Starting phenix.real_space_refine on Sun Dec 29 09:59:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.map" model { file = "/net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qri_18619/12_2024/8qri_18619.cif" } resolution = 3.5 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= 1.005 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 192 5.16 5 C 17484 2.51 5 N 4693 2.21 5 O 4835 1.98 5 H 27845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 55049 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 52887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3246, 52887 Classifications: {'peptide': 3246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 141, 'TRANS': 3104} Chain breaks: 32 Chain: "A" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2162 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain breaks: 2 Time building chain proxies: 19.26, per 1000 atoms: 0.35 Number of scatterers: 55049 At special positions: 0 Unit cell: (131.886, 149.988, 197.398, 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 192 16.00 O 4835 8.00 N 4693 7.00 C 17484 6.00 H 27845 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=2.07 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: 11.24 Conformation dependent library (CDL) restraints added in 3.4 seconds 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6550 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 3 sheets defined 76.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.825A pdb=" N GLN C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 61 through 73 Proline residue: C 67 - end of helix Processing helix chain 'C' and resid 85 through 91 removed outlier: 4.168A pdb=" N LEU C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 91 " --> pdb=" O GLN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 removed outlier: 4.265A pdb=" N ILE C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 120 through 121 No H-bonds generated for 'chain 'C' and resid 120 through 121' Processing helix chain 'C' and resid 128 through 128 No H-bonds generated for 'chain 'C' and resid 128 through 128' Processing helix chain 'C' and resid 129 through 142 removed outlier: 4.393A pdb=" N ILE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 237 through 243 removed outlier: 4.388A pdb=" N LYS C 240 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU C 241 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C 242 " --> pdb=" O TYR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.506A pdb=" N ALA C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 4.669A pdb=" N MET C 313 " --> pdb=" O MET C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 342 through 347 Processing helix chain 'C' and resid 348 through 353 removed outlier: 3.913A pdb=" N MET C 351 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.919A pdb=" N SER C 358 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 387 Proline residue: C 373 - end of helix removed outlier: 3.705A pdb=" N HIS C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 Processing helix chain 'C' and resid 412 through 435 removed outlier: 4.243A pdb=" N GLN C 416 " --> pdb=" O PRO C 412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU C 435 " --> pdb=" O ARG C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 463 removed outlier: 3.562A pdb=" N ARG C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 452 " --> pdb=" O MET C 448 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 461 " --> pdb=" O HIS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 467 removed outlier: 3.591A pdb=" N ILE C 467 " --> pdb=" O LEU C 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 464 through 467' Processing helix chain 'C' and resid 542 through 566 Processing helix chain 'C' and resid 581 through 604 removed outlier: 3.773A pdb=" N MET C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 602 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 638 removed outlier: 4.139A pdb=" N GLU C 633 " --> pdb=" O LYS C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 653 removed outlier: 4.089A pdb=" N GLU C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 663 removed outlier: 3.590A pdb=" N MET C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 678 removed outlier: 4.144A pdb=" N ALA C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'C' and resid 683 through 697 removed outlier: 3.544A pdb=" N THR C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.667A pdb=" N LEU C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 721 " --> pdb=" O VAL C 717 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 722 " --> pdb=" O PHE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 removed outlier: 3.717A pdb=" N ASN C 728 " --> pdb=" O PHE C 724 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 729 " --> pdb=" O ALA C 725 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN C 730 " --> pdb=" O ALA C 726 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET C 731 " --> pdb=" O GLU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 748 removed outlier: 3.634A pdb=" N SER C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 748 " --> pdb=" O MET C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 768 removed outlier: 3.712A pdb=" N PHE C 757 " --> pdb=" O PRO C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 780 removed outlier: 4.085A pdb=" N GLN C 777 " --> pdb=" O ASP C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 795 removed outlier: 3.839A pdb=" N GLN C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 811 Processing helix chain 'C' and resid 820 through 826 Proline residue: C 825 - end of helix Processing helix chain 'C' and resid 827 through 836 removed outlier: 3.666A pdb=" N ASN C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 854 Processing helix chain 'C' and resid 857 through 866 Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.879A pdb=" N GLN C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 898 removed outlier: 4.019A pdb=" N VAL C 890 " --> pdb=" O SER C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 903 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 974 Processing helix chain 'C' and resid 980 through 989 