Starting phenix.real_space_refine on Thu Jan 16 06:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.map" model { file = "/net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c47_45176/01_2025/9c47_45176.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 187 5.16 5 C 16560 2.51 5 N 4449 2.21 5 O 4591 1.98 5 H 26380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 1.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 52167 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 50044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3079, 50044 Classifications: {'peptide': 3079} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 132, 'TRANS': 2946} Chain breaks: 31 Chain: "G" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2123 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 2 Time building chain proxies: 17.89, per 1000 atoms: 0.34 Number of scatterers: 52167 At special positions: 0 Unit cell: (129.15, 183.75, 153.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 187 16.00 O 4591 8.00 N 4449 7.00 C 16560 6.00 H 26380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C1868 " - pdb=" SG CYS C1874 " distance=2.04 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: 11.28 Conformation dependent library (CDL) restraints added in 3.3 seconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6218 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 3 sheets defined 79.3% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'C' and resid 243 through 255 removed outlier: 3.755A pdb=" N VAL C 247 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Proline residue: C 252 - end of helix removed outlier: 3.645A pdb=" N MET C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 293 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.517A pdb=" N SER C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 346 through 352 removed outlier: 4.336A pdb=" N CYS C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 387 removed outlier: 3.630A pdb=" N ARG C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.603A pdb=" N GLN C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 437 removed outlier: 3.505A pdb=" N GLN C 416 " --> pdb=" O PRO C 412 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 463 removed outlier: 3.600A pdb=" N VAL C 444 " --> pdb=" O ASN C 440 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 461 " --> pdb=" O HIS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 467 Processing helix chain 'C' and resid 542 through 566 removed outlier: 3.975A pdb=" N CYS C 555 " --> pdb=" O LYS C 551 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 removed outlier: 3.925A pdb=" N ILE C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 605 removed outlier: 3.735A pdb=" N VAL C 605 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 639 removed outlier: 3.661A pdb=" N VAL C 638 " --> pdb=" O HIS C 634 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE C 639 " --> pdb=" O PHE C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 665 removed outlier: 3.765A pdb=" N GLN C 652 " --> pdb=" O LYS C 648 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Proline residue: C 656 - end of helix removed outlier: 4.113A pdb=" N LYS C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 676 removed outlier: 3.571A pdb=" N ALA C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 697 removed outlier: 3.953A pdb=" N LEU C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 700 No H-bonds generated for 'chain 'C' and resid 698 through 700' Processing helix chain 'C' and resid 703 through 724 removed outlier: 4.049A pdb=" N LEU C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 735 through 750 removed outlier: 3.606A pdb=" N ILE C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 768 Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 782 through 796 Processing helix chain 'C' and resid 799 through 811 Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 823 through 836 removed outlier: 3.932A pdb=" N ASP C 829 " --> pdb=" O PRO C 825 " (cutoff:3.500A) Proline residue: C 830 - end of helix removed outlier: 3.552A pdb=" N ASN C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 856 removed outlier: 3.509A pdb=" N ASP C 854 " --> pdb=" O GLU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 866 Processing helix chain 'C' and resid 868 through 881 removed outlier: 3.986A pdb=" N GLN C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 881 " --> pdb=" O TRP C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 898 Processing helix chain 'C' and resid 929 through 932 Processing helix chain 'C' and resid 939 through 952 Processing helix chain 'C' and resid 956 through 975 Processing helix chain 'C' and resid 980 through 989 removed outlier: 3.566A pdb=" N LEU C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'C' and resid 1012 through 1031 Processing helix chain 'C' and resid 1034 through 1058 Proline residue: C1040 - end of helix Processing helix chain 'C' and resid 1063 through 1067 Processing helix chain 'C' and resid 1073 through 1077 removed outlier: 3.720A pdb=" N MET C1076 " --> pdb=" O SER C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1102 Processing helix chain 'C' and resid 1106 through 1127 removed outlier: 4.102A pdb=" N ILE C1110 " --> pdb=" O GLU C1106 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1134 Processing helix chain 'C' and resid 1135 through 1148 removed outlier: 3.965A pdb=" N SER C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C1148 " --> pdb=" O ARG C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1151 No H-bonds generated for 'chain 'C' and resid 1149 through 1151' Processing helix chain 'C' and resid 1153 through 1171 Processing helix chain 'C' and resid 1172 through 1179 Processing helix chain 'C' and resid 1179 through 1194 Processing helix chain 'C' and resid 1202 through 1219 removed outlier: 3.554A pdb=" N THR C1208 " --> pdb=" O ALA C1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 1227 through 1248 Processing helix chain 'C' and resid 1253 through 1271 removed outlier: 3.748A pdb=" N GLN C1265 " --> pdb=" O MET C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1274 through 1280 Processing helix chain 'C' and resid 1282 through 1287 removed outlier: 4.059A pdb=" N LEU C1286 " --> pdb=" O HIS C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1318 removed outlier: 3.620A pdb=" N LEU C1318 " --> pdb=" O PHE C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1332 through 1345 Processing helix chain 'C' and resid 1347 through 1352 Processing helix chain 'C' and resid 1355 through 1359 removed outlier: 4.209A pdb=" N SER C1358 " --> pdb=" O CYS C1355 " (cutoff:3.500A) Processing helix chain 'C' and resid 1362 through 1376 removed outlier: 3.508A pdb=" N CYS C1376 " --> pdb=" O ALA C1372 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1395 removed outlier: 3.515A pdb=" N ARG C1383 " --> pdb=" O LEU C1379 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C1384 " --> pdb=" O PRO C1380 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS C1385 " --> pdb=" O GLN C1381 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C1388 " --> pdb=" O GLU C1384 " (cutoff:3.500A) Processing helix chain 'C' and resid 1398 through 1416 removed outlier: 3.743A pdb=" N GLY C1415 " --> pdb=" O LYS C1411 " (cutoff:3.500A) Processing helix chain 'C' and resid 1419 through 1427 Processing helix chain 'C' and resid 1427 through 1433 removed outlier: 3.702A pdb=" N MET C1433 " --> pdb=" O PRO C1429 " (cutoff:3.500A) Processing helix chain 'C' and resid 1434 through 1435 No H-bonds generated for 'chain 'C' and resid 1434 through 1435' Processing helix chain 'C' and resid 1436 through 1440 Processing helix chain 'C' and resid 1441 through 1453 removed outlier: 3.561A pdb=" N ASN C1446 " --> pdb=" O LEU C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1455 through 1459 Processing helix chain 'C' and resid 1460 through 1483 removed outlier: 3.584A pdb=" N GLN C1466 " --> pdb=" O LYS C1462 