 2 Bond angle restraints: 61234 Sorted by residual: angle pdb=" PB ANP B3101 " pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 126.95 108.73 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 108.73 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C LEU B 409 " pdb=" N VAL B 410 " pdb=" CA VAL B 410 " ideal model delta sigma weight residual 120.24 123.12 -2.88 6.30e-01 2.52e+00 2.09e+01 angle pdb=" C LEU A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta sigma weight residual 120.24 123.12 -2.88 6.30e-01 2.52e+00 2.09e+01 angle pdb=" CG ARG A1312 " pdb=" CD ARG A1312 " pdb=" NE ARG A1312 " ideal model delta sigma weight residual 112.00 120.14 -8.14 2.20e+00 2.07e-01 1.37e+01 ... (remaining 61229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 23588 17.87 - 35.74: 3022 35.74 - 53.61: 790 53.61 - 71.48: 190 71.48 - 89.36: 82 Dihedral angle restraints: 27672 sinusoidal: 11314 harmonic: 16358 Sorted by residual: dihedral pdb=" CG ARG B1312 " pdb=" CD ARG B1312 " pdb=" NE ARG B1312 " pdb=" CZ ARG B1312 " ideal model delta sinusoidal sigma weight residual 90.00 9.27 80.73 2 1.50e+01 4.44e-03 2.08e+01 dihedral pdb=" CG ARG A1312 " pdb=" CD ARG A1312 " pdb=" NE ARG A1312 " pdb=" CZ ARG A1312 " ideal model delta sinusoidal sigma weight residual 90.00 9.27 80.73 2 1.50e+01 4.44e-03 2.08e+01 dihedral pdb=" CA ASN B1377 " pdb=" C ASN B1377 " pdb=" N PRO B1378 " pdb=" CA PRO B1378 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 27669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6062 0.053 - 0.107: 894 0.107 - 0.160: 64 0.160 - 0.214: 0 0.214 - 0.267: 2 Chirality restraints: 7022 Sorted by residual: chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE B2511 " pdb=" N ILE B2511 " pdb=" C ILE B2511 " pdb=" CB ILE B2511 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 7019 not shown) Planarity restraints: 7708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 595 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 596 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 596 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 596 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 595 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 596 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B2055 " -0.030 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO B2056 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B2056 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B2056 " -0.026 5.00e-02 4.00e+02 ... (remaining 7705 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 772 2.70 - 3.25: 44135 3.25 - 3.80: 73096 3.80 - 4.35: 92232 4.35 - 4.90: 153139 Nonbonded interactions: 363374 Sorted by model distance: nonbonded pdb=" OH TYR A2969 " pdb=" O2G ANP A3101 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR B2969 " pdb=" O2G ANP B3101 " model vdw 2.151 3.040 nonbonded pdb=" O THR A2142 " pdb=" OG SER A2146 " model vdw 2.186 3.040 nonbonded pdb=" O THR B2142 " pdb=" OG SER B2146 " model vdw 2.186 3.040 nonbonded pdb=" N ASN A 272 " pdb=" OD1 ASN A 272 " model vdw 2.190 3.120 ... (remaining 363369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 81.710 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 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 : 0.003 0.144 45314 Z= 0.137 Angle : 0.577 18.216 61234 Z= 0.296 Chirality : 0.036 0.267 7022 Planarity : 0.004 0.051 7708 Dihedral : 17.753 89.356 17004 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.04 % Allowed : 22.52 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.12), residues: 5470 helix: 2.21 (0.09), residues: 3836 sheet: 0.00 (0.58), residues: 66 loop : -0.13 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 62 TYR 0.015 0.001 TYR B 959 PHE 0.018 0.001 PHE A2799 TRP 0.013 0.001 TRP B2104 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00283 (45314) covalent geometry : angle 0.57700 (61234) hydrogen bonds : bond 0.13900 ( 2839) hydrogen bonds : angle 4.75641 ( 8379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 586 time to evaluate : 1.718 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 94 MET cc_start: 0.1503 (mmt) cc_final: 0.1042 (mtm) REVERT: A 1063 VAL cc_start: 0.2530 (OUTLIER) cc_final: 0.1947 (p) REVERT: A 1134 MET cc_start: 0.1920 (mtm) cc_final: 0.0921 (ptm) REVERT: A 1321 MET cc_start: 0.3980 (tmt) cc_final: 0.3712 (ppp) REVERT: A 1322 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4620 (mp) REVERT: A 1540 ASP cc_start: 0.7395 (m-30) cc_final: 0.7177 (t0) REVERT: A 1669 GLU cc_start: 0.7553 (tt0) cc_final: 0.7286 (tm-30) REVERT: A 1701 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7408 (mmtt) REVERT: A 1721 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 1773 LYS cc_start: 0.6605 (tmmt) cc_final: 0.6342 (ttpt) REVERT: A 1991 GLU cc_start: 0.6295 (mt-10) cc_final: 0.6057 (mm-30) REVERT: A 2007 GLU cc_start: 0.7081 (mp0) cc_final: 0.6791 (mm-30) REVERT: A 2034 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7230 (mtp180) REVERT: A 2057 SER cc_start: 0.7913 (m) cc_final: 0.7664 (m) REVERT: A 2141 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6871 (m) REVERT: A 2189 PHE cc_start: 0.7841 (t80) cc_final: 0.7417 (t80) REVERT: A 2232 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 2266 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7832 (mmpt) REVERT: A 2314 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7042 (tm-30) REVERT: A 2315 MET cc_start: 0.7637 (mtp) cc_final: 0.7394 (mtp) REVERT: A 2377 ASP cc_start: 0.6932 (t70) cc_final: 0.6665 (t0) REVERT: A 2378 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: A 2406 LYS cc_start: 0.6817 (mtmt) cc_final: 0.6553 (mmtm) REVERT: A 2529 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6523 (p) REVERT: A 2531 MET cc_start: 0.5530 (ttm) cc_final: 0.5105 (ttp) REVERT: A 2636 THR cc_start: 0.7464 (t) cc_final: 0.7098 (t) REVERT: A 2670 LYS cc_start: 0.7986 (tppt) cc_final: 0.7781 (tmtt) REVERT: A 2703 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: A 2710 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7289 (ttpp) REVERT: A 2810 LYS cc_start: 0.6882 (mtpt) cc_final: 0.6680 (mppt) REVERT: A 2935 MET cc_start: 0.8457 (tpp) cc_final: 0.7292 (tpp) REVERT: A 2966 LYS cc_start: 0.7102 (ttmt) cc_final: 0.6695 (ttmm) REVERT: A 3004 LYS cc_start: 0.7444 (mttm) cc_final: 0.7017 (ttpt) REVERT: A 3007 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6732 (mt-10) REVERT: A 3043 LYS cc_start: 0.6057 (tptp) cc_final: 0.5850 (tptp) REVERT: B 94 MET cc_start: 0.1507 (mmt) cc_final: 0.1044 (mtm) REVERT: B 1063 VAL cc_start: 0.2538 (OUTLIER) cc_final: 0.1954 (p) REVERT: B 1134 MET cc_start: 0.1913 (mtm) cc_final: 0.0919 (ptm) REVERT: B 1321 MET cc_start: 0.3985 (tmt) cc_final: 0.3715 (ppp) REVERT: B 1322 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4616 (mp) REVERT: B 1540 