removed outlier: 3.777A pdb=" N LEU C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.561A pdb=" N TYR C1007 " --> pdb=" O SER C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1031 removed outlier: 3.502A pdb=" N ILE C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1057 Proline residue: C1040 - end of helix removed outlier: 3.757A pdb=" N SER C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET C1051 " --> pdb=" O ARG C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1067 Processing helix chain 'C' and resid 1073 through 1077 removed outlier: 3.599A pdb=" N MET C1076 " --> pdb=" O SER C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1102 removed outlier: 3.552A pdb=" N ASP C1094 " --> pdb=" O LEU C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1106 No H-bonds generated for 'chain 'C' and resid 1104 through 1106' Processing helix chain 'C' and resid 1107 through 1127 removed outlier: 3.598A pdb=" N VAL C1113 " --> pdb=" O LYS C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1135 removed outlier: 3.689A pdb=" N LEU C1135 " --> pdb=" O ARG C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1148 removed outlier: 3.517A pdb=" N TYR C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) removed outlier: 3.726A 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 1194 removed outlier: 4.051A pdb=" N GLN C1178 " --> pdb=" O THR C1174 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C1179 " --> pdb=" O TRP C1175 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN C1181 " --> pdb=" O LEU C1177 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR C1182 " --> pdb=" O GLN C1178 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C1194 " --> pdb=" O VAL C1190 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1219 Processing helix chain 'C' and resid 1227 through 1248 removed outlier: 3.936A pdb=" N GLU C1248 " --> pdb=" O ASP C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1271 removed outlier: 3.619A pdb=" N GLN C1259 " --> pdb=" O THR C1255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C1271 " --> pdb=" O LEU C1267 " (cutoff:3.500A) Processing helix chain 'C' and resid 1274 through 1280 Processing helix chain 'C' and resid 1281 through 1287 removed outlier: 5.328A pdb=" N GLU C1284 " --> pdb=" O PRO C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1300 Processing helix chain 'C' and resid 1301 through 1318 removed outlier: 3.555A pdb=" N LEU C1318 " --> pdb=" O PHE C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1345 Processing helix chain 'C' and resid 1353 through 1358 removed outlier: 4.042A pdb=" N SER C1358 " --> pdb=" O PRO C1354 " (cutoff:3.500A) Processing helix chain 'C' and resid 1362 through 1376 Processing helix chain 'C' and resid 1377 through 1378 No H-bonds generated for 'chain 'C' and resid 1377 through 1378' Processing helix chain 'C' and resid 1379 through 1381 No H-bonds generated for 'chain 'C' and resid 1379 through 1381' Processing helix chain 'C' and resid 1382 through 1395 Processing helix chain 'C' and resid 1398 through 1413 removed outlier: 3.514A pdb=" N ARG C1410 " --> pdb=" O GLU C1406 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C1411 " --> pdb=" O ALA C1407 " (cutoff:3.500A) Processing helix chain 'C' and resid 1418 through 1424 Processing helix chain 'C' and resid 1427 through 1435 removed outlier: 3.501A pdb=" N LEU C1431 " --> pdb=" O MET C1427 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C1432 " --> pdb=" O ARG C1428 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N MET C1433 " --> pdb=" O PRO C1429 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C1435 " --> pdb=" O LEU C1431 " (cutoff:3.500A) Processing helix chain 'C' and resid 1441 through 1454 Processing helix chain 'C' and resid 1455 through 1459 removed outlier: 4.210A pdb=" N PHE C1459 " --> pdb=" O PRO C1456 " (cutoff:3.500A) Processing helix chain 'C' and resid 1460 through 1482 removed outlier: 3.794A pdb=" N LYS C1473 " --> pdb=" O GLN C1469 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP C1474 " --> pdb=" O HIS C1470 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C1479 " --> pdb=" O MET C1475 " (cutoff:3.500A) Processing helix chain 'C' and resid 1510 through 1524 removed outlier: 3.512A pdb=" N ALA C1516 " --> pdb=" O LYS C1512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE C1521 " --> pdb=" O ILE C1517 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS C1522 " --> pdb=" O ILE C1518 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C1523 " --> pdb=" O ASN C1519 " (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: 3.931A pdb=" N ARG C1564 " --> pdb=" O LYS C1560 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS C1565 " --> pdb=" O PHE C1561 " (cutoff:3.500A) Processing helix chain 'C' and resid 1568 through 1573 removed outlier: 3.825A pdb=" N PHE C1573 " --> pdb=" O THR C1569 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1579 Processing helix chain 'C' and resid 1581 through 1594 Processing helix chain 'C' and resid 1597 through 1606 removed outlier: 4.427A pdb=" N LEU C1604 " --> pdb=" O LEU C1600 " (cutoff:3.500A) Processing helix chain 'C' and resid 1608 through 1613 Processing helix chain 'C' and resid 1636 through 1653 Processing helix chain 'C' and resid 1659 through 1678 removed outlier: 4.709A pdb=" N SER C1665 " --> pdb=" O HIS C1661 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN C1666 " --> pdb=" O SER C1662 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C1669 " --> pdb=" O SER C1665 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN C1675 " --> pdb=" O TRP C1671 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE C1676 " --> pdb=" O VAL C1672 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1705 Processing helix chain 'C' and resid 1710 through 1716 Processing helix chain 'C' and resid 1722 through 1724 No H-bonds generated for 'chain 'C' and resid 1722 through 1724' Processing helix chain 'C' and resid 1725 through 1740 removed outlier: 4.314A pdb=" N GLU C1737 " --> pdb=" O LYS C1733 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU C1738 " --> pdb=" O GLU C1734 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1757 Processing helix chain 