Starting phenix.real_space_refine on Tue Nov 19 18:30:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_45176.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_45176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_45176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_45176.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c47_45176/11_2024/9c47_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): 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 22.71, per 1000 atoms: 0.44 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: 14.14 Conformation dependent library (CDL) restraints added in 3.8 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: 5.17 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: 23.47 Time building geometry restraints manager: 16.66 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: 2.680 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: 0.850 Extract box with map and model: 1.950 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 104.520 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.140 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.780 ------------------------------------------------------------------------------- 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 : 3.800 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: 0.9177 time to fit residues: 445.5041 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 : 4.583 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 4.106 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: 0.9036 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: C 1123 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8584 (m) REVERT: C 1287 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: C 1737 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: C 3043 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8286 (tp-100) REVERT: C 3099 MET cc_start: 0.8035 (tpp) cc_final: 0.7620 (tpp) REVERT: C 3416 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6690 (pp) REVERT: C 3828 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8817 (t80) outliers start: 76 outliers final: 51 residues processed: 345 average time/residue: 0.8965 time to fit residues: 496.8531 Evaluate side-chains 326 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 4.095 ------------------------------------------------------------------------------- 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 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 161 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 291 optimal weight: 0.3980 chunk 314 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26317 Z= 0.213 Angle : 0.600 6.928 35598 Z= 0.321 Chirality : 0.037 0.150 4098 Planarity : 0.004 0.055 4463 Dihedral : 5.381 88.121 3449 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % Rotamer: Outliers : 2.48 % Allowed : 22.33 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.15), residues: 3142 helix: 0.80 (0.11), residues: 2215 sheet: -1.32 (0.69), residues: 63 loop : -0.94 (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 0.022 0.001 PHE C1335 TYR 0.024 0.001 TYR C2243 ARG 0.003 0.000 ARG C1668 *********************** 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 376 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 305 time to evaluate : 4.693 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: 0.8975 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: C 1287 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 2218 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8636 (mtt180) REVERT: C 2417 PHE cc_start: 0.8410 (t80) cc_final: 0.8163 (t80) REVERT: C 2865 MET cc_start: 0.9033 (tpt) cc_final: 0.8815 (tpt) REVERT: C 3099 MET cc_start: 0.7944 (tpp) cc_final: 0.7500 (tpp) REVERT: C 3152 LEU cc_start: 0.8646 (tp) cc_final: 0.8428 (tp) REVERT: C 3416 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6709 (pp) REVERT: C 3828 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8787 (t80) outliers start: 71 outliers final: 43 residues processed: 359 average time/residue: 0.8785 time to fit residues: 502.2796 Evaluate side-chains 331 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 4.359 ------------------------------------------------------------------------------- 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 758 LEU 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 2218 ARG 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 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 287 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3043 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26317 Z= 0.328 Angle : 0.617 7.010 35598 Z= 0.333 Chirality : 0.038 0.201 4098 Planarity : 0.004 0.058 4463 Dihedral : 5.361 89.374 3448 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.30 % Favored : 93.32 % Rotamer: Outliers : 3.01 % Allowed : 22.26 % Favored : 74.73 % 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: 0.34 (0.15), residues: 3142 helix: 0.81 (0.11), residues: 2227 sheet: -1.56 (0.68), residues: 63 loop : -1.01 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1671 HIS 0.008 0.001 HIS C2987 PHE 0.017 0.002 PHE C 675 TYR 0.026 0.001 TYR C2243 ARG 0.004 0.000 ARG C1719 *********************** 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 375 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 4.098 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: C 450 GLU cc_start: 0.8400 (mp0) cc_final: 0.8110 (mp0) REVERT: C 1094 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: C 1123 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8549 (m) REVERT: C 1729 MET cc_start: 0.6067 (pmm) cc_final: 0.5453 (mpp) REVERT: C 2218 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mtt180) REVERT: C 2417 PHE cc_start: 0.8392 (t80) cc_final: 0.8175 (t80) REVERT: C 2506 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8319 (t) REVERT: C 2865 MET cc_start: 0.9103 (tpt) cc_final: 0.8823 (tpt) REVERT: C 3099 MET cc_start: 0.7975 (tpp) cc_final: 0.7522 (tpp) REVERT: C 3416 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6783 (pp) REVERT: C 3828 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8782 (t80) outliers start: 86 outliers final: 66 residues processed: 356 average time/residue: 0.8673 time to fit residues: 496.2188 Evaluate side-chains 348 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 4.081 ------------------------------------------------------------------------------- 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 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 945 THR 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 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 1289 MET Chi-restraints excluded: chain C residue 1290 VAL Chi-restraints excluded: chain C residue 1313 THR 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 2209 LEU 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 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 2593 ASN 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 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9681 > 50: distance: 48 - 114: 4.007 distance: 68 - 125: 7.287 distance: 85 - 147: 10.635 distance: 106 - 162: 10.601 distance: 114 - 115: 8.302 distance: 114 - 120: 4.648 distance: 115 - 116: 12.161 distance: 115 - 118: 7.126 distance: 115 - 121: 6.019 distance: 116 - 117: 16.613 distance: 116 - 125: 20.136 distance: 118 - 119: 11.148 distance: 118 - 122: 6.515 distance: 118 - 123: 10.407 distance: 119 - 124: 6.168 distance: 125 - 126: 3.740 distance: 125 - 134: 22.408 distance: 126 - 127: 6.339 distance: 126 - 129: 4.010 distance: 126 - 135: 7.833 distance: 127 - 128: 6.049 distance: 127 - 147: 3.211 distance: 129 - 130: 4.022 distance: 129 - 136: 5.110 distance: 129 - 137: 6.001 distance: 130 - 131: 7.670 distance: 130 - 139: 5.995 distance: 131 - 132: 15.175 distance: 131 - 140: 14.350 distance: 131 - 141: 17.134 distance: 132 - 133: 7.749 distance: 132 - 142: 7.889 distance: 132 - 143: 7.660 distance: 133 - 145: 7.927 distance: 133 - 146: 8.063 distance: 147 - 148: 4.678 distance: 147 - 156: 4.821 distance: 148 - 149: 4.459 distance: 148 - 151: 3.566 distance: 151 - 152: 4.520 distance: 151 - 159: 6.765 distance: 152 - 153: 3.971 distance: 152 - 160: 5.045 distance: 162 - 163: 5.171 distance: 162 - 170: 5.895 distance: 163 - 164: 7.685 distance: 163 - 166: 4.041 distance: 163 - 171: 6.363 distance: 166 - 172: 4.942 distance: 166 - 173: 3.455 distance: 167 - 168: 4.235 distance: 167 - 169: 4.652 distance: 167 - 174: 3.065 distance: 168 - 176: 3.011 distance: 169 - 178: 3.718 distance: 169 - 179: 4.462 distance: 181 - 189: 3.987 distance: 183 - 195: 3.877 distance: 185 - 191: 5.072 distance: 185 - 192: 5.739 distance: 186 - 188: 6.343 distance: 196 - 199: 3.115 distance: 196 - 205: 3.732 distance: 197 - 212: 3.284 distance: 198 - 261: 5.009 distance: 200 - 208: 3.689 distance: 201 - 203: 4.203 distance: 203 - 210: 3.239 distance: 214 - 236: 4.082 distance: 215 - 280: 9.547 distance: 216 - 217: 3.423 distance: 216 - 229: 3.319 distance: 219 - 222: 4.967 distance: 220 - 221: 4.659 distance: 221 - 223: 3.172 distance: 223 - 225: 3.140 distance: 236 - 237: 3.067 distance: 236 - 245: 3.914 distance: 237 - 238: 3.830 distance: 237 - 240: 5.449 distance: 237 - 246: 4.465 distance: 238 - 239: 4.611 distance: 238 - 251: 4.101 distance: 239 - 293: 6.359 distance: 240 - 241: 5.648 distance: 240 - 247: 3.636 distance: 240 - 248: 7.658 distance: 241 - 242: 6.975 distance: 241 - 249: 6.783 distance: 241 - 250: 5.730 distance: 242 - 243: 6.667 distance: 242 - 244: 3.387 distance: 252 - 253: 4.364 distance: 252 - 257: 3.621 distance: 253 - 254: 3.509 distance: 253 - 261: 4.662 distance: 254 - 308: 7.502 distance: 255 - 258: 6.889 distance: 261 - 269: 7.621 distance: 262 - 265: 3.763 distance: 263 - 264: 3.677 distance: 263 - 280: 4.100 distance: 264 - 322: 8.128 distance: 265 - 271: 3.675 distance: 266 - 268: 3.858 distance: 267 - 274: 4.631 distance: 267 - 275: 4.752 distance: 268 - 278: 3.196 distance: 268 - 279: 3.897