ASP cc_start: 0.7409 (m-30) cc_final: 0.7184 (t0) REVERT: B 1669 GLU cc_start: 0.7550 (tt0) cc_final: 0.7284 (tm-30) REVERT: B 1701 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7400 (mmtt) REVERT: B 1721 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8513 (t) REVERT: B 1773 LYS cc_start: 0.6592 (tmmt) cc_final: 0.6320 (ttpt) REVERT: B 1991 GLU cc_start: 0.6284 (mt-10) cc_final: 0.6044 (mm-30) REVERT: B 2007 GLU cc_start: 0.7072 (mp0) cc_final: 0.6780 (mm-30) REVERT: B 2034 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7230 (mtp180) REVERT: B 2057 SER cc_start: 0.7901 (m) cc_final: 0.7654 (m) REVERT: B 2141 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6870 (m) REVERT: B 2189 PHE cc_start: 0.7838 (t80) cc_final: 0.7418 (t80) REVERT: B 2232 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 2266 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7846 (mmpt) REVERT: B 2314 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7057 (tm-30) REVERT: B 2315 MET cc_start: 0.7640 (mtp) cc_final: 0.7395 (mtp) REVERT: B 2377 ASP cc_start: 0.6933 (t70) cc_final: 0.6665 (t0) REVERT: B 2378 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6652 (tp30) REVERT: B 2406 LYS cc_start: 0.6825 (mtmt) cc_final: 0.6564 (mmtm) REVERT: B 2529 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6527 (p) REVERT: B 2531 MET cc_start: 0.5533 (ttm) cc_final: 0.5106 (ttp) REVERT: B 2636 THR cc_start: 0.7474 (t) cc_final: 0.7108 (t) REVERT: B 2703 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: B 2710 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7296 (ttpp) REVERT: B 2935 MET cc_start: 0.8462 (tpp) cc_final: 0.7295 (tpp) REVERT: B 2966 LYS cc_start: 0.7119 (ttmt) cc_final: 0.6718 (ttmm) REVERT: B 3004 LYS cc_start: 0.7454 (mttm) cc_final: 0.7034 (ttpt) REVERT: B 3007 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6743 (mt-10) outliers start: 150 outliers final: 36 residues processed: 722 average time/residue: 0.8047 time to fit residues: 715.7247 Evaluate side-chains 483 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2378 GLU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2703 ASP Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 917 SER Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1143 THR Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1989 LEU Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2378 GLU Chi-restraints excluded: chain B residue 2529 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2703 ASP Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2920 ILE Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 0.5980 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A1116 GLN A1311 GLN A1653 GLN A1801 ASN A2038 HIS A2412 ASN ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2881 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B1116 GLN B1311 GLN B1653 GLN B1801 ASN B2038 HIS B2412 ASN ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.257732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.211249 restraints weight = 52558.128| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.13 r_work: 0.3793 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 45314 Z= 0.148 Angle : 0.558 9.649 61234 Z= 0.285 Chirality : 0.039 0.172 7022 Planarity : 0.004 0.050 7708 Dihedral : 5.594 88.873 6090 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.93 % Allowed : 21.93 % Favored : 74.14 % 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 are not related in a simple way. whole: 2.43 (0.12), residues: 5470 helix: 2.23 (0.08), residues: 3900 sheet: 0.16 (0.59), residues: 66 loop : 0.10 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 919 TYR 0.014 0.001 TYR B1556 PHE 0.027 0.001 PHE B 918 TRP 0.013 0.001 TRP A 156 HIS 0.006 0.001 HIS A2538 Details of bonding type rmsd covalent geometry : bond 0.00335 (45314) covalent geometry : angle 0.55819 (61234) hydrogen bonds : bond 0.04520 ( 2839) hydrogen bonds : angle 3.65966 ( 8379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 465 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1543 (mmt) cc_final: 0.1144 (mtm) REVERT: A 125 MET cc_start: 0.2383 (mmt) cc_final: 0.0853 (mtt) REVERT: A 230 ASN cc_start: 0.1351 (OUTLIER) cc_final: 0.1081 (m-40) REVERT: A 577 MET cc_start: 0.2234 (tmt) cc_final: 0.1992 (tmm) REVERT: A 1040 MET cc_start: 0.4560 (ptm) cc_final: 0.3638 (ttm) REVERT: A 1134 MET cc_start: 0.2476 (mtm) cc_final: 0.1311 (ptm) REVERT: A 1190 VAL cc_start: 0.4848 (OUTLIER) cc_final: 0.4647 (p) REVERT: A 1529 TYR cc_start: 0.7667 (m-80) cc_final: 0.6928 (m-80) REVERT: A 1792 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 1796 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 1920 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7973 (tptt) REVERT: A 2007 GLU cc_start: 0.8110 (mp0) cc_final: 0.7833 (mm-30) REVERT: A 2026 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.5246 (mtp) REVERT: A 2189 PHE cc_start: 0.7653 (t80) cc_final: 0.7286 (t80) REVERT: A 2531 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5391 (ttp) REVERT: A 2636 THR cc_start: 0.7691 (t) cc_final: 0.7413 (t) REVERT: A 2935 MET cc_start: 0.8768 (tpp) cc_final: 0.7784 (tpp) REVERT: A 2966 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7544 (ttmm) REVERT: B 94 MET cc_start: 0.1556 (mmt) cc_final: 0.1153 (mtm) REVERT: B 230 ASN cc_start: 0.1361 (OUTLIER) cc_final: 0.1090 (m-40) REVERT: B 577 MET cc_start: 0.2223 (tmt) cc_final: 0.1979 (tmm) REVERT: B 1040 MET cc_start: 0.4544 (ptm) cc_final: 0.3626 (ttm) REVERT: B 1134 MET cc_start: 0.2468 (mtm) cc_final: 0.1301 (ptm) REVERT: B 1529 TYR cc_start: 0.7669 (m-80) cc_final: 0.6924 (m-80) REVERT: B 1669 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: B 1792 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7910 (mt) REVERT: B 1796 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7104 (mt) REVERT: B 1920 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7980 (tptt) REVERT: B 2007 GLU cc_start: 0.8101 (mp0) cc_final: 0.7823 (mm-30) REVERT: B 2026 MET cc_start: 0.5556 (OUTLIER) cc_final: 0.5254 (mtp) REVERT: B 2189 PHE cc_start: 0.7650 (t80) cc_final: 0.7283 (t80) REVERT: B 2531 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.5382 (ttp) REVERT: B 2636 THR cc_start: 0.7692 (t) cc_final: 0.7412 (t) REVERT: B 2935 MET cc_start: 0.8777 (tpp) cc_final: 0.7797 (tpp) REVERT: B 2966 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7534 (ttmm) outliers start: 194 outliers final: 54 residues processed: 603 average time/residue: 0.8252 time to fit residues: 606.3028 Evaluate side-chains 486 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2531 MET Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 966 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1143 THR Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1465 