'C' and resid 1767 through 1784 Proline residue: C1779 - end of helix Processing helix chain 'C' and resid 1807 through 1817 removed outlier: 4.042A pdb=" N PHE C1811 " --> pdb=" O ILE C1807 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C1815 " --> pdb=" O PHE C1811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1826 through 1837 Processing helix chain 'C' and resid 1858 through 1866 removed outlier: 3.769A pdb=" N PHE C1864 " --> pdb=" O ARG C1860 " (cutoff:3.500A) Processing helix chain 'C' and resid 1867 through 1870 removed outlier: 3.736A pdb=" N LEU C1870 " --> pdb=" O PRO C1867 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1867 through 1870' Processing helix chain 'C' and resid 1876 through 1894 removed outlier: 4.019A pdb=" N LYS C1880 " --> pdb=" O ASP C1876 " (cutoff:3.500A) Processing helix chain 'C' and resid 1900 through 1909 removed outlier: 3.874A pdb=" N PHE C1905 " --> pdb=" O VAL C1901 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS C1906 " --> pdb=" O LEU C1902 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C1907 " --> pdb=" O GLN C1903 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C1909 " --> pdb=" O PHE C1905 " (cutoff:3.500A) Processing helix chain 'C' and resid 1916 through 1931 removed outlier: 3.520A pdb=" N ARG C1921 " --> pdb=" O ARG C1917 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN C1922 " --> pdb=" O ALA C1918 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C1923 " --> pdb=" O ILE C1919 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C1926 " --> pdb=" O GLN C1922 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C1927 " --> pdb=" O ALA C1923 " (cutoff:3.500A) Proline residue: C1929 - end of helix Processing helix chain 'C' and resid 1932 through 1939 removed outlier: 3.661A pdb=" N MET C1935 " --> pdb=" O PRO C1932 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C1936 " --> pdb=" O ALA C1933 " (cutoff:3.500A) Processing helix chain 'C' and resid 1940 through 1941 No H-bonds generated for 'chain 'C' and resid 1940 through 1941' Processing helix chain 'C' and resid 1942 through 1953 removed outlier: 3.694A pdb=" N LYS C1948 " --> pdb=" O HIS C1944 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C1951 " --> pdb=" O ARG C1947 " (cutoff:3.500A) Processing helix chain 'C' and resid 1965 through 1971 Processing helix chain 'C' and resid 1980 through 1985 removed outlier: 3.506A pdb=" N GLN C1983 " --> pdb=" O HIS C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 1991 Processing helix chain 'C' and resid 2003 through 2020 removed outlier: 3.980A pdb=" N VAL C2007 " --> pdb=" O ARG C2003 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C2011 " --> pdb=" O VAL C2007 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C2012 " --> pdb=" O ASP C2008 " (cutoff:3.500A) Processing helix chain 'C' and resid 2091 through 2106 removed outlier: 3.890A pdb=" N ASP C2095 " --> pdb=" O LYS C2091 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C2096 " --> pdb=" O GLN C2092 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C2098 " --> pdb=" O THR C2094 " (cutoff:3.500A) Processing helix chain 'C' and resid 2120 through 2131 removed outlier: 4.382A pdb=" N ARG C2124 " --> pdb=" O GLU C2120 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C2127 " --> pdb=" O SER C2123 " (cutoff:3.500A) Processing helix chain 'C' and resid 2143 through 2154 removed outlier: 3.715A pdb=" N PHE C2149 " --> pdb=" O LYS C2145 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP C2150 " --> pdb=" O LEU C2146 " (cutoff:3.500A) Processing helix chain 'C' and resid 2163 through 2181 removed outlier: 4.767A pdb=" N GLY C2170 " --> pdb=" O ASN C2166 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU C2171 " --> pdb=" O ILE C2167 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE C2176 " --> pdb=" O GLU C2172 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR C2179 " --> pdb=" O SER C2175 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C2181 " --> pdb=" O LEU C2177 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2189 removed outlier: 3.950A pdb=" N SER C2189 " --> pdb=" O ALA C2185 " (cutoff:3.500A) Processing helix chain 'C' and resid 2190 through 2198 Processing helix chain 'C' and resid 2199 through 2205 removed outlier: 4.983A pdb=" N THR C2202 " --> pdb=" O ALA C2199 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN C2205 " --> pdb=" O THR C2202 " (cutoff:3.500A) Processing helix chain 'C' and resid 2206 through 2223 removed outlier: 3.693A pdb=" N ARG C2210 " --> pdb=" O THR C2206 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2254 removed outlier: 3.681A pdb=" N LEU C2254 " --> pdb=" O ILE C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2279 Processing helix chain 'C' and resid 2282 through 2285 removed outlier: 3.760A pdb=" N TYR C2285 " --> pdb=" O ASN C2282 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2282 through 2285' Processing helix chain 'C' and resid 2286 through 2291 Processing helix chain 'C' and resid 2292 through 2306 removed outlier: 4.137A pdb=" N SER C2296 " --> pdb=" O VAL C2292 " (cutoff:3.500A) Processing helix chain 'C' and resid 2319 through 2335 removed outlier: 3.610A pdb=" N LEU C2323 " --> pdb=" O GLY C2319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C2325 " --> pdb=" O SER C2321 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C2328 " --> pdb=" O VAL C2324 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C2330 " --> pdb=" O LEU C2326 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C2331 " --> pdb=" O SER C2327 " (cutoff:3.500A) Processing helix chain 'C' and resid 2339 through 2356 removed outlier: 3.690A pdb=" N ARG C2343 " --> pdb=" O SER C2339 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASN C2345 " --> pdb=" O GLU C2341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE C2346 " --> pdb=" O MET C2342 " (cutoff:3.500A) Processing helix chain 'C' and resid 2360 through 2375 removed outlier: 3.907A pdb=" N LYS C2369 " --> pdb=" O ARG C2365 " (cutoff:3.500A) Processing helix chain 'C' and resid 2388 through 2403 removed outlier: 4.750A pdb=" N LEU C2395 " --> pdb=" O GLU C2391 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C2396 " --> pdb=" O LYS C2392 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS C2398 " --> pdb=" O ILE C2394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C2401 " --> pdb=" O VAL C2397 " (cutoff:3.500A) Processing helix chain 'C' and resid 2412 through 2425 Processing helix chain 'C' and resid 2439 through 2448 Processing helix chain 'C' and resid 2451 through 2463 removed outlier: 3.705A pdb=" N VAL C2461 " --> pdb=" O LYS C2457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2469 through 2477 removed outlier: 3.772A pdb=" N ARG C2473 " --> pdb=" O ARG C2469 " (cutoff:3.500A) Processing helix chain 'C' and resid 2482 through 2486 removed outlier: 4.136A pdb=" N ALA C2485 " --> pdb=" O ASN C2482 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET C2486 " --> pdb=" O TRP C2483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2482 through 2486' Processing helix chain 'C' and resid 2491 through 2501 Processing helix chain 'C' and resid 2522 through 2528 removed outlier: 3.654A pdb=" N ASN C2526 " --> pdb=" O THR C2522 " (cutoff:3.500A) Processing helix chain 'C' and resid 2587 through 2602 removed outlier: 3.980A pdb=" N THR C2601 " --> pdb=" O LYS C2597 " (cutoff:3.500A) Processing helix chain 'C' and resid 2607 through 2621 removed outlier: 3.701A pdb=" N VAL C2615 " --> pdb=" O LEU C2611 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C2616 " --> pdb=" O SER C2612 " (cutoff:3.500A) Processing helix chain 'C' and resid 2621 through 2640 Proline residue: C2634 - end of helix removed outlier: 3.519A pdb=" N ILE C2639 " --> pdb=" O ARG C2635 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C2640 " --> pdb=" O LEU C2636 " (cutoff:3.500A) Processing helix chain 'C' and resid 2641 through 2658 removed outlier: 4.423A pdb=" N ALA C2647 " --> pdb=" O ARG C2643 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C2651 " --> pdb=" O ALA C2647 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C2653 " --> pdb=" O ALA C2649 " (cutoff:3.500A) Proline residue: C2654 - end of helix Processing helix chain 'C' and resid 2659 through 2667 removed outlier: 4.489A pdb=" N VAL C2663 " --> pdb=" O SER C2660 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C2666 " --> pdb=" O VAL C2663 " (cutoff:3.500A) Processing helix chain 'C' and resid 2670 through 2680 removed outlier: 3.528A pdb=" N PHE C2675 " --> pdb=" O ALA C2671 " (cutoff:3.500A) Processing helix chain 'C' and resid 2691 through 2700 removed outlier: 3.592A pdb=" N TYR C2695 " --> pdb=" O CYS C2691 " (cutoff:3.500A) Processing helix chain 'C' and resid 2702 through 2718 Processing helix chain 'C' and resid 2742 through 2755 Processing helix chain 'C' and resid 2757 through 2766 Processing helix chain 'C' and resid 2771 through 2783 removed outlier: 4.359A pdb=" N ALA C2775 " --> pdb=" O TYR C2771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C2783 " --> pdb=" O ALA C2779 " (cutoff:3.500A) Processing helix chain 'C' and resid 2785 through 2805 removed outlier: 3.606A pdb=" N GLU C2791 " --> pdb=" O GLU C2787 " (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 removed outlier: 3.974A pdb=" N TRP C2820 " --> pdb=" O GLU C2816 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C2821 " --> pdb=" O TYR C2817 " (cutoff:3.500A) Processing helix chain 'C' and resid 2833 through 2842 Processing helix chain 'C' and resid 2848 through 2857 removed outlier: 3.935A pdb=" N VAL C2852 " --> pdb=" O ASN C2848 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP C2857 " --> pdb=" O LEU C2853 " (cutoff:3.500A) Processing helix chain 'C' and resid 2863 through 2869 Processing helix chain 'C' and resid 2869 through 2876 removed outlier: 3.558A pdb=" N VAL C2874 " --> pdb=" O VAL C2870 " (cutoff:3.500A) Processing helix chain 'C' and resid 2880 through 2894 removed outlier: 4.100A pdb=" N VAL C2884 " --> pdb=" O MET C2880 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C2889 " --> pdb=" O ASN C2885 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C2890 " --> pdb=" O MET C2886 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C2891 " --> pdb=" O TYR C2887 " (cutoff:3.500A) Processing helix chain 'C' and resid 2903 through 2920 removed outlier: 3.537A 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 2952 removed outlier: 4.380A pdb=" N GLN C2938 " --> pdb=" O LEU C2934 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN C2939 " --> pdb=" O GLN C2935 " (cutoff:3.500A) Processing helix chain 'C' and resid 2960 through 2975 Processing helix chain 'C' and resid 2984 through 3006 removed outlier: 3.800A pdb=" N HIS C2998 " --> pdb=" O TRP C2994 " (cutoff:3.500A) Proline residue: C3003 - end of helix Processing helix chain 'C' and resid 3027 through 3051 removed outlier: 4.239A pdb=" N MET C3031 " --> pdb=" O SER C3027 " (cutoff:3.500A) Processing helix chain 'C' and resid 3053 through 3063 Processing helix chain 'C' and resid 3064 through 3067 Processing helix chain 'C' and resid 3071 through 3088 Processing helix chain 'C' and resid 3097 through 3107 removed outlier: 3.561A pdb=" N ILE C3105 " --> pdb=" O GLY C3101 " (cutoff:3.500A) Processing helix chain 'C' and resid 3116 through 3132 removed outlier: 4.050A pdb=" N GLU C3120 " --> pdb=" O GLU C3116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3135 through 3146 Processing helix chain 'C' and resid 3152 through 3168 Processing helix chain 'C' and resid 3172 through 3190 removed outlier: 3.855A pdb=" N GLY C3176 " --> pdb=" O GLN C3172 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C3177 " --> pdb=" O LEU C3173 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C3180 " --> pdb=" O GLY C3176 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS C3189 " --> pdb=" O HIS C3185 " (cutoff:3.500A) Processing helix chain 'C' and resid 3195 through 3206 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 3232 removed outlier: 4.497A pdb=" N TRP C3231 " --> pdb=" O PRO C3227 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C3232 " --> pdb=" O PRO C3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3234 through 3243 Processing helix chain 'C' and resid 3246 through 3261 removed outlier: 4.352A pdb=" N LEU C3250 " --> pdb=" O GLU C3246 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C3252 " --> pdb=" O LYS C3248 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C3253 " --> pdb=" O LEU C3249 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C3254 " --> pdb=" O LEU C3250 " (cutoff:3.500A) Processing helix chain 'C' and resid 3261 through 3283 removed outlier: 3.671A pdb=" N VAL C3265 " --> pdb=" O TYR C3261 " (cutoff:3.500A) removed outlier: 4.148A 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 3308 removed outlier: 3.632A pdb=" N MET C3306 " --> pdb=" O ARG C3302 " (cutoff:3.500A) Processing helix chain 'C' and resid 3311 through 3326 removed outlier: 3.624A 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 removed outlier: 3.763A pdb=" N GLN C3339 " --> pdb=" O GLU C3335 " (cutoff:3.500A) Processing helix chain 'C' and resid 3364 through 3379 removed outlier: 3.507A pdb=" N VAL C3375 " --> pdb=" O VAL C3371 " (cutoff:3.500A) Processing helix chain 'C' and resid 3416 through 3426 removed outlier: 3.792A pdb=" N ASP C3423 " --> pdb=" O GLN C3419 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C3424 " --> pdb=" O PHE C3420 " (cutoff:3.500A) Processing helix chain 'C' and resid 3427 through 3431 Processing helix chain 'C' and resid 3433 through 3452 removed outlier: 3.675A pdb=" N SER C3439 " --> pdb=" O HIS C3435 " (cutoff:3.500A) Processing helix chain 'C' and resid 3453 through 3455 No H-bonds generated for 'chain 'C' and resid 3453 through 3455' Processing helix chain 'C' and resid 3466 through 3471 removed outlier: 3.530A pdb=" N ASN C3470 " --> pdb=" O ARG C3466 " (cutoff:3.500A) Processing helix chain 'C' and resid 3482 through 3486 removed outlier: 4.352A pdb=" N MET C3486 " --> pdb=" O GLU C3483 " (cutoff:3.500A) Processing helix chain 'C' and resid 3535 through 3553 removed outlier: 4.010A pdb=" N ARG C3541 " --> pdb=" O THR C3537 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU C3542 " --> pdb=" O GLU C3538 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C3543 " --> pdb=" O SER C3539 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C3544 " --> pdb=" O ARG C3540 " (cutoff:3.500A) Processing helix chain 'C' and resid 3554 through 3558 Processing helix chain 'C' and resid 3559 through 3564 Processing helix chain 'C' and resid 3593 through 3603 Processing helix chain 'C' and resid 3609 through 3625 removed outlier: 3.775A pdb=" N ARG C3625 " --> pdb=" O THR C3621 " (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 3746 removed outlier: 4.113A pdb=" N PHE C3738 " --> pdb=" O ASN C3734 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR C3741 " --> pdb=" O GLU C3737 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE C3742 " --> pdb=" O PHE C3738 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C3743 " --> pdb=" O LEU C3739 " (cutoff:3.500A) Processing helix chain 'C' and resid 3746 through 3760 Processing helix chain 'C' and resid 3767 through 3772 Processing helix chain 'C' and resid 3772 through 3785 removed outlier: 3.706A pdb=" N ILE C3779 " --> pdb=" O ARG C3775 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C3780 " --> pdb=" O ASP C3776 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C3781 " --> pdb=" O GLU C3777 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3824 removed outlier: 3.599A pdb=" N VAL C3808 " --> pdb=" O SER C3804 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3834 through 3844 removed outlier: 3.585A pdb=" N ASN C3843 " --> pdb=" O VAL C3839 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3849 Processing helix chain 'C' and resid 3852 through 3856 Processing helix chain 'A' and resid 2369 through 2383 Processing helix chain 'A' and resid 2400 through 2410 removed outlier: 3.786A pdb=" N VAL A2404 " --> pdb=" O ASN A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2417 through 2428 Processing helix chain 'A' and resid 2428 through 2435 removed outlier: 4.108A pdb=" N GLY A2435 " --> pdb=" O PRO A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2452 removed outlier: 4.039A pdb=" N GLN A2447 " --> pdb=" O LEU A2443 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A2448 " --> pdb=" O ARG A2444 " (cutoff:3.500A) Processing helix chain 'A' and resid 2454 through 2474 removed outlier: 3.560A pdb=" N TYR A2461 " --> pdb=" O HIS A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2521 removed outlier: 3.792A pdb=" N SER A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG A2518 " --> pdb=" O VAL A2514 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A2519 " --> pdb=" O ALA A2515 " (cutoff:3.500A) 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 3459 through 3460 removed outlier: 3.543A pdb=" N PHE C3459 " --> pdb=" O VAL C3503 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N MET C3500 " --> pdb=" O ARG C3519 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ARG C3519 " --> pdb=" O MET C3500 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG C3502 " --> pdb=" O TYR C3517 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR C3517 " --> pdb=" O ARG C3502 " (cutoff:3.500A) removed outlier: 4.070A 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 1524 hydrogen bonds defined for protein. 4437 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: 23.67 Time building geometry restraints manager: 13.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 27773 1.04 - 1.25: 4421 1.25 - 1.46: 8425 1.46 - 1.66: 14680 1.66 - 1.87: 310 Bond restraints: 55609 Sorted by residual: bond pdb=" CA LEU C2831 " pdb=" C LEU C2831 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.41e-02 5.03e+03 5.67e+00 bond pdb=" CA SER C2480 " pdb=" C SER C2480 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.66e-02 3.63e+03 3.57e+00 bond pdb=" CB CYS C1874 " pdb=" SG CYS C1874 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" N GLU A2367 " pdb=" CA GLU A2367 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N LYS C 38 " pdb=" CA LYS C 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 55604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 100379 2.61 - 5.23: 405 5.23 - 7.84: 30 7.84 - 10.45: 4 10.45 - 13.07: 1 Bond angle restraints: 100819 Sorted by residual: angle pdb=" CB MET C2340 " pdb=" CG MET C2340 " pdb=" SD MET C2340 " ideal model delta sigma weight