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C1479 " --> pdb=" O MET C1475 " (cutoff:3.500A) Processing helix chain 'C' and resid 1510 through 1524 removed outlier: 3.515A pdb=" N PHE C1521 " --> pdb=" O ILE C1517 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS C1522 " --> pdb=" O ILE C1518 " (cutoff:3.500A) Processing helix chain 'C' and resid 1528 through 1530 No H-bonds generated for 'chain 'C' and resid 1528 through 1530' Processing helix chain 'C' and resid 1531 through 1547 Processing helix chain 'C' and resid 1554 through 1565 removed outlier: 3.685A pdb=" N PHE C1561 " --> pdb=" O PRO C1557 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C1564 " --> pdb=" O LYS C1560 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1574 removed outlier: 3.793A pdb=" N THR C1569 " --> pdb=" O HIS C1565 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C1571 " --> pdb=" O SER C1567 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1581 removed outlier: 3.555A pdb=" N ASP C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) Processing helix chain 'C' and resid 1581 through 1594 removed outlier: 3.581A pdb=" N MET C1587 " --> pdb=" O GLN C1583 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS C1594 " --> pdb=" O SER C1590 " (cutoff:3.500A) Processing helix chain 'C' and resid 1596 through 1607 removed outlier: 4.423A pdb=" N LEU C1600 " --> pdb=" O ASP C1596 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C1603 " --> pdb=" O PRO C1599 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C1604 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C1607 " --> pdb=" O VAL C1603 " (cutoff:3.500A) Processing helix chain 'C' and resid 1607 through 1616 removed outlier: 3.974A pdb=" N PHE C1611 " --> pdb=" O ASN C1607 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C1614 " --> pdb=" O ARG C1610 " (cutoff:3.500A) Processing helix chain 'C' and resid 1636 through 1653 removed outlier: 3.592A pdb=" N ASN C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) Processing helix chain 'C' and resid 1661 through 1674 removed outlier: 4.243A pdb=" N SER C1665 " --> pdb=" O HIS C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1675 through 1679 removed outlier: 3.745A pdb=" N GLU C1678 " --> pdb=" O ASN C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1707 removed outlier: 3.925A pdb=" N CYS C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C1700 " --> pdb=" O LEU C1696 " (cutoff:3.500A) Processing helix chain 'C' and resid 1710 through 1721 removed outlier: 3.555A pdb=" N GLN C1716 " --> pdb=" O GLU C1712 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C1721 " --> pdb=" O LEU C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1732 through 1740 removed outlier: 4.086A pdb=" N MET C1736 " --> pdb=" O LEU C1732 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C1740 " --> pdb=" O MET C1736 " (cutoff:3.500A) Processing helix chain 'C' and resid 1749 through 1760 removed outlier: 3.567A pdb=" N ARG C1755 " --> pdb=" O ALA C1751 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE C1756 " --> pdb=" O LEU C1752 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C1757 " --> pdb=" O PHE C1753 " (cutoff:3.500A) Processing helix chain 'C' and resid 1766 through 1782 Proline residue: C1779 - end of helix Processing helix chain 'C' and resid 1805 through 1815 removed outlier: 4.166A pdb=" N SER C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C1812 " --> pdb=" O THR C1808 " (cutoff:3.500A) Processing helix chain 'C' and resid 1826 through 1843 removed outlier: 4.246A pdb=" N ILE C1830 " --> pdb=" O ASP C1826 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C1841 " --> pdb=" O THR C1837 " (cutoff:3.500A) Processing helix chain 'C' and resid 1858 through 1862 Processing helix chain 'C' and resid 1865 through 1870 Processing helix chain 'C' and resid 1876 through 1891 Processing helix chain 'C' and resid 1897 through 1910 removed outlier: 3.848A pdb=" N GLN C1903 " --> pdb=" O LYS C1899 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C1906 " --> pdb=" O LEU C1902 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C1907 " --> pdb=" O GLN C1903 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C1909 " --> pdb=" O PHE C1905 " (cutoff:3.500A) Processing helix chain 'C' and resid 1913 through 1928 removed outlier: 3.733A pdb=" N ILE C1919 " --> pdb=" O GLU C1915 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C1926 " --> pdb=" O GLN C1922 " (cutoff:3.500A) Processing helix chain 'C' and resid 1930 through 1938 removed outlier: 4.070A pdb=" N ARG C1934 " --> pdb=" O ALA C1930 " (cutoff:3.500A) Processing helix chain 'C' and resid 1941 through 1953 removed outlier: 3.801A pdb=" N TRP C1945 " --> pdb=" O MET C1941 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1971 removed outlier: 3.548A pdb=" N HIS C1970 " --> pdb=" O LEU C1966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1980 through 1994 removed outlier: 3.801A pdb=" N HIS C1984 " --> pdb=" O HIS C1980 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C1991 " --> pdb=" O SER C1987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2020 removed outlier: 4.119A pdb=" N ALA C2006 " --> pdb=" O GLN C2002 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C2007 " --> pdb=" O ARG C2003 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C2008 " --> pdb=" O ARG C2004 " (cutoff:3.500A) Processing helix chain 'C' and resid 2091 through 2108 removed outlier: 3.629A pdb=" N ASP C2095 " --> pdb=" O LYS C2091 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR C2096 " --> pdb=" O GLN C2092 " (cutoff:3.500A) Processing helix chain 'C' and resid 2123 through 2132 removed outlier: 4.244A pdb=" N VAL C2127 " --> pdb=" O SER C2123 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C2128 " --> pdb=" O ARG C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2143 through 2155 removed outlier: 4.005A pdb=" N GLN C2147 " --> pdb=" O GLU C2143 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C2150 " --> pdb=" O LEU C2146 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS C2151 " --> pdb=" O GLN C2147 " (cutoff:3.500A) Processing helix chain 'C' and resid 2163 through 2183 removed outlier: 3.978A pdb=" N ILE C2167 " --> pdb=" O ASN C2163 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU C2178 " --> pdb=" O LEU C2174 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C2179 " --> pdb=" O SER C2175 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2190 Processing helix chain 'C' and resid 2190 through 2198 Processing helix chain 'C' and resid 2199 through 2205 Processing helix chain 'C' and resid 2208 through 2223 removed outlier: 3.505A pdb=" N VAL C2212 " --> pdb=" O VAL C2208 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C2223 " --> pdb=" O LEU C2219 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2253 removed outlier: 3.533A pdb=" N LEU C2242 " --> pdb=" O GLU C2238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C2249 " --> pdb=" O ALA C2245 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2282 removed outlier: 3.809A pdb=" N MET C2273 " --> pdb=" O PHE C2269 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C2274 " --> pdb=" O GLY C2270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C2277 " --> pdb=" O MET C2273 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2287 through 2305 removed outlier: 3.926A pdb=" N SER C2291 " --> pdb=" O ASP C2287 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C2292 " --> pdb=" O ARG C2288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C2302 " --> pdb=" O GLN C2298 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C2305 " --> pdb=" O VAL C2301 " (cutoff:3.500A) Processing helix chain 'C' and resid 2317 through 2334 removed outlier: 3.516A pdb=" N SER C2327 " --> pdb=" O LEU C2323 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C2331 " --> pdb=" O SER C2327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C2334 " --> pdb=" O LEU C2330 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2357 removed outlier: 