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2531 MET Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 493 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 436 optimal weight: 7.9990 chunk 453 optimal weight: 0.0270 chunk 151 optimal weight: 0.9990 chunk 307 optimal weight: 9.9990 chunk 415 optimal weight: 1.9990 chunk 462 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1549 ASN A1653 GLN A1801 ASN A2038 HIS ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2881 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN B1549 ASN B1653 GLN B1801 ASN B2038 HIS B2881 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.257323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.207675 restraints weight = 52726.681| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.28 r_work: 0.3764 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 45314 Z= 0.114 Angle : 0.508 8.835 61234 Z= 0.257 Chirality : 0.037 0.149 7022 Planarity : 0.003 0.050 7708 Dihedral : 4.932 86.833 6041 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.28 % Allowed : 22.17 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.12), residues: 5470 helix: 2.36 (0.08), residues: 3878 sheet: 0.30 (0.60), residues: 66 loop : 0.16 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3047 TYR 0.013 0.001 TYR B1556 PHE 0.019 0.001 PHE B2571 TRP 0.015 0.001 TRP A2104 HIS 0.004 0.001 HIS B2038 Details of bonding type rmsd covalent geometry : bond 0.00249 (45314) covalent geometry : angle 0.50765 (61234) hydrogen bonds : bond 0.03817 ( 2839) hydrogen bonds : angle 3.47932 ( 8379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 449 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1594 (mmt) cc_final: 0.0994 (mtp) REVERT: A 230 ASN cc_start: 0.1248 (OUTLIER) cc_final: 0.1013 (m-40) REVERT: A 389 ILE cc_start: -0.1055 (OUTLIER) cc_final: -0.1499 (mm) REVERT: A 577 MET cc_start: 0.2259 (tmt) cc_final: 0.1980 (tmm) REVERT: A 1040 MET cc_start: 0.4664 (ptm) cc_final: 0.3866 (mtt) REVERT: A 1134 MET cc_start: 0.2534 (mtm) cc_final: 0.1327 (ptm) REVERT: A 1432 VAL cc_start: 0.7359 (m) cc_final: 0.7047 (m) REVERT: A 1539 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7821 (mm) REVERT: A 1633 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7230 (mtm110) REVERT: A 1706 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6976 (tptt) REVERT: A 1792 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7892 (mt) REVERT: A 1796 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7057 (mt) REVERT: A 1820 LYS cc_start: 0.7246 (tppt) cc_final: 0.7036 (mptt) REVERT: A 1920 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8066 (tptt) REVERT: A 2007 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: A 2026 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5489 (mtp) REVERT: A 2189 PHE cc_start: 0.7392 (t80) cc_final: 0.7111 (t80) REVERT: A 2531 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5441 (ttp) REVERT: A 2636 THR cc_start: 0.7559 (t) cc_final: 0.7308 (t) REVERT: A 2859 SER cc_start: 0.7800 (p) cc_final: 0.7600 (m) REVERT: A 2935 MET cc_start: 0.8811 (tpp) cc_final: 0.8127 (tpp) REVERT: B 94 MET cc_start: 0.1613 (mmt) cc_final: 0.1000 (mtp) REVERT: B 230 ASN cc_start: 0.1256 (OUTLIER) cc_final: 0.1025 (m-40) REVERT: B 577 MET cc_start: 0.2249 (tmt) cc_final: 0.1967 (tmm) REVERT: B 1040 MET cc_start: 0.4647 (ptm) cc_final: 0.3864 (mtt) REVERT: B 1134 MET cc_start: 0.2525 (mtm) cc_final: 0.1327 (ptm) REVERT: B 1432 VAL cc_start: 0.7366 (m) cc_final: 0.7056 (m) REVERT: B 1539 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7829 (mm) REVERT: B 1633 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7252 (mtm110) REVERT: B 1706 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6977 (tptt) REVERT: B 1792 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7884 (mt) REVERT: B 1796 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7056 (mt) REVERT: B 1820 LYS cc_start: 0.7246 (tppt) cc_final: 0.7035 (mptt) REVERT: B 1920 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8066 (tptt) REVERT: B 2007 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: B 2026 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5531 (mtp) REVERT: B 2189 PHE cc_start: 0.7388 (t80) cc_final: 0.7110 (t80) REVERT: B 2531 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5444 (ttp) REVERT: B 2636 THR cc_start: 0.7565 (t) cc_final: 0.7318 (t) REVERT: B 2935 MET cc_start: 0.8826 (tpp) cc_final: 0.8139 (tpp) outliers start: 162 outliers final: 51 residues processed: 563 average time/residue: 0.7974 time to fit residues: 551.0692 Evaluate side-chains 469 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 403 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2531 MET Chi-restraints excluded: chain A residue 2594 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1143 THR Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2531 MET Chi-restraints excluded: chain B residue 2594 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 33 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 459 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A 996 HIS A1117 GLN A1128 GLN A1653 GLN A1719 ASN A2038 HIS A2241 ASN A2277 GLN A2480 HIS A3014 GLN B 354 HIS ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 996 HIS B1117 GLN B1128 GLN B1653 GLN B1719 ASN B2038 HIS B2241 ASN B2277 GLN B2480 HIS B3014 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.254506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.206054 restraints weight = 51999.673| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.12 r_work: 0.3672 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 45314 Z= 0.180 Angle : 0.595 18.013 61234 Z= 0.297 Chirality : 0.041 0.184 7022 Planarity : 0.004 0.048 7708 Dihedral : 4.947 84.959 6034 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.83 % Allowed : 22.54 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.11), residues: 5470 helix: 2.03 (0.08), residues: 3910 sheet: 0.26 (0.58), residues: 66 loop : 0.11 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 981 TYR 0.019 0.002 TYR A 980 PHE 0.021 0.002 PHE B2571 TRP 0.015 0.002 TRP B2104 HIS 0.007 0.001 HIS A2538 Details of bonding type rmsd covalent geometry : bond 0.00425 (45314) covalent geometry : angle 0.59504 (61234) hydrogen bonds : bond 0.04562 ( 2839) hydrogen bonds : angle 3.59033 ( 8379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 424 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1798 (mmt) cc_final: 0.1171 (mtp) REVERT: A 230 ASN cc_start: 0.1338 (OUTLIER) cc_final: 0.1068 (m110) REVERT: A 1040 MET cc_start: 0.4675 (ptm) cc_final: 0.3873 (mtt) REVERT: A 1134 MET cc_start: 0.2596 (mtm) cc_final: 0.1294 (ptm) REVERT: A 1547 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 1706 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7242 (tptt) REVERT: A 1789 