residual 112.70 125.77 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CA CYS C1868 " pdb=" CB CYS C1868 " pdb=" SG CYS C1868 " ideal model delta sigma weight residual 114.40 124.12 -9.72 2.30e+00 1.89e-01 1.79e+01 angle pdb=" N GLU C 727 " pdb=" CA GLU C 727 " pdb=" CB GLU C 727 " ideal model delta sigma weight residual 114.17 109.47 4.70 1.14e+00 7.69e-01 1.70e+01 angle pdb=" N LYS C 163 " pdb=" CA LYS C 163 " pdb=" C LYS C 163 " ideal model delta sigma weight residual 113.43 108.81 4.62 1.26e+00 6.30e-01 1.34e+01 angle pdb=" N SER C 771 " pdb=" CA SER C 771 " pdb=" C SER C 771 " ideal model delta sigma weight residual 112.97 109.09 3.88 1.06e+00 8.90e-01 1.34e+01 ... (remaining 100814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 23290 17.78 - 35.57: 1976 35.57 - 53.35: 533 53.35 - 71.13: 143 71.13 - 88.92: 62 Dihedral angle restraints: 26004 sinusoidal: 14291 harmonic: 11713 Sorted by residual: dihedral pdb=" CB CYS C1868 " pdb=" SG CYS C1868 " pdb=" SG CYS C1874 " pdb=" CB CYS C1874 " ideal model delta sinusoidal sigma weight residual -86.00 -5.04 -80.96 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CA TRP C1866 " pdb=" C TRP C1866 " pdb=" N PRO C1867 " pdb=" CA PRO C1867 " ideal model delta harmonic sigma weight residual -180.00 -145.00 -35.00 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CA VAL C1290 " pdb=" C VAL C1290 " pdb=" N PRO C1291 " pdb=" CA PRO C1291 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 26001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2886 0.030 - 0.061: 980 0.061 - 0.091: 331 0.091 - 0.122: 117 0.122 - 0.152: 10 Chirality restraints: 4324 Sorted by residual: chirality pdb=" CA PRO C 858 " pdb=" N PRO C 858 " pdb=" C PRO C 858 " pdb=" CB PRO C 858 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB VAL C3083 " pdb=" CA VAL C3083 " pdb=" CG1 VAL C3083 " pdb=" CG2 VAL C3083 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE C3480 " pdb=" N ILE C3480 " pdb=" C ILE C3480 " pdb=" CB ILE C3480 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 4321 not shown) Planarity restraints: 7909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 678 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO C 679 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 679 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 679 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 438 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C SER C 438 " 0.046 2.00e-02 2.50e+03 pdb=" O SER C 438 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 439 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C2358 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C2359 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C2359 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C2359 " 0.024 5.00e-02 4.00e+02 ... (remaining 7906 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1201 2.09 - 2.71: 94327 2.71 - 3.34: 166262 3.34 - 3.97: 195278 3.97 - 4.60: 314560 Nonbonded interactions: 771628 Sorted by model distance: nonbonded pdb=" OD2 ASP C2410 " pdb=" H ASN C2414 " model vdw 1.458 2.450 nonbonded pdb=" OE1 GLU C 627 " pdb=" H GLU C 627 " model vdw 1.462 2.450 nonbonded pdb=" OE1 GLU C1248 " pdb=" H GLU C1248 " model vdw 1.492 2.450 nonbonded pdb="HH12 ARG C 107 " pdb=" OE1 GLU C 150 " model vdw 1.550 2.450 nonbonded pdb=" OD1 ASP C2410 " pdb=" H GLU C2412 " model vdw 1.551 2.450 ... (remaining 771623 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 group one per residue 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: 7.700 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: 0.700 Extract box with map and model: 1.590 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 99.930 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.170 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: 0.030 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.004 0.062 27764 Z= 0.232 Angle : 0.666 13.065 37552 Z= 0.380 Chirality : 0.037 0.152 4324 Planarity : 0.004 0.069 4710 Dihedral : 15.156 88.877 10400 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 0.20 % Allowed : 12.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.38 % 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: -0.30 (0.15), residues: 3308 helix: 0.28 (0.11), residues: 2178 sheet: -0.52 (0.76), residues: 53 loop : -0.99 (0.21), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 964 HIS 0.011 0.001 HIS C 772 PHE 0.020 0.002 PHE C3121 TYR 0.014 0.001 TYR C2251 ARG 0.003 0.000 ARG C3730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 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: C 1862 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9041 (tpt) REVERT: C 3158 MET cc_start: 0.8503 (mmm) cc_final: 0.8280 (mmm) REVERT: C 3645 MET cc_start: 0.8237 (mmm) cc_final: 0.7765 (ptp) outliers start: 6 outliers final: 2 residues processed: 142 average time/residue: 0.7481 time to fit residues: 171.8522 Evaluate side-chains 133 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 1862 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 2.9990 chunk 255 optimal weight: 0.0570 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN C 284 GLN C 992 ASN C1082 ASN C1470 HIS C1970 HIS C2093 HIS C2464 ASN C2593 ASN C2700 HIS C2804 HIS C2976 ASN C3213 ASN C3419 GLN ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27764 Z= 0.255 Angle : 0.617 7.308 37552 Z= 0.332 Chirality : 0.038 0.157 4324 Planarity : 0.004 0.064 4710 Dihedral : 5.292 70.715 3620 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 1.03 % Allowed : 12.53 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.38 % 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: -0.19 (0.15), residues: 3308 helix: 0.38 (0.11), residues: 2198 sheet: -1.15 (0.69), residues: 55 loop : -0.95 (0.21), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 964 HIS 0.006 0.001 HIS C2998 PHE 0.028 0.002 PHE C3121 TYR 0.014 0.001 TYR C1140 ARG 0.004 0.000 ARG C2705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 3.292 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: C 446 MET cc_start: 0.7944 (mmm) cc_final: 0.7688 (ppp) REVERT: C 1289 MET cc_start: 0.7827 (pmm) cc_final: 0.7608 (pmm) REVERT: C 1540 MET cc_start: 