3.761A pdb=" N THR C2352 " --> pdb=" O GLN C2348 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C2357 " --> pdb=" O SER C2353 " (cutoff:3.500A) Processing helix chain 'C' and resid 2360 through 2377 removed outlier: 4.248A pdb=" N LEU C2364 " --> pdb=" O ASP C2360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C2365 " --> pdb=" O ALA C2361 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C2366 " --> pdb=" O LYS C2362 " (cutoff:3.500A) Processing helix chain 'C' and resid 2388 through 2407 removed outlier: 3.518A pdb=" N ILE C2394 " --> pdb=" O ARG C2390 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C2401 " --> pdb=" O VAL C2397 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C2402 " --> pdb=" O LYS C2398 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS C2405 " --> pdb=" O THR C2401 " (cutoff:3.500A) Processing helix chain 'C' and resid 2411 through 2427 removed outlier: 3.624A pdb=" N ASP C2419 " --> pdb=" O ALA C2415 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C2422 " --> pdb=" O LEU C2418 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR C2423 " --> pdb=" O ASP C2419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C2424 " --> pdb=" O LEU C2420 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C2426 " --> pdb=" O ASN C2422 " (cutoff:3.500A) Processing helix chain 'C' and resid 2436 through 2438 No H-bonds generated for 'chain 'C' and resid 2436 through 2438' Processing helix chain 'C' and resid 2439 through 2449 removed outlier: 3.899A pdb=" N SER C2445 " --> pdb=" O PRO C2441 " (cutoff:3.500A) Processing helix chain 'C' and resid 2451 through 2465 removed outlier: 4.098A pdb=" N VAL C2461 " --> pdb=" O LYS C2457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2469 through 2479 Processing helix chain 'C' and resid 2483 through 2487 removed outlier: 3.587A pdb=" N MET C2486 " --> pdb=" O TRP C2483 " (cutoff:3.500A) Processing helix chain 'C' and resid 2491 through 2501 removed outlier: 3.544A pdb=" N CYS C2495 " --> pdb=" O TRP C2491 " (cutoff:3.500A) Processing helix chain 'C' and resid 2513 through 2517 Processing helix chain 'C' and resid 2522 through 2528 removed outlier: 3.638A pdb=" N ASN C2526 " --> pdb=" O THR C2522 " (cutoff:3.500A) Processing helix chain 'C' and resid 2587 through 2604 removed outlier: 3.606A pdb=" N LYS C2597 " --> pdb=" O ASN C2593 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C2598 " --> pdb=" O ARG C2594 " (cutoff:3.500A) Processing helix chain 'C' and resid 2606 through 2621 removed outlier: 3.940A pdb=" N LEU C2610 " --> pdb=" O LYS C2606 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C2619 " --> pdb=" O VAL C2615 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C2620 " --> pdb=" O GLN C2616 " (cutoff:3.500A) Processing helix chain 'C' and resid 2621 through 2640 Proline residue: C2634 - end of helix removed outlier: 3.828A pdb=" N ILE C2639 " --> pdb=" O ARG C2635 " (cutoff:3.500A) Processing helix chain 'C' and resid 2641 through 2657 removed outlier: 3.529A pdb=" N SER C2653 " --> pdb=" O ALA C2649 " (cutoff:3.500A) Proline residue: C2654 - end of helix removed outlier: 3.616A pdb=" N CYS C2657 " --> pdb=" O SER C2653 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2665 Processing helix chain 'C' and resid 2670 through 2681 removed outlier: 3.960A pdb=" N GLN C2681 " --> pdb=" O GLU C2677 " (cutoff:3.500A) Processing helix chain 'C' and resid 2689 through 2700 Processing helix chain 'C' and resid 2702 through 2717 removed outlier: 3.580A pdb=" N GLN C2713 " --> pdb=" O MET C2709 " (cutoff:3.500A) Processing helix chain 'C' and resid 2742 through 2756 Processing helix chain 'C' and resid 2757 through 2769 Processing helix chain 'C' and resid 2771 through 2784 removed outlier: 3.887A pdb=" N ALA C2775 " --> pdb=" O TYR C2771 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C2783 " --> pdb=" O ALA C2779 " (cutoff:3.500A) Processing helix chain 'C' and resid 2785 through 2807 removed outlier: 3.619A pdb=" N GLU C2805 " --> pdb=" O LYS C2801 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) Processing helix chain 'C' and resid 2810 through 2812 No H-bonds generated for 'chain 'C' and resid 2810 through 2812' Processing helix chain 'C' and resid 2813 through 2831 Processing helix chain 'C' and resid 2833 through 2842 Processing helix chain 'C' and resid 2848 through 2857 removed outlier: 4.172A pdb=" N TRP C2857 " --> pdb=" O LEU C2853 " (cutoff:3.500A) Processing helix chain 'C' and resid 2861 through 2874 removed outlier: 3.712A pdb=" N VAL C2874 " --> pdb=" O VAL C2870 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2894 removed outlier: 4.032A pdb=" N LYS C2883 " --> pdb=" O GLU C2879 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C2889 " --> pdb=" O ASN C2885 " (cutoff:3.500A) Processing helix chain 'C' and resid 2903 through 2920 removed outlier: 3.588A pdb=" N LEU C2907 " --> pdb=" O PHE C2903 " (cutoff:3.500A) Processing helix chain 'C' and resid 2927 through 2929 No H-bonds generated for 'chain 'C' and resid 2927 through 2929' Processing helix chain 'C' and resid 2930 through 2954 removed outlier: 3.761A pdb=" N GLN C2938 " --> pdb=" O LEU C2934 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C2939 " --> pdb=" O GLN C2935 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C2942 " --> pdb=" O GLN C2938 " (cutoff:3.500A) Processing helix chain 'C' and resid 2960 through 2977 removed outlier: 3.550A pdb=" N VAL C2970 " --> pdb=" O ASP C2966 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C2976 " --> pdb=" O LYS C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2984 through 3007 removed outlier: 3.938A pdb=" N HIS C2998 " --> pdb=" O TRP C2994 " (cutoff:3.500A) Proline residue: C3003 - end of helix Processing helix chain 'C' and resid 3028 through 3051 removed outlier: 3.713A pdb=" N ALA C3048 " --> pdb=" O TYR C3044 " (cutoff:3.500A) Processing helix chain 'C' and resid 3053 through 3064 removed outlier: 3.972A pdb=" N ILE C3064 " --> pdb=" O ILE C3060 " (cutoff:3.500A) Processing helix chain 'C' and resid 3065 through 3067 No H-bonds generated for 'chain 'C' and resid 3065 through 3067' Processing helix chain 'C' and resid 3071 through 3089 removed outlier: 3.627A pdb=" N LEU C3089 " --> pdb=" O CYS C3085 " (cutoff:3.500A) Processing helix chain 'C' and resid 3097 through 3108 Processing helix chain 'C' and resid 3114 through 3132 removed outlier: 3.526A pdb=" N GLY C3126 " --> pdb=" O TYR C3122 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C3132 " --> pdb=" O PHE C3128 " (cutoff:3.500A) Processing helix chain 'C' and resid 3135 through 3150 removed outlier: 3.793A pdb=" N LYS C3140 " --> pdb=" O GLU C3136 " (cutoff:3.500A) Processing helix chain 'C' and resid 3152 through 3169 removed outlier: 4.351A pdb=" N LYS C3169 " --> pdb=" O ASN C3165 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3190 removed outlier: 3.870A pdb=" N HIS C3189 " --> pdb=" O HIS C3185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C3190 " --> pdb=" O ALA C3186 " (cutoff:3.500A) Processing helix chain 'C' and resid 3195 through 3206 removed outlier: 3.611A pdb=" N LYS C3201 " --> pdb=" O LYS C3197 " (cutoff:3.500A) Processing helix chain 'C' and resid 3207 through 3209 No H-bonds generated for 'chain 'C' and resid 3207 through 3209' Processing helix chain 'C' and resid 3213 through 3223 Processing helix chain 'C' and resid 3227 through 3233 removed outlier: 3.973A pdb=" N ALA C3233 " --> pdb=" O GLN C3230 " (cutoff:3.500A) Processing helix chain 'C' and resid 3234 through 3244 Processing helix chain 'C' and resid 3246 through 3261 removed outlier: 3.760A pdb=" N LEU C3250 " --> pdb=" O GLU C3246 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C3252 " --> pdb=" O LYS C3248 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C3253 " --> pdb=" O LEU C3249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN C3256 " --> pdb=" O ASN C3252 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C3260 " --> pdb=" O GLN C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3261 