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7950 (mm) REVERT: A 1792 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7784 (mt) REVERT: A 1796 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 2007 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: A 2187 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: A 2189 PHE cc_start: 0.7606 (t80) cc_final: 0.7191 (t80) REVERT: A 2198 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 2458 ASP cc_start: 0.7794 (m-30) cc_final: 0.7551 (m-30) REVERT: A 2636 THR cc_start: 0.7648 (t) cc_final: 0.7400 (t) REVERT: A 2935 MET cc_start: 0.8904 (tpp) cc_final: 0.7951 (tpp) REVERT: B 94 MET cc_start: 0.1798 (mmt) cc_final: 0.1169 (mtp) REVERT: B 230 ASN cc_start: 0.1355 (OUTLIER) cc_final: 0.1082 (m110) REVERT: B 811 LEU cc_start: 0.0863 (OUTLIER) cc_final: 0.0598 (mt) REVERT: B 1040 MET cc_start: 0.4684 (ptm) cc_final: 0.3879 (mtt) REVERT: B 1134 MET cc_start: 0.2587 (mtm) cc_final: 0.1286 (ptm) REVERT: B 1547 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7401 (mm) REVERT: B 1706 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7244 (tptt) REVERT: B 1789 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7947 (mm) REVERT: B 1792 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7792 (mt) REVERT: B 1796 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7226 (mt) REVERT: B 2007 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: B 2187 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: B 2189 PHE cc_start: 0.7604 (t80) cc_final: 0.7186 (t80) REVERT: B 2198 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7471 (mm) REVERT: B 2458 ASP cc_start: 0.7779 (m-30) cc_final: 0.7539 (m-30) REVERT: B 2636 THR cc_start: 0.7642 (t) cc_final: 0.7397 (t) REVERT: B 2734 MET cc_start: 0.8148 (tpp) cc_final: 0.7943 (mmp) REVERT: B 2935 MET cc_start: 0.8894 (tpp) cc_final: 0.7936 (tpp) outliers start: 189 outliers final: 79 residues processed: 547 average time/residue: 0.8100 time to fit residues: 541.5886 Evaluate side-chains 501 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 405 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1819 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2280 GLN Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2594 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2836 MET Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3014 GLN Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 1066 LYS Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1547 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1789 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1819 THR Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2280 GLN Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2594 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2836 MET Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3014 GLN Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 390 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 368 optimal weight: 7.9990 chunk 552 optimal weight: 0.8980 chunk 531 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 445 optimal weight: 2.9990 chunk 480 optimal weight: 0.5980 chunk 384 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 414 GLN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1653 GLN A2038 HIS ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 414 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 ASN B1653 GLN B2038 HIS ** B2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.255205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.207561 restraints weight = 51970.071| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.05 r_work: 0.3694 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45314 Z= 0.128 Angle : 0.541 11.895 61234 Z= 0.271 Chirality : 0.038 0.174 7022 Planarity : 0.004 0.048 7708 Dihedral : 4.820 86.748 6032 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.28 % Allowed : 23.31 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.11), residues: 5470 helix: 2.15 (0.08), residues: 3894 sheet: 0.20 (0.57), residues: 66 loop : 0.10 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3047 TYR 0.013 0.001 TYR A1544 PHE 0.015 0.001 PHE A1381 TRP 0.018 0.001 TRP A2104 HIS 0.003 0.001 HIS A2038 Details of bonding type rmsd covalent geometry : bond 0.00293 (45314) covalent geometry : angle 0.54116 (61234) hydrogen bonds : bond 0.03842 ( 2839) hydrogen bonds : angle 3.48271 ( 8379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 426 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1754 (mmt) cc_final: 0.1151 (mtp) REVERT: A 389 ILE cc_start: -0.0708 (OUTLIER) cc_final: -0.0912 (mt) REVERT: A 528 THR cc_start: 0.1239 (OUTLIER) cc_final: 0.0668 (t) REVERT: A 753 MET cc_start: 0.2911 (tpp) cc_final: 0.2162 (ttm) REVERT: A 1040 MET cc_start: 0.4666 (ptm) cc_final: 0.3957 (mtt) REVERT: A 1134 MET cc_start: 0.2521 (mtm) cc_final: 0.1247 (ptm) REVERT: A 1706 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7327 (tptt) REVERT: A 1747 HIS cc_start: 0.6468 (m90) cc_final: 0.6085 (m-70) REVERT: A 1774 PHE cc_start: 0.7303 (m-80) cc_final: 0.6702 (m-80) REVERT: A 1792 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7798 (mt) REVERT: A 1796 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 2007 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: A 2026 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5577 (mtp) REVERT: A 2061 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: A 2187 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: A 2189 PHE cc_start: 0.7475 (t80) cc_final: 0.7169 (t80) REVERT: A 2314 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 2458 ASP cc_start: 0.7835 (m-30) cc_final: 0.7596 (m-30) REVERT: A 2636 THR cc_start: 0.7671 (t) cc_final: 0.7467 (t) REVERT: A 2935 MET cc_start: 0.8901 (tpp) cc_final: 0.8121 (tpp) REVERT: B 94 MET cc_start: 0.1750 (mmt) cc_final: 0.1144 (mtp) REVERT: B 230 ASN cc_start: 0.1070 (OUTLIER) cc_final: 0.0869 (m-40) REVERT: B 528 THR cc_start: 0.1230 (OUTLIER) cc_final: 0.0657 (t) REVERT: B 753 MET cc_start: 0.2907 (tpp) cc_final: 0.2145 (ttm) REVERT: B 1040 MET cc_start: 0.4687 (ptm) cc_final: 0.3964 (mtt) REVERT: B 1134 MET cc_start: 0.2538 (mtm) cc_final: 0.1259 (ptm) REVERT: B 1706 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7288 (tptt) REVERT: B 1747 HIS cc_start: 0.6472 (m90) cc_final: 0.6094 (m-70) REVERT: B 1774 PHE cc_start: 0.7303 (m-80) cc_final: 0.6691 (m-80) REVERT: B 1792 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 1796 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7219 (mt) REVERT: B 2007 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 2026 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5614 (mtp) REVERT: B 2061 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: B 2187 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: B 2189 PHE cc_start: 0.7419 (t80) cc_final: 0.7144 (t80) REVERT: B 2314 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: B 2458 ASP cc_start: 0.7833 (m-30) cc_final: 0.7598 (m-30) REVERT: B 2636 THR cc_start: 0.7667 (t) cc_final: 0.7464 (t) REVERT: B 2734 MET cc_start: 0.8239 (tpp) cc_final: 0.8032 (mmp) REVERT: B 2935 MET cc_start: 0.8900 (tpp) cc_final: 0.8117 (tpp) outliers start: 162 outliers final: 76 residues processed: 545 average time/residue: 0.7279 time to fit residues: 487.7144 Evaluate side-chains 495 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 401 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2460 LYS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1702 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2460 LYS Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2719 ARG Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 372 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 508 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 462 optimal weight: 0.6980 chunk 552 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 302 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 HIS A1653 GLN A1689 GLN A2210 GLN A2243 GLN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 GLN B 683 HIS B1653 GLN B1689 GLN B2210 GLN B2243 GLN ** B2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN B3014 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.253954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.205782 restraints weight = 52015.557| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.00 r_work: 0.3693 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45314 Z= 0.161 Angle : 0.585 14.185 61234 Z= 0.289 Chirality : 0.040 0.176 7022 Planarity : 0.004 0.047 7708 Dihedral : 4.889 86.238 6032 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.67 % Allowed : 22.96 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.11), residues: 5470 helix: 2.05 (0.08), residues: 3884 sheet: 0.17 (0.57), residues: 66 loop : 0.06 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B3047 TYR 0.017 0.002 TYR B1556 PHE 0.023 0.002 PHE B2571 TRP 0.016 0.001 TRP A2104 HIS 0.006 0.001 HIS B1213 Details of bonding type rmsd covalent geometry : bond 0.00380 (45314) covalent geometry : angle 0.58509 (61234) hydrogen bonds : bond 0.04213 ( 2839) hydrogen bonds : angle 3.52917 ( 8379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 416 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1593 (mmt) cc_final: 0.1047 (mtp) REVERT: A 617 MET cc_start: 0.1695 (OUTLIER) cc_final: 0.0400 (mtt) REVERT: A 753 MET cc_start: 0.3055 (OUTLIER) cc_final: 0.2242 (ttm) REVERT: A 1040 MET cc_start: 0.4673 (ptm) cc_final: 0.3950 (mtt) REVERT: A 1134 MET cc_start: 0.2560 (mtm) cc_final: 0.1290 (ptm) REVERT: A 1191 LYS cc_start: 0.4728 (OUTLIER) cc_final: 0.3657 (mttt) REVERT: A 1677 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: A 1706 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7355 (tptt) REVERT: A 1792 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 2026 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5603 (mtp) REVERT: A 2061 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 2187 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 2189 PHE cc_start: 0.7545 (t80) cc_final: 0.7172 (t80) REVERT: A 2198 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7374 (mm) REVERT: A 2314 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 2357 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: A 2458 ASP cc_start: 0.7881 (m-30) cc_final: 0.7654 (m-30) REVERT: A 2531 MET cc_start: 0.6173 (ttp) cc_final: 0.5809 (ttt) REVERT: A 2636 THR cc_start: 0.7744 (t) cc_final: 0.7544 (t) REVERT: A 2935 MET cc_start: 0.8904 (tpp) cc_final: 0.8140 (tpp) REVERT: B 94 MET cc_start: 0.1595 (mmt) cc_final: 0.1049 (mtp) REVERT: B 617 MET cc_start: 0.1690 (OUTLIER) cc_final: 0.0398 (mtt) REVERT: B 753 MET cc_start: 0.3053 (OUTLIER) cc_final: 0.2231 (ttm) REVERT: B 1040 MET cc_start: 0.4687 (ptm) cc_final: 0.3959 (mtt) REVERT: B 1134 MET cc_start: 0.2576 (mtm) cc_final: 0.1290 (ptm) REVERT: B 1677 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: B 1706 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7341 (tptt) REVERT: B 1792 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7814 (mt) REVERT: B 2026 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5619 (mtp) REVERT: B 2061 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: B 2187 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: B 2189 PHE cc_start: 0.7545 (t80) cc_final: 0.7173 (t80) REVERT: B 2198 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 2314 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: B 2357 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: B 2458 ASP cc_start: 0.7880 (m-30) cc_final: 0.7655 (m-30) REVERT: B 2531 MET cc_start: 0.6081 (ttp) cc_final: 0.5703 (ttt) REVERT: B 2935 MET cc_start: 0.8905 (tpp) cc_final: 0.8140 (tpp) outliers start: 181 outliers final: 89 residues processed: 540 average time/residue: 0.6925 time to fit residues: 457.9785 Evaluate side-chains 510 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 400 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1819 THR Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2460 LYS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2594 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1465 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1677 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1698 LYS Chi-restraints excluded: chain B residue 1702 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1819 THR Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2460 LYS Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2594 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 274 optimal weight: 0.9980 chunk 440 optimal weight: 0.7980 chunk 229 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 476 optimal weight: 0.9980 chunk 551 optimal weight: 0.0970 chunk 493 optimal weight: 0.5980 chunk 337 optimal weight: 9.9990 chunk 538 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 GLN A2243 GLN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2881 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1380 HIS B1653 GLN B2243 GLN ** B2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.255238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.204315 restraints weight = 52091.015| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.15 r_work: 0.3604 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 45314 Z= 0.107 Angle : 0.527 15.397 61234 Z= 0.260 Chirality : 0.037 0.176 7022 Planarity : 0.003 0.048 7708 Dihedral : 4.639 86.489 6028 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.75 % Allowed : 24.04 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.12), residues: 5470 helix: 2.22 (0.08), residues: 