0.8730 (tpp) cc_final: 0.8524 (tpp) REVERT: C 2294 MET cc_start: 0.9538 (mpp) cc_final: 0.9213 (mpp) REVERT: C 3158 MET cc_start: 0.8554 (mmm) cc_final: 0.8311 (mmm) REVERT: C 3645 MET cc_start: 0.8137 (mmm) cc_final: 0.7560 (ptp) REVERT: C 3731 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (tt) outliers start: 31 outliers final: 18 residues processed: 165 average time/residue: 0.6892 time to fit residues: 188.3080 Evaluate side-chains 150 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1638 LEU Chi-restraints excluded: chain C residue 1866 TRP Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3731 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1897 HIS C2128 ASN C2589 HIS C2727 GLN ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.004 0.041 27764 Z= 0.238 Angle : 0.584 7.179 37552 Z= 0.312 Chirality : 0.037 0.144 4324 Planarity : 0.004 0.065 4710 Dihedral : 5.129 62.905 3617 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 1.12 % Allowed : 13.10 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.38 % 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: -0.12 (0.15), residues: 3308 helix: 0.47 (0.11), residues: 2201 sheet: -1.32 (0.68), residues: 55 loop : -1.01 (0.21), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 964 HIS 0.017 0.001 HIS C2804 PHE 0.025 0.002 PHE C3121 TYR 0.012 0.001 TYR C1140 ARG 0.004 0.000 ARG C1668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 3.370 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: C 1289 MET cc_start: 0.7832 (pmm) cc_final: 0.7560 (pmm) REVERT: C 1587 MET cc_start: 0.8702 (tmm) cc_final: 0.8355 (tmm) REVERT: C 1862 MET cc_start: 0.9482 (tpt) cc_final: 0.8114 (tpt) REVERT: C 2354 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 2681 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: C 3158 MET cc_start: 0.8569 (mmm) cc_final: 0.8335 (mmm) REVERT: C 3645 MET cc_start: 0.8119 (mmm) cc_final: 0.7564 (ptp) REVERT: C 3731 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8666 (tt) outliers start: 34 outliers final: 17 residues processed: 168 average time/residue: 0.7160 time to fit residues: 199.3268 Evaluate side-chains 152 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3731 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 794 GLN C2727 GLN C2804 HIS ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27764 Z= 0.302 Angle : 0.608 8.044 37552 Z= 0.326 Chirality : 0.038 0.142 4324 Planarity : 0.004 0.065 4710 Dihedral : 5.125 62.546 3617 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 1.72 % Allowed : 12.96 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.27 (0.15), residues: 3308 helix: 0.41 (0.11), residues: 2200 sheet: -1.61 (0.67), residues: 55 loop : -1.21 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C1866 HIS 0.007 0.001 HIS C2823 PHE 0.025 0.002 PHE C3121 TYR 0.012 0.001 TYR C1140 ARG 0.004 0.000 ARG C1544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 4.486 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: C 309 MET cc_start: 0.7890 (ppp) cc_final: 0.7563 (ppp) REVERT: C 446 MET cc_start: 0.7967 (mmm) cc_final: 0.7687 (tmm) REVERT: C 1289 MET cc_start: 0.7819 (pmm) cc_final: 0.7499 (pmm) REVERT: C 1587 MET cc_start: 0.8749 (tmm) cc_final: 0.8442 (tmm) REVERT: C 1862 MET cc_start: 0.9146 (tpt) cc_final: 0.8915 (tpt) REVERT: C 1935 MET cc_start: 0.4897 (tpp) cc_final: 0.4547 (tpt) REVERT: C 2294 MET cc_start: 0.9534 (mpp) cc_final: 0.9199 (mpp) REVERT: C 2354 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8792 (mt) REVERT: C 2681 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: C 2803 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: C 3158 MET cc_start: 0.8588 (mmm) cc_final: 0.8344 (mmm) REVERT: C 3645 MET cc_start: 0.8194 (mmm) cc_final: 0.7529 (ptp) REVERT: C 3731 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8719 (tt) outliers start: 52 outliers final: 31 residues processed: 179 average time/residue: 0.7240 time to fit residues: 213.2688 Evaluate side-chains 164 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2706 SER Chi-restraints excluded: chain C residue 2721 LEU Chi-restraints excluded: chain C residue 2803 GLU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3235 ILE Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3731 LEU Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 242 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 277 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2727 GLN ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27764 Z= 0.209 Angle : 0.570 7.583 37552 Z= 0.299 Chirality : 0.036 0.145 4324 Planarity : 0.004 0.064 4710 Dihedral : 4.963 60.902 3617 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 1.69 % Allowed : 13.36 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.01 (0.15), residues: 3308 helix: 0.63 (0.11), residues: 2206 sheet: -1.65 (0.67), residues: 55 loop : -1.09 (0.21), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1866 HIS 0.015 0.001 HIS C2804 PHE 0.024 0.001 PHE C3121 TYR 0.012 0.001 TYR C1140 ARG 0.002 0.000 ARG C3502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 3.199 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: C 309 MET cc_start: 0.7949 (ppp) cc_final: 0.7608 (ppp) REVERT: C 446 MET cc_start: 0.7988 (mmm) cc_final: 0.7774 (tmm) REVERT: C 1289 MET cc_start: 0.7767 (pmm) cc_final: 0.7399 (pmm) REVERT: C 1587 MET cc_start: 0.8726 (tmm) cc_final: 0.8403 (tmm) REVERT: C 2294 MET cc_start: 0.9540 (mpp) cc_final: 0.9184 (mpp) REVERT: C 2354 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 2681 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: C 2803 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: C 3158 MET cc_start: 0.8571 (mmm) cc_final: 0.8320 (mmm) REVERT: C 3325 MET cc_start: 0.8400 (mpp) cc_final: 0.8122 (mpp) REVERT: C 3645 MET cc_start: 0.8158 (mmm) cc_final: 0.7510 (ptp) REVERT: C 3731 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8687 (tt) REVERT: A 2433 GLU cc_start: 0.8435 (pt0) cc_final: 0.8216 (pt0) outliers start: 51 outliers final: 33 residues processed: 181 average time/residue: 0.7019 time to fit residues: 208.3688 Evaluate side-chains 167 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2803 