through 3282 removed outlier: 3.988A pdb=" N PHE C3267 " --> pdb=" O GLN C3263 " (cutoff:3.500A) Proline residue: C3268 - end of helix Processing helix chain 'C' and resid 3294 through 3310 Processing helix chain 'C' and resid 3311 through 3326 removed outlier: 3.899A pdb=" N VAL C3326 " --> pdb=" O VAL C3322 " (cutoff:3.500A) Processing helix chain 'C' and resid 3327 through 3329 No H-bonds generated for 'chain 'C' and resid 3327 through 3329' Processing helix chain 'C' and resid 3331 through 3354 Processing helix chain 'C' and resid 3364 through 3379 Processing helix chain 'C' and resid 3416 through 3426 removed outlier: 3.978A pdb=" N THR C3421 " --> pdb=" O LYS C3417 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C3424 " --> pdb=" O PHE C3420 " (cutoff:3.500A) Processing helix chain 'C' and resid 3433 through 3454 removed outlier: 3.979A pdb=" N SER C3439 " --> pdb=" O HIS C3435 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C3454 " --> pdb=" O ALA C3450 " (cutoff:3.500A) Processing helix chain 'C' and resid 3466 through 3471 Processing helix chain 'C' and resid 3535 through 3559 removed outlier: 3.505A pdb=" N VAL C3545 " --> pdb=" O ARG C3541 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C3546 " --> pdb=" O GLU C3542 " (cutoff:3.500A) Proline residue: C3554 - end of helix removed outlier: 3.618A pdb=" N GLU C3557 " --> pdb=" O ASN C3553 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C3558 " --> pdb=" O PRO C3554 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG C3559 " --> pdb=" O CYS C3555 " (cutoff:3.500A) Processing helix chain 'C' and resid 3559 through 3564 Processing helix chain 'C' and resid 3593 through 3604 Processing helix chain 'C' and resid 3609 through 3626 removed outlier: 3.668A pdb=" N GLY C3626 " --> pdb=" O VAL C3622 " (cutoff:3.500A) Processing helix chain 'C' and resid 3630 through 3645 Processing helix chain 'C' and resid 3649 through 3659 Processing helix chain 'C' and resid 3661 through 3686 Processing helix chain 'C' and resid 3732 through 3738 Processing helix chain 'C' and resid 3746 through 3761 removed outlier: 3.589A pdb=" N GLN C3761 " --> pdb=" O ARG C3757 " (cutoff:3.500A) Processing helix chain 'C' and resid 3765 through 3786 Processing helix chain 'C' and resid 3805 through 3827 Processing helix chain 'C' and resid 3834 through 3844 removed outlier: 3.635A pdb=" N LEU C3838 " --> pdb=" O LYS C3834 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3849 Processing helix chain 'C' and resid 3850 through 3851 No H-bonds generated for 'chain 'C' and resid 3850 through 3851' Processing helix chain 'C' and resid 3852 through 3856 Processing helix chain 'G' and resid 2370 through 2382 Processing helix chain 'G' and resid 2400 through 2410 removed outlier: 3.752A pdb=" N SER G2410 " --> pdb=" O ASP G2406 " (cutoff:3.500A) Processing helix chain 'G' and resid 2417 through 2428 Processing helix chain 'G' and resid 2428 through 2435 Processing helix chain 'G' and resid 2444 through 2453 Processing helix chain 'G' and resid 2454 through 2474 removed outlier: 3.859A pdb=" N LYS G2474 " --> pdb=" O MET G2470 " (cutoff:3.500A) Processing helix chain 'G' and resid 2496 through 2501 Processing helix chain 'G' and resid 2510 through 2523 Processing sheet with id=AA1, first strand: chain 'C' and resid 923 through 927 Processing sheet with id=AA2, first strand: chain 'C' and resid 3458 through 3460 removed outlier: 3.584A pdb=" N PHE C3459 " --> pdb=" O VAL C3503 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C3503 " --> pdb=" O PHE C3459 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET C3500 " --> pdb=" O ARG C3519 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ARG C3519 " --> pdb=" O MET C3500 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG C3502 " --> pdb=" O TYR C3517 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C3517 " --> pdb=" O ARG C3502 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA C3512 " --> pdb=" O ASN C3532 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN C3532 " --> pdb=" O ALA C3512 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C3514 " --> pdb=" O VAL C3530 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3590 through 3592 1586 hydrogen bonds defined for protein. 4671 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: 20.20 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26309 1.03 - 1.23: 102 1.23 - 1.43: 10660 1.43 - 1.62: 15324 1.62 - 1.82: 302 Bond restraints: 52697 Sorted by residual: bond pdb=" N PRO G2387 " pdb=" CD PRO G2387 " ideal model delta sigma weight residual 1.473 1.708 -0.235 1.40e-02 5.10e+03 2.81e+02 bond pdb=" C LEU G2386 " pdb=" N PRO G2387 " ideal model delta sigma weight residual 1.334 1.506 -0.172 2.34e-02 1.83e+03 5.42e+01 bond pdb=" C VAL C1290 " pdb=" O VAL C1290 " ideal model delta sigma weight residual 1.240 1.189 0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" C PRO C1291 " pdb=" O PRO C1291 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" C ARG G2444 " pdb=" O ARG G2444 " ideal model delta sigma weight residual 1.234 1.196 0.038 1.27e-02 6.20e+03 8.87e+00 ... (remaining 52692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 95154 2.54 - 5.07: 336 5.07 - 7.61: 24 7.61 - 10.14: 7 10.14 - 12.68: 2 Bond angle restraints: 95523 Sorted by residual: angle pdb=" N PRO C1291 " pdb=" CA PRO C1291 " pdb=" C PRO C1291 " ideal model delta sigma weight residual 110.70 98.02 12.68 1.22e+00 6.72e-01 1.08e+02 angle pdb=" C PRO C1291 " pdb=" CA PRO C1291 " pdb=" CB PRO C1291 " ideal model delta sigma weight residual 110.92 121.51 -10.59 1.22e+00 6.72e-01 7.54e+01 angle pdb=" CA HIS C1295 " pdb=" C HIS C1295 " pdb=" O HIS C1295 " ideal model delta sigma weight residual 122.36 113.55 8.81 1.21e+00 6.83e-01 5.30e+01 angle pdb=" C LEU G2386 " pdb=" N PRO G2387 " pdb=" CA PRO G2387 " ideal model delta sigma weight residual 119.84 127.76 -7.92 1.25e+00 6.40e-01 4.02e+01 angle pdb=" C ARG G2444 " pdb=" N THR G2445 " pdb=" CA THR G2445 " ideal model delta sigma weight residual 120.28 127.78 -7.50 1.34e+00 5.57e-01 3.13e+01 ... (remaining 95518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 21717 17.98 - 35.96: 2100 35.96 - 53.94: 627 53.94 - 71.91: 161 71.91 - 89.89: 58 Dihedral angle restraints: 24663 sinusoidal: 13532 harmonic: 11131 Sorted by residual: dihedral pdb=" CD ARG G2444 " pdb=" NE ARG G2444 " pdb=" CZ ARG G2444 " pdb=" NH1 ARG G2444 " ideal model delta sinusoidal sigma weight residual 0.00 58.63 -58.63 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA SER C3578 " pdb=" C SER C3578 " pdb=" N PRO C3579 " pdb=" CA PRO C3579 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA LEU C3739 " pdb=" C LEU C3739 " pdb=" N THR C3740 " pdb=" CA THR C3740 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 24660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3328 0.042 - 0.083: 597 0.083 - 0.125: 154 0.125 - 0.167: 17 0.167 - 0.209: 2 Chirality restraints: 4098 Sorted by residual: chirality pdb=" CA LEU G2390 " pdb=" N LEU G2390 " pdb=" C LEU G2390 " pdb=" CB LEU G2390 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL C1290 " pdb=" N VAL C1290 " pdb=" C VAL C1290 " pdb=" CB VAL C1290 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA LEU C1296 " pdb=" N LEU C1296 " pdb=" C LEU C1296 " pdb=" CB LEU C1296 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 4095 not shown) Planarity restraints: 7505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G2444 " 0.544 9.50e-02 1.11e+02 4.01e-01 2.91e+03 pdb=" NE ARG G2444 " -0.320 2.00e-02 2.50e+03 pdb=" CZ ARG G2444 " -0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG G2444 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG G2444 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG G2444 " 0.761 2.00e-02 2.50e+03 pdb="HH12 ARG G2444 " -0.615 2.00e-02 2.50e+03 pdb="HH21 ARG G2444 " 0.268 2.00e-02 2.50e+03 pdb="HH22 ARG G2444 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G2389 " -0.249 2.00e-02 2.50e+03 3.23e-01 1.56e+03 pdb=" CG ASN