3910 sheet: 0.18 (0.57), residues: 66 loop : 0.06 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B3047 TYR 0.016 0.001 TYR B1544 PHE 0.012 0.001 PHE A2143 TRP 0.020 0.001 TRP A2104 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00235 (45314) covalent geometry : angle 0.52689 (61234) hydrogen bonds : bond 0.03468 ( 2839) hydrogen bonds : angle 3.39061 ( 8379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 414 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1572 (mmt) cc_final: 0.0999 (mtp) REVERT: A 389 ILE cc_start: -0.0530 (OUTLIER) cc_final: -0.0820 (mt) REVERT: A 617 MET cc_start: 0.1834 (OUTLIER) cc_final: 0.0321 (mtt) REVERT: A 753 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.2156 (ttm) REVERT: A 779 MET cc_start: 0.2513 (mmt) cc_final: 0.1783 (mmm) REVERT: A 1040 MET cc_start: 0.4811 (ptm) cc_final: 0.4048 (mtt) REVERT: A 1134 MET cc_start: 0.2631 (mtm) cc_final: 0.1291 (ptm) REVERT: A 1191 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.3542 (mttt) REVERT: A 1633 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7288 (mtm110) REVERT: A 1706 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7342 (tptt) REVERT: A 1735 THR cc_start: 0.8654 (p) cc_final: 0.8399 (t) REVERT: A 1789 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 1792 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 2007 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: A 2014 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 2026 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5793 (mtp) REVERT: A 2187 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: A 2314 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: A 2357 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: A 2458 ASP cc_start: 0.7966 (m-30) cc_final: 0.7747 (m-30) REVERT: A 2531 MET cc_start: 0.6331 (ttp) cc_final: 0.5953 (ttt) REVERT: A 2636 THR cc_start: 0.7789 (t) cc_final: 0.7580 (t) REVERT: A 2929 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8408 (mmp80) REVERT: A 2935 MET cc_start: 0.8882 (tpp) cc_final: 0.8126 (tpp) REVERT: B 94 MET cc_start: 0.1580 (mmt) cc_final: 0.0998 (mtp) REVERT: B 617 MET cc_start: 0.1824 (OUTLIER) cc_final: 0.0312 (mtt) REVERT: B 753 MET cc_start: 0.3034 (OUTLIER) cc_final: 0.2154 (ttm) REVERT: B 779 MET cc_start: 0.2515 (mmt) cc_final: 0.1787 (mmm) REVERT: B 1040 MET cc_start: 0.4821 (ptm) cc_final: 0.4055 (mtt) REVERT: B 1134 MET cc_start: 0.2546 (mtm) cc_final: 0.1236 (ptm) REVERT: B 1191 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.3551 (mptt) REVERT: B 1633 ARG cc_start: 0.7508 (ttm110) cc_final: 0.7288 (mtm110) REVERT: B 1706 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7327 (tptt) REVERT: B 1735 THR cc_start: 0.8643 (p) cc_final: 0.8384 (t) REVERT: B 1789 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (mm) REVERT: B 1792 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7706 (mt) REVERT: B 2007 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: B 2026 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5786 (mtp) REVERT: B 2187 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: B 2314 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: B 2357 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: B 2458 ASP cc_start: 0.7972 (m-30) cc_final: 0.7754 (m-30) REVERT: B 2531 MET cc_start: 0.6303 (ttp) cc_final: 0.5899 (ttt) REVERT: B 2670 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7393 (tmmt) REVERT: B 2929 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8395 (mmp80) REVERT: B 2935 MET cc_start: 0.8894 (tpp) cc_final: 0.8138 (tpp) outliers start: 136 outliers final: 67 residues processed: 504 average time/residue: 0.6738 time to fit residues: 414.7511 Evaluate side-chains 480 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 390 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2243 GLN Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1191 LYS Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1465 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1702 LEU Chi-restraints excluded: chain B residue 1789 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2243 GLN Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2670 LYS Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 60 optimal weight: 5.9990 chunk 292 optimal weight: 0.0030 chunk 384 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 513 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 354 optimal weight: 30.0000 overall best weight: 3.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A1395 ASN A1653 GLN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B1395 ASN B1653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.252562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.202268 restraints weight = 51748.678| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.17 r_work: 0.3643 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 45314 Z= 0.235 Angle : 0.662 14.922 61234 Z= 0.330 Chirality : 0.044 0.184 7022 Planarity : 0.005 0.047 7708 Dihedral : 5.051 86.505 6028 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.40 % Allowed : 23.67 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.11), residues: 5470 helix: 1.76 (0.08), residues: 3904 sheet: 0.10 (0.57), residues: 66 loop : -0.09 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2244 TYR 0.019 0.002 TYR A1544 PHE 0.022 0.002 PHE B2571 TRP 0.015 0.002 TRP B 156 HIS 0.007 0.002 HIS A2538 Details of bonding type rmsd covalent geometry : bond 0.00567 (45314) covalent geometry : angle 0.66245 (61234) hydrogen bonds : bond 0.05022 ( 2839) hydrogen bonds : angle 3.70488 ( 8379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 401 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1626 (mmt) cc_final: 0.1022 (mtp) REVERT: A 753 MET cc_start: 0.2977 (OUTLIER) cc_final: 0.2112 (ttm) REVERT: A 779 MET cc_start: 0.2297 (mmt) cc_final: 0.1585 (mmm) REVERT: A 780 MET cc_start: 0.1760 (mmt) cc_final: 0.0807 (tmt) REVERT: A 1134 MET cc_start: 0.2198 (mtm) cc_final: 0.0884 (ptm) REVERT: A 1191 LYS cc_start: 0.4924 (OUTLIER) cc_final: 0.3772 (mttt) REVERT: A 1706 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7404 (tptt) REVERT: A 1792 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 1971 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6588 (mm-30) REVERT: A 2026 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5993 (mtp) REVERT: A 2061 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: A 2187 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: A 2189 PHE cc_start: 0.7563 (t80) cc_final: 0.7146 (t80) REVERT: A 2198 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7575 (mm) REVERT: A 2314 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: A 2458 ASP cc_start: 0.7871 (m-30) cc_final: 0.7650 (m-30) REVERT: A 2531 MET cc_start: 0.6406 (ttp) cc_final: 