G2389 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN G2389 " 0.248 2.00e-02 2.50e+03 pdb=" ND2 ASN G2389 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN G2389 " 0.498 2.00e-02 2.50e+03 pdb="HD22 ASN G2389 " -0.503 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C1287 " 0.176 2.00e-02 2.50e+03 1.93e-01 5.58e+02 pdb=" CD GLN C1287 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C1287 " -0.167 2.00e-02 2.50e+03 pdb=" NE2 GLN C1287 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C1287 " -0.284 2.00e-02 2.50e+03 pdb="HE22 GLN C1287 " 0.290 2.00e-02 2.50e+03 ... (remaining 7502 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1057 2.08 - 2.71: 89085 2.71 - 3.34: 162847 3.34 - 3.97: 195417 3.97 - 4.60: 309390 Nonbonded interactions: 757796 Sorted by model distance: nonbonded pdb=" OE1 GLU C 450 " pdb=" H GLU C 450 " model vdw 1.448 2.450 nonbonded pdb=" O ASN C 992 " pdb=" H LYS C 996 " model vdw 1.508 2.450 nonbonded pdb=" O MET C 446 " pdb=" H LEU C 449 " model vdw 1.552 2.450 nonbonded pdb=" H MET C1325 " pdb=" OH TYR C1378 " model vdw 1.584 2.450 nonbonded pdb=" O SER C2189 " pdb=" H LYS C2191 " model vdw 1.584 2.450 ... (remaining 757791 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.670 Extract box with map and model: 1.610 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 87.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.130 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.235 26317 Z= 0.198 Angle : 0.551 12.676 35598 Z= 0.298 Chirality : 0.035 0.209 4098 Planarity : 0.007 0.421 4463 Dihedral : 17.242 89.892 9837 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.98 % Favored : 93.51 % Rotamer: Outliers : 0.63 % Allowed : 23.45 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 3142 helix: 1.13 (0.12), residues: 2084 sheet: -0.89 (0.71), residues: 63 loop : -0.66 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G2374 HIS 0.013 0.001 HIS C1522 PHE 0.033 0.001 PHE C 675 TYR 0.010 0.001 TYR C 603 ARG 0.010 0.000 ARG C3338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 3.153 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: 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: C 1192 MET cc_start: 0.8805 (tmm) cc_final: 0.8542 (tmm) REVERT: C 1287 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: C 1293 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7992 (tptp) REVERT: C 3432 MET cc_start: 0.3881 (tmt) cc_final: 0.3534 (tmt) outliers start: 18 outliers final: 12 residues processed: 306 average time/residue: 0.7406 time to fit residues: 356.8515 Evaluate side-chains 294 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 280 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 1287 GLN Chi-restraints excluded: chain C residue 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1293 LYS Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2466 MET Chi-restraints excluded: chain C residue 2670 SER Chi-restraints excluded: chain C residue 2924 HIS Chi-restraints excluded: chain G residue 2384 LEU Chi-restraints excluded: chain G residue 2390 LEU Chi-restraints excluded: chain G residue 2394 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN C 405 ASN C 425 ASN C 801 HIS C 855 ASN C 920 GLN C1005 HIS C1179 ASN C1234 GLN C1312 ASN C1371 ASN C1443 ASN C1652 ASN C1707 ASN C1728 ASN C1803 ASN C1834 GLN C2166 ASN C2306 ASN C2377 ASN C2464 ASN C2832 ASN C2928 HIS C3088 GLN ** C3189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2427 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079801 restraints weight = 194468.005| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.97 r_work: 0.3120 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 26317 Z= 0.469 Angle : 0.703 6.624 35598 Z= 0.393 Chirality : 0.042 0.164 4098 Planarity : 0.005 0.056 4463 Dihedral : 5.712 88.233 3462 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.59 % Favored : 93.06 % Rotamer: Outliers : 2.66 % Allowed : 22.37 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3142 helix: 0.72 (0.11), residues: 2226 sheet: -1.24 (0.69), residues: 63 loop : -1.09 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G2374 HIS 0.007 0.001 HIS C2987 PHE 0.018 0.002 PHE C1189 TYR 0.021 0.002 TYR C2243 ARG 0.010 0.001 ARG G2444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 286 time to evaluate : 3.173 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: 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: C 1094 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8836 (m-30) REVERT: C 1123 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8676 (m) REVERT: C 1287 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 1574 MET cc_start: 0.7515 (mmm) cc_final: 0.7312 (mmm) REVERT: C 1737 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: C 3043 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8482 (tp-100) REVERT: C 3099 MET cc_start: 0.8500 (tpp) cc_final: 0.8111 (tpp) REVERT: C 3416 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7189 (pp) REVERT: C 3828 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8891 (t80) REVERT: G 2385 GLU cc_start: 0.8212 (pt0) cc_final: 0.7994 (pt0) REVERT: G 2433 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7997 (tm-30) REVERT: G 2457 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.9112 (t-90) outliers start: 76 outliers final: 51 residues processed: 345 average time/residue: 0.7125 time to fit residues: 390.5983 Evaluate side-chains 327 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 944 GLU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1287 GLN Chi-restraints excluded: chain C residue 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1701 LEU Chi-restraints excluded: chain C residue 1728 ASN Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1753 PHE Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2298 GLN Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2593 ASN Chi-restraints excluded: chain C residue 2670 SER Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2792 SER Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3127 MET Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3511 THR Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2370 ILE Chi-restraints excluded: chain G residue 2384 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2424 ARG Chi-restraints excluded: chain G residue 2446 SER Chi-restraints excluded: chain G residue 2457 HIS Chi-restraints excluded: chain G residue 2517 LEU Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 255 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 231 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1707 ASN C1728 ASN C1763 ASN C1842 HIS ** C3435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3474 GLN G2378 GLN G2382 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.112770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082416 restraints weight = 192987.207| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.99 r_work: 0.3177 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26317 Z= 0.207 Angle : 0.597 7.037 35598 Z= 0.318 Chirality : 0.037 0.164 4098 Planarity : 0.004 0.055 4463 Dihedral : 5.357 87.779 3449 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.25 % Favored : 94.40 % Rotamer: Outliers : 2.34 % Allowed : 22.37 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3142 helix: 0.83 (0.11), residues: 2215 sheet: -1.30 (0.69), residues: 63 loop : -0.92 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1671 HIS 0.009 0.001 HIS C2987 PHE 0.023 0.001 PHE C1335 TYR 0.024 0.001 TYR C2243 ARG 0.004 0.000 ARG C1586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 3.137 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: 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: C 1094 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8802 (m-30) REVERT: C 1287 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 2417 PHE cc_start: 0.8774 (t80) cc_final: 0.8521 (t80) REVERT: C 2708 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 2865 MET cc_start: 0.9257 (tpt) cc_final: 0.9043 (tpt) REVERT: C 3099 MET cc_start: 0.8440 (tpp) cc_final: 0.8018 (tpp) REVERT: C 3152 LEU cc_start: 0.8660 (tp) cc_final: 0.8406 (tp) REVERT: C 3416 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7226 (pp) REVERT: C 3828 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8835 (t80) REVERT: G 2385 GLU cc_start: 0.8281 (pt0) cc_final: 0.7956 (pt0) outliers start: 67 outliers final: 42 residues processed: 361 average time/residue: 0.7197 time to fit residues: 412.9998 Evaluate side-chains 333 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1287 GLN Chi-restraints excluded: chain C residue 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2298 GLN Chi-restraints excluded: chain C residue 2342 MET Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2593 ASN Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3474 GLN Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3613 SER Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2370 ILE Chi-restraints excluded: chain G residue 2384 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2513 GLN Chi-restraints excluded: chain G residue 2517 LEU Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 258 optimal weight: 0.6980 chunk 289 optimal weight: 0.0370 chunk 64 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3043 GLN G2382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.112863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082497 restraints weight = 192881.436| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.19 r_work: 0.3173 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26317 Z= 0.200 Angle : 0.579 6.884 35598 Z= 0.306 Chirality : 0.036 0.237 4098 Planarity : 0.004 0.056 4463 Dihedral : 5.223 88.028 3448 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.76 % Favored : 93.89 % Rotamer: Outliers : 2.52 % Allowed : 22.47 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3142 helix: 0.97 (0.11), residues: 2215 sheet: -1.36 (0.71), residues: 55 loop : -0.97 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1671 HIS 0.008 0.001 HIS C2987 PHE 0.020 0.001 PHE C 675 TYR 0.026 0.001 TYR C2243 ARG 0.013 0.000 ARG C1668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 3.153 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: 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: C 450 GLU cc_start: 0.8661 (mp0) cc_final: 0.8326 (mp0) REVERT: C 758 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8953 (mt) REVERT: C 1094 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.8826 (m-30) REVERT: C 1123 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8621 (m) REVERT: C 1574 MET cc_start: 0.7738 (mmm) cc_final: 0.7379 (mmm) REVERT: C 1668 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7419 (ttp80) REVERT: C 1729 MET cc_start: 0.6226 (pmm) cc_final: 0.5505 (mpp) REVERT: C 1737 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: C 2417 PHE cc_start: 0.8716 (t80) cc_final: 0.8489 (t80) REVERT: C 2708 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 3099 MET cc_start: 0.8434 (tpp) cc_final: 0.7999 (tpp) REVERT: C 3416 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7310 (pp) REVERT: C 3828 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8848 (t80) outliers start: 72 outliers final: 49 residues processed: 360 average time/residue: 0.7084 time to fit residues: 407.4947 Evaluate side-chains 343 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1668 ARG Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2218 ARG Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2298 GLN Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2342 MET Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 2924 HIS Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3124 LEU Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2370 ILE Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2384 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 239 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS C1707 ASN G2378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.112520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082407 restraints weight = 192483.548| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.93 r_work: 0.3185 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26317 Z= 0.229 Angle : 0.576 6.935 35598 Z= 0.304 Chirality : 0.036 0.150 4098 Planarity : 0.004 0.055 4463 Dihedral : 5.073 88.675 3445 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.73 % Favored : 93.92 % Rotamer: Outliers : 2.80 % Allowed : 22.51 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3142 helix: 1.05 (0.11), residues: 2226 sheet: -1.59 (0.67), residues: 55 loop : -0.98 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1671 HIS 0.009 0.001 HIS C1424 PHE 0.019 0.001 PHE C 675 TYR 0.026 0.001 TYR C2243 ARG 0.003 0.000 ARG C2218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 3.172 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: 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: C 758 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8952 (mt) REVERT: C 1094 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: C 1123 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (m) REVERT: C 1192 MET cc_start: 0.9006 (tmm) cc_final: 0.8703 (tmm) REVERT: C 1574 MET cc_start: 0.7755 (mmm) cc_final: 0.7410 (mmm) REVERT: C 2417 PHE cc_start: 0.8700 (t80) cc_final: 0.8489 (t80) REVERT: C 2506 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8462 (t) REVERT: C 2708 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (mt) REVERT: C 2880 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8462 (ttp) REVERT: C 3099 MET cc_start: 0.8418 (tpp) cc_final: 0.7975 (tpp) REVERT: C 3152 LEU cc_start: 0.8666 (tp) cc_final: 0.8401 (tp) REVERT: C 3416 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7006 (tt) REVERT: C 3828 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8790 (t80) REVERT: G 2444 ARG cc_start: 0.6858 (tpp80) cc_final: 0.6466 (tpp80) REVERT: G 2447 GLN cc_start: 0.8399 (mt0) cc_final: 0.8190 (mt0) outliers start: 80 outliers final: 59 residues processed: 354 average time/residue: 0.7047 time to fit residues: 403.3759 Evaluate side-chains 350 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 283 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1195 THR Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2298 GLN Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2342 MET Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2506 SER Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2652 ILE Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 2924 HIS Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3124 LEU Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3460 LEU Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3511 THR Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2384 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1078 HIS C1469 GLN C1707 ASN C3786 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080836 restraints weight = 193763.765| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.03 r_work: 0.3148 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26317 Z= 0.321 Angle : 0.600 7.084 35598 Z= 0.321 Chirality : 0.038 0.149 4098 Planarity : 0.004 0.057 4463 Dihedral : 5.146 89.894 3445 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.24 % Favored : 93.38 % Rotamer: Outliers : 3.01 % Allowed : 22.54 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3142 helix: 1.03 (0.11), residues: 2228 sheet: -1.75 (0.65), residues: 63 loop : -1.02 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1671 HIS 0.010 0.001 HIS C1889 PHE 0.020 0.002 PHE C 675 TYR 0.028 0.001 TYR C2243 ARG 0.003 0.000 ARG C2768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 3.121 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: 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: C 758 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8977 (mt) REVERT: C 1094 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8819 (m-30) REVERT: C 1123 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8624 (m) REVERT: C 1574 MET cc_start: 0.7738 (mmm) cc_final: 0.7411 (mmm) REVERT: C 1889 HIS cc_start: 0.7456 (t70) cc_final: 0.7244 (t-90) REVERT: C 2417 PHE cc_start: 0.8730 (t80) cc_final: 0.8495 (t80) REVERT: C 2506 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8461 (t) REVERT: C 2708 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8332 (mt) REVERT: C 3099 MET cc_start: 0.8429 (tpp) cc_final: 0.8120 (tpp) REVERT: C 3152 LEU cc_start: 0.8743 (tp) cc_final: 0.8494 (tp) REVERT: C 3828 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8791 (t80) REVERT: G 2444 ARG cc_start: 0.6859 (tpp80) cc_final: 0.6458 (tpp80) REVERT: G 2447 GLN cc_start: 0.8422 (mt0) cc_final: 0.8189 (mt0) outliers start: 86 outliers final: 69 residues processed: 353 average time/residue: 0.7028 time to fit residues: 398.2802 Evaluate side-chains 350 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 275 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 HIS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1195 THR Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1344 GLU Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1835 TYR Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2209 LEU Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2342 MET Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2460 GLU Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2506 SER Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2851 LEU Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3124 LEU Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3455 LEU Chi-restraints excluded: chain C residue 3460 LEU Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3511 THR Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3590 SER Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2370 ILE Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS C 578 ASN C1707 ASN ** C2987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080919 restraints weight = 192665.669| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.02 r_work: 0.3153 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26317 Z= 0.301 Angle : 0.593 6.846 35598 Z= 0.315 Chirality : 0.037 0.142 4098 Planarity : 0.004 0.056 4463 Dihedral : 5.064 88.838 3440 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.27 % Favored : 93.35 % Rotamer: Outliers : 3.08 % Allowed : 22.61 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3142 helix: 1.02 (0.11), residues: 2229 sheet: -1.79 (0.67), residues: 55 loop : -1.06 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1671 HIS 0.007 0.001 HIS C2998 PHE 0.021 0.002 PHE C 675 TYR 0.028 0.001 TYR C2243 ARG 0.005 0.000 ARG G2521 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 285 time to evaluate : 3.179 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: 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: symmetry clash REVERT: C 1094 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: C 1123 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8611 (m) REVERT: C 1574 MET cc_start: 0.7776 (mmm) cc_final: 0.7412 (mmm) REVERT: C 2506 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8458 (t) REVERT: C 2708 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8331 (mt) REVERT: C 2880 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8613 (ttp) REVERT: C 3043 GLN cc_start: 0.8906 (tp40) cc_final: 0.8659 (tp40) REVERT: C 3099 MET cc_start: 0.8348 (tpp) cc_final: 0.8068 (tpp) REVERT: C 3152 LEU cc_start: 0.8735 (tp) cc_final: 0.8485 (tp) REVERT: C 3416 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7050 (tt) REVERT: C 3828 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8819 (t80) REVERT: G 2444 ARG cc_start: 0.6908 (tpp80) cc_final: 0.6625 (tpp80) outliers start: 88 outliers final: 74 residues processed: 355 average time/residue: 0.7277 time to fit residues: 414.7582 Evaluate side-chains 362 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 281 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 HIS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1012 THR Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1195 THR Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1313 THR Chi-restraints excluded: chain C residue 1344 GLU Chi-restraints excluded: chain C residue 1442 LEU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1841 GLU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2342 MET Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2460 GLU Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2506 SER Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2880 MET Chi-restraints excluded: chain C residue 2924 HIS Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3124 LEU Chi-restraints excluded: chain C residue 3207 SER Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3282 GLU Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3460 LEU Chi-restraints excluded: chain C residue 3477 GLU Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3511 THR Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3590 SER Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3825 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2370 ILE Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 217 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1707 ASN C2939 GLN ** C2987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.112968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082500 restraints weight = 192664.187| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.12 r_work: 0.3180 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26317 Z= 0.191 Angle : 0.562 6.854 35598 Z= 0.293 Chirality : 0.036 0.143 4098 Planarity : 0.004 0.056 4463 Dihedral : 4.927 86.714 3440 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.70 % Favored : 93.92 % Rotamer: Outliers : 2.41 % Allowed : 23.35 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3142 helix: 1.21 (0.11), residues: 2224 sheet: -1.72 (0.67), residues: 55 loop : -1.01 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1671 HIS 0.007 0.001 HIS C2987 PHE 0.020 0.001 PHE C 675 TYR 0.029 0.001 TYR C2243 ARG 0.005 0.000 ARG G2521 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 3.219 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: 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: C 1094 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: C 1574 MET cc_start: 0.7779 (mmm) cc_final: 0.7401 (mmm) REVERT: C 1598 ARG cc_start: 0.8965 (ttt90) cc_final: 0.8764 (mtp180) REVERT: C 2708 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 3099 MET cc_start: 0.8324 (tpp) cc_final: 0.8043 (tpp) REVERT: C 3152 LEU cc_start: 0.8676 (tp) cc_final: 0.8442 (tp) REVERT: C 3416 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7049 (tt) REVERT: C 3432 MET cc_start: 0.4623 (tmt) cc_final: 0.4142 (tmt) REVERT: C 3828 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8795 (t80) REVERT: G 2444 ARG cc_start: 0.6983 (tpp80) cc_final: 0.6693 (tpp80) outliers start: 69 outliers final: 58 residues processed: 362 average time/residue: 0.7468 time to fit residues: 426.6555 Evaluate side-chains 349 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1344 GLU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1841 GLU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2924 HIS Chi-restraints excluded: chain C residue 2949 ILE Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3282 GLU Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 196 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1707 ASN ** C2987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.112590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082232 restraints weight = 192384.892| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.96 r_work: 0.3183 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26317 Z= 0.236 Angle : 0.576 10.778 35598 Z= 0.301 Chirality : 0.036 0.205 4098 Planarity : 0.004 0.073 4463 Dihedral : 4.913 88.251 3439 