0.6053 (ttt) REVERT: A 2636 THR cc_start: 0.7858 (t) cc_final: 0.7652 (t) REVERT: A 2660 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 2935 MET cc_start: 0.8973 (tpp) cc_final: 0.8241 (tpp) REVERT: B 94 MET cc_start: 0.1627 (mmt) cc_final: 0.1019 (mtp) REVERT: B 753 MET cc_start: 0.2980 (OUTLIER) cc_final: 0.2114 (ttm) REVERT: B 779 MET cc_start: 0.2289 (mmt) cc_final: 0.1576 (mmm) REVERT: B 780 MET cc_start: 0.1753 (mmt) cc_final: 0.0809 (tmt) REVERT: B 1134 MET cc_start: 0.2195 (mtm) cc_final: 0.0877 (ptm) REVERT: B 1191 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.3719 (mtmm) REVERT: B 1706 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7405 (tptt) REVERT: B 1792 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 1971 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6578 (mm-30) REVERT: B 2026 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5992 (mtp) REVERT: B 2061 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: B 2187 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: B 2189 PHE cc_start: 0.7560 (t80) cc_final: 0.7145 (t80) REVERT: B 2198 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7580 (mm) REVERT: B 2314 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: B 2458 ASP cc_start: 0.7894 (m-30) cc_final: 0.7673 (m-30) REVERT: B 2531 MET cc_start: 0.6418 (ttp) cc_final: 0.6056 (ttt) REVERT: B 2660 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: B 2935 MET cc_start: 0.8963 (tpp) cc_final: 0.8227 (tpp) outliers start: 168 outliers final: 88 residues processed: 517 average time/residue: 0.5056 time to fit residues: 323.0326 Evaluate side-chains 501 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 395 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1819 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2660 GLU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3004 LYS Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1191 LYS Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1698 LYS Chi-restraints excluded: chain B residue 1702 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1819 THR Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2198 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2660 GLU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2719 ARG Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3004 LYS Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 76 optimal weight: 8.9990 chunk 277 optimal weight: 50.0000 chunk 169 optimal weight: 0.8980 chunk 432 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 515 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 chunk 268 optimal weight: 0.5980 chunk 419 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A1380 HIS A1395 ASN A1653 GLN A2099 HIS ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B1395 ASN B1653 GLN B2099 HIS ** B2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.253181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.204480 restraints weight = 51647.857| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.07 r_work: 0.3667 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45314 Z= 0.122 Angle : 0.560 14.146 61234 Z= 0.277 Chirality : 0.038 0.211 7022 Planarity : 0.004 0.047 7708 Dihedral : 4.805 87.577 6028 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.57 % Allowed : 24.44 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.11), residues: 5470 helix: 2.10 (0.08), residues: 3876 sheet: 0.18 (0.57), residues: 66 loop : -0.10 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 925 TYR 0.019 0.001 TYR A1556 PHE 0.013 0.001 PHE B2143 TRP 0.022 0.001 TRP A2104 HIS 0.003 0.001 HIS A2125 Details of bonding type rmsd covalent geometry : bond 0.00277 (45314) covalent geometry : angle 0.55963 (61234) hydrogen bonds : bond 0.03719 ( 2839) hydrogen bonds : angle 3.49715 ( 8379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 395 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1612 (mmt) cc_final: 0.0999 (mtp) REVERT: A 753 MET cc_start: 0.3043 (OUTLIER) cc_final: 0.2129 (ttm) REVERT: A 779 MET cc_start: 0.2262 (mmt) cc_final: 0.1716 (mmm) REVERT: A 780 MET cc_start: 0.2094 (mmt) cc_final: 0.1164 (tmt) REVERT: A 1040 MET cc_start: 0.4542 (ptt) cc_final: 0.4028 (mtt) REVERT: A 1134 MET cc_start: 0.2389 (mtm) cc_final: 0.1117 (ptm) REVERT: A 1191 LYS cc_start: 0.4616 (OUTLIER) cc_final: 0.3497 (mttt) REVERT: A 1622 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: A 1706 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7452 (tptt) REVERT: A 1792 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7767 (mt) REVERT: A 1971 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 2026 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5696 (mtp) REVERT: A 2187 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: A 2314 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: A 2531 MET cc_start: 0.6392 (ttp) cc_final: 0.6052 (ttt) REVERT: A 2660 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 2935 MET cc_start: 0.8883 (tpp) cc_final: 0.8158 (tpp) REVERT: B 94 MET cc_start: 0.1631 (mmt) cc_final: 0.1010 (mtp) REVERT: B 753 MET cc_start: 0.3014 (OUTLIER) cc_final: 0.2124 (ttm) REVERT: B 779 MET cc_start: 0.2258 (mmt) cc_final: 0.1717 (mmm) REVERT: B 780 MET cc_start: 0.1865 (mmt) cc_final: 0.0987 (tmt) REVERT: B 1040 MET cc_start: 0.4517 (ptt) cc_final: 0.4023 (mtt) REVERT: B 1134 MET cc_start: 0.2473 (mtm) cc_final: 0.1216 (ptm) REVERT: B 1191 LYS cc_start: 0.4800 (OUTLIER) cc_final: 0.3656 (mttt) REVERT: B 1208 ASP cc_start: 0.4245 (OUTLIER) cc_final: 0.3932 (p0) REVERT: B 1622 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: B 1706 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7446 (tptt) REVERT: B 1792 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 1971 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6639 (mm-30) REVERT: B 2026 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5678 (mtp) REVERT: B 2187 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: B 2314 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: B 2458 ASP cc_start: 0.8054 (m-30) cc_final: 0.7848 (m-30) REVERT: B 2531 MET cc_start: 0.6401 (ttp) cc_final: 0.6071 (ttt) REVERT: B 2636 THR cc_start: 0.7849 (t) cc_final: 0.7587 (m) REVERT: B 2660 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 2670 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7530 (tmmt) REVERT: B 2935 MET cc_start: 0.8895 (tpp) cc_final: 0.8162 (tpp) outliers start: 127 outliers final: 73 residues processed: 483 average time/residue: 0.5202 time to fit residues: 307.8732 Evaluate side-chains 482 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 392 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1622 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2460 LYS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2660 GLU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3004 LYS Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1191 LYS Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1622 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2460 LYS Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2660 GLU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2719 ARG Chi-restraints excluded: chain B residue 3004 LYS Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 21 optimal weight: 4.9990 chunk 413 optimal weight: 2.9990 chunk 448 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 476 optimal weight: 0.9990 chunk 419 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 347 optimal weight: 5.