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.98 % Favored : 93.67 % Rotamer: Outliers : 2.59 % Allowed : 23.38 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3142 helix: 1.22 (0.11), residues: 2229 sheet: -1.78 (0.67), residues: 55 loop : -1.03 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1671 HIS 0.007 0.001 HIS C2987 PHE 0.024 0.001 PHE C2293 TYR 0.029 0.001 TYR C2243 ARG 0.010 0.000 ARG C3625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 290 time to evaluate : 3.147 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: 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: symmetry clash revert: symmetry clash REVERT: C 1094 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8806 (m-30) REVERT: C 1574 MET cc_start: 0.7766 (mmm) cc_final: 0.7384 (mmm) REVERT: C 1598 ARG cc_start: 0.8941 (ttt90) cc_final: 0.8716 (mtp180) REVERT: C 2506 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8394 (t) REVERT: C 2708 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 3043 GLN cc_start: 0.8902 (tp40) cc_final: 0.8669 (tp40) REVERT: C 3099 MET cc_start: 0.8292 (tpp) cc_final: 0.8011 (tpp) REVERT: C 3416 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7050 (tt) REVERT: C 3432 MET cc_start: 0.4861 (tmt) cc_final: 0.4360 (tmt) REVERT: C 3828 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8792 (t80) REVERT: G 2444 ARG cc_start: 0.6898 (tpp80) cc_final: 0.6589 (tpp80) outliers start: 74 outliers final: 65 residues processed: 353 average time/residue: 0.7222 time to fit residues: 406.0145 Evaluate side-chains 354 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 HIS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1120 ASP Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1195 THR Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1344 GLU Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1841 GLU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2401 THR Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2506 SER Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2772 SER Chi-restraints excluded: chain C residue 2913 SER Chi-restraints excluded: chain C residue 2949 ILE Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3207 SER Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3275 THR Chi-restraints excluded: chain C residue 3282 GLU Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3503 VAL Chi-restraints excluded: chain C residue 3511 THR Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3590 SER Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3825 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2389 ASN Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 26 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 234 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 281 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.114023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083653 restraints weight = 191060.142| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.02 r_work: 0.3208 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26317 Z= 0.176 Angle : 0.565 12.084 35598 Z= 0.290 Chirality : 0.036 0.147 4098 Planarity : 0.004 0.056 4463 Dihedral : 4.811 86.180 3439 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.51 % Favored : 94.14 % Rotamer: Outliers : 2.24 % Allowed : 23.80 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 3142 helix: 1.34 (0.11), residues: 2227 sheet: -1.68 (0.67), residues: 55 loop : -0.95 (0.24), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1671 HIS 0.007 0.001 HIS C2987 PHE 0.024 0.001 PHE C2293 TYR 0.030 0.001 TYR C2243 ARG 0.010 0.000 ARG C3625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 3.221 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: 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: symmetry clash revert: symmetry clash REVERT: C 376 TYR cc_start: 0.8678 (m-80) cc_final: 0.8333 (m-80) REVERT: C 635 PHE cc_start: 0.8998 (t80) cc_final: 0.8707 (t80) REVERT: C 669 GLN cc_start: 0.9385 (tt0) cc_final: 0.9113 (tt0) REVERT: C 758 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8884 (mt) REVERT: C 1094 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: C 1574 MET cc_start: 0.7765 (mmm) cc_final: 0.7225 (mmm) REVERT: C 1833 LEU cc_start: 0.7197 (mt) cc_final: 0.6821 (pp) REVERT: C 2329 GLU cc_start: 0.8926 (pt0) cc_final: 0.8476 (pt0) REVERT: C 2484 GLU cc_start: 0.8495 (tp30) cc_final: 0.8225 (tp30) REVERT: C 2708 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 3099 MET cc_start: 0.8225 (tpp) cc_final: 0.7957 (tpp) REVERT: C 3416 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7054 (tt) REVERT: C 3432 MET cc_start: 0.4589 (tmt) cc_final: 0.4126 (tmt) REVERT: C 3828 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (t80) REVERT: G 2444 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6671 (tpp80) REVERT: G 2518 ARG cc_start: 0.8271 (ttt180) cc_final: 0.7991 (ttt180) outliers start: 64 outliers final: 53 residues processed: 363 average time/residue: 0.7196 time to fit residues: 418.1398 Evaluate side-chains 350 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 882 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain C residue 1195 THR Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1344 GLU Chi-restraints excluded: chain C residue 1546 MET Chi-restraints excluded: chain C residue 1589 MET Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1696 LEU Chi-restraints excluded: chain C residue 1710 ASP Chi-restraints excluded: chain C residue 1718 LEU Chi-restraints excluded: chain C residue 1737 GLU Chi-restraints excluded: chain C residue 1773 LEU Chi-restraints excluded: chain C residue 1841 GLU Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2190 PHE Chi-restraints excluded: chain C residue 2289 LEU Chi-restraints excluded: chain C residue 2330 LEU Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2422 ASN Chi-restraints excluded: chain C residue 2425 TYR Chi-restraints excluded: chain C residue 2502 VAL Chi-restraints excluded: chain C residue 2648 LEU Chi-restraints excluded: chain C residue 2708 LEU Chi-restraints excluded: chain C residue 2913 SER Chi-restraints excluded: chain C residue 2949 ILE Chi-restraints excluded: chain C residue 2961 ASN Chi-restraints excluded: chain C residue 3005 TRP Chi-restraints excluded: chain C residue 3041 ILE Chi-restraints excluded: chain C residue 3047 ILE Chi-restraints excluded: chain C residue 3207 SER Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3282 GLU Chi-restraints excluded: chain C residue 3370 PHE Chi-restraints excluded: chain C residue 3416 LEU Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3555 CYS Chi-restraints excluded: chain C residue 3590 SER Chi-restraints excluded: chain C residue 3739 LEU Chi-restraints excluded: chain C residue 3820 THR Chi-restraints excluded: chain C residue 3825 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain G residue 2377 LEU Chi-restraints excluded: chain G residue 2392 ILE Chi-restraints excluded: chain G residue 2394 SER Chi-restraints excluded: chain G residue 2522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 294 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.113539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082563 restraints weight = 192909.630| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.90 r_work: 0.3209 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26317 Z= 0.199 Angle : 0.564 8.639 35598 Z= 0.291 Chirality : 0.036 0.152 4098 Planarity : 0.004 0.057 4463 Dihedral : 4.787 87.965 3439 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 2.10 % Allowed : 23.94 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 3142 helix: 1.37 (0.11), residues: 2227 sheet: -1.72 (0.67), residues: 55 loop : -0.96 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1671 HIS 0.006 0.001 HIS C2987 PHE 0.023 0.001 PHE C2293 TYR 0.030 0.001 TYR C2243 ARG 0.011 0.000 ARG C3625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18907.32 seconds wall clock time: 323 minutes 29.66 seconds (19409.66 seconds total)