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 GLN A1660 ASN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN B1660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.253591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.204047 restraints weight = 51822.415| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.12 r_work: 0.3685 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45314 Z= 0.159 Angle : 0.592 13.731 61234 Z= 0.294 Chirality : 0.040 0.183 7022 Planarity : 0.004 0.046 7708 Dihedral : 4.892 87.144 6028 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.17 % Allowed : 25.07 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.11), residues: 5470 helix: 1.99 (0.08), residues: 3882 sheet: 0.13 (0.57), residues: 66 loop : -0.09 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3047 TYR 0.020 0.002 TYR B1556 PHE 0.020 0.002 PHE B1381 TRP 0.015 0.001 TRP B2104 HIS 0.004 0.001 HIS B2538 Details of bonding type rmsd covalent geometry : bond 0.00376 (45314) covalent geometry : angle 0.59166 (61234) hydrogen bonds : bond 0.04202 ( 2839) hydrogen bonds : angle 3.58158 ( 8379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 408 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1658 (mmt) cc_final: 0.1041 (mtp) REVERT: A 617 MET cc_start: 0.0784 (pp-130) cc_final: 0.0278 (ptt) REVERT: A 753 MET cc_start: 0.2989 (OUTLIER) cc_final: 0.2126 (ttm) REVERT: A 779 MET cc_start: 0.2287 (mmt) cc_final: 0.1746 (mmm) REVERT: A 780 MET cc_start: 0.1615 (mmt) cc_final: 0.0715 (tmt) REVERT: A 1040 MET cc_start: 0.4463 (ptt) cc_final: 0.4007 (mtt) REVERT: A 1134 MET cc_start: 0.2394 (mtm) cc_final: 0.1191 (ptm) REVERT: A 1191 LYS cc_start: 0.4690 (OUTLIER) cc_final: 0.3547 (mttt) REVERT: A 1706 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7347 (tptt) REVERT: A 1792 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7800 (mt) REVERT: A 1971 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6549 (mm-30) REVERT: A 2026 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5813 (mtp) REVERT: A 2187 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 2189 PHE cc_start: 0.7450 (t80) cc_final: 0.7111 (t80) REVERT: A 2314 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 2531 MET cc_start: 0.6374 (ttp) cc_final: 0.6044 (ttt) REVERT: A 2935 MET cc_start: 0.8939 (tpp) cc_final: 0.8217 (tpp) REVERT: B 94 MET cc_start: 0.1677 (mmt) cc_final: 0.1050 (mtp) REVERT: B 617 MET cc_start: 0.0784 (pp-130) cc_final: 0.0274 (ptt) REVERT: B 753 MET cc_start: 0.3039 (OUTLIER) cc_final: 0.2165 (ttm) REVERT: B 779 MET cc_start: 0.2289 (mmt) cc_final: 0.1747 (mmm) REVERT: B 780 MET cc_start: 0.1615 (mmt) cc_final: 0.0715 (tmt) REVERT: B 1040 MET cc_start: 0.4473 (ptt) cc_final: 0.4011 (mtt) REVERT: B 1134 MET cc_start: 0.2380 (mtm) cc_final: 0.1185 (ptm) REVERT: B 1191 LYS cc_start: 0.4586 (OUTLIER) cc_final: 0.3437 (mttt) REVERT: B 1437 ARG cc_start: 0.7335 (ttp80) cc_final: 0.7121 (tmt170) REVERT: B 1706 LYS cc_start: 0.7605 (tmtt) cc_final: 0.7346 (tptt) REVERT: B 1792 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7815 (mt) REVERT: B 1971 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6565 (mm-30) REVERT: B 2026 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5802 (mtp) REVERT: B 2187 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: B 2189 PHE cc_start: 0.7459 (t80) cc_final: 0.7120 (t80) REVERT: B 2314 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: B 2531 MET cc_start: 0.6312 (ttp) cc_final: 0.5997 (ttt) REVERT: B 2636 THR cc_start: 0.7737 (t) cc_final: 0.7505 (m) REVERT: B 2935 MET cc_start: 0.8940 (tpp) cc_final: 0.8212 (tpp) outliers start: 107 outliers final: 77 residues processed: 478 average time/residue: 0.5190 time to fit residues: 303.9044 Evaluate side-chains 485 residues out of total 5040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 396 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2187 GLU Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2460 LYS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2719 ARG Chi-restraints excluded: chain A residue 3004 LYS Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1191 LYS Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2187 GLU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2460 LYS Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2719 ARG Chi-restraints excluded: chain B residue 2836 MET Chi-restraints excluded: chain B residue 3004 LYS Chi-restraints excluded: chain B residue 3011 MET Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 33 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 345 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 316 optimal weight: 0.9990 chunk 126 optimal weight: 0.0970 chunk 317 optimal weight: 0.3980 chunk 325 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 GLN A2243 GLN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 GLN B 230 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1579 GLN B1653 GLN B2243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.254083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.203397 restraints weight = 52189.413| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.21 r_work: 0.3678 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45314 Z= 0.116 Angle : 0.548 13.388 61234 Z= 0.270 Chirality : 0.038 0.200 7022 Planarity : 0.003 0.047 7708 Dihedral : 4.747 87.008 6028 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.96 % Allowed : 25.29 % Favored : 72.74 % 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 are not related in a simple way. whole: 2.29 (0.12), residues: 5470 helix: 2.16 (0.08), residues: 3894 sheet: 0.19 (0.57), residues: 66 loop : -0.07 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2642 TYR 0.018 0.001 TYR A1544 PHE 0.026 0.001 PHE B2571 TRP 0.021 0.001 TRP A2104 HIS 0.003 0.001 HIS B 945 Details of bonding type rmsd covalent geometry : bond 0.00261 (45314) covalent geometry : angle 0.54806 (61234) hydrogen bonds : bond 0.03580 ( 2839) hydrogen bonds : angle 3.45757 ( 8379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14040.12 seconds wall clock time: 239 minutes 42.53 seconds (14382.53 seconds total)