GLU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3235 ILE Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3445 ILE Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3731 LEU Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2727 GLN ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27764 Z= 0.192 Angle : 0.559 7.898 37552 Z= 0.291 Chirality : 0.036 0.146 4324 Planarity : 0.004 0.064 4710 Dihedral : 4.822 60.044 3615 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 1.75 % Allowed : 13.59 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.17 (0.15), residues: 3308 helix: 0.77 (0.11), residues: 2215 sheet: -1.62 (0.66), residues: 55 loop : -1.11 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 964 HIS 0.005 0.001 HIS C 864 PHE 0.023 0.001 PHE C3121 TYR 0.011 0.001 TYR C2251 ARG 0.004 0.000 ARG C1438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 3.269 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: C 309 MET cc_start: 0.8006 (ppp) cc_final: 0.7642 (ppp) REVERT: C 437 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.5082 (mp0) REVERT: C 625 MET cc_start: 0.8115 (tpp) cc_final: 0.7895 (tpp) REVERT: C 1289 MET cc_start: 0.7758 (pmm) cc_final: 0.7353 (pmm) REVERT: C 1587 MET cc_start: 0.8720 (tmm) cc_final: 0.8397 (tmm) REVERT: C 2354 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8790 (mt) REVERT: C 2681 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: C 2835 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: C 3158 MET cc_start: 0.8571 (mmm) cc_final: 0.8327 (mmm) REVERT: C 3325 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: C 3731 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8693 (tt) outliers start: 53 outliers final: 38 residues processed: 182 average time/residue: 0.7000 time to fit residues: 210.8716 Evaluate side-chains 175 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1734 GLU Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2281 ASN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2721 LEU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2835 GLU Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3235 ILE Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3325 MET Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3442 LYS Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3731 LEU Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27764 Z= 0.205 Angle : 0.560 8.691 37552 Z= 0.291 Chirality : 0.036 0.145 4324 Planarity : 0.004 0.063 4710 Dihedral : 4.754 59.637 3615 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 1.75 % Allowed : 13.72 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.20 (0.15), residues: 3308 helix: 0.81 (0.11), residues: 2215 sheet: -1.60 (0.66), residues: 55 loop : -1.14 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 964 HIS 0.006 0.001 HIS C 864 PHE 0.023 0.001 PHE C3121 TYR 0.011 0.001 TYR C2251 ARG 0.002 0.000 ARG A2518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 3.225 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: C 309 MET cc_start: 0.7995 (ppp) cc_final: 0.7595 (ppp) REVERT: C 625 MET cc_start: 0.8038 (tpp) cc_final: 0.7831 (tpp) REVERT: C 1289 MET cc_start: 0.7712 (pmm) cc_final: 0.7292 (pmm) REVERT: C 1587 MET cc_start: 0.8709 (tmm) cc_final: 0.8386 (tmm) REVERT: C 2681 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: C 2803 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: C 2835 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: C 3158 MET cc_start: 0.8571 (mmm) cc_final: 0.8340 (mmm) REVERT: C 3325 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8261 (mpp) REVERT: C 3645 MET cc_start: 0.8258 (mmm) cc_final: 0.7597 (ptp) REVERT: C 3731 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8703 (tt) outliers start: 53 outliers final: 44 residues processed: 181 average time/residue: 0.7094 time to fit residues: 212.6924 Evaluate side-chains 178 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1734 GLU Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2142 SER Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2721 LEU Chi-restraints excluded: chain C residue 2803 GLU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2835 GLU Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3235 ILE Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3325 MET Chi-restraints excluded: chain C residue 3347 CYS Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3442 LYS Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3731 LEU Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 160 optimal weight: 0.0970 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27764 Z= 0.205 Angle : 0.565 9.600 37552 Z= 0.293 Chirality : 0.036 0.146 4324 Planarity : 0.004 0.062 4710 Dihedral : 4.698 59.453 3615 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 1.79 % Allowed : 13.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.26 (0.15), residues: 3308 helix: 0.87 (0.11), residues: 2218 sheet: -1.55 (0.66), residues: 53 loop : -1.18 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 964 HIS 0.006 0.001 HIS C 864 PHE 0.023 0.001 PHE C3121 TYR 0.011 0.001 TYR C2251 ARG 0.002 0.000 ARG C3502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 3.330 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: C 309 MET cc_start: 0.8006 (ppp) cc_final: 0.7575 (ppp) REVERT: C 625 MET cc_start: 0.8040 (tpp) cc_final: 0.7798 (tpp) REVERT: C 1289 MET cc_start: 0.7684 (pmm) cc_final: 0.7248 (pmm) REVERT: C 1587 MET cc_start: 0.8644 (tmm) cc_final: 0.8320 (tmm) REVERT: C 2681 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: C 2803 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: C 2835 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: C 3158 MET cc_start: 0.8563 (mmm) cc_final: 0.8344 (mmm) REVERT: C 3731 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8702 (tt) outliers start: 54 outliers final: 46 residues processed: 183 average time/residue: 0.7071 time to fit residues: 214.5085 Evaluate side-chains 182 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1734 GLU Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2142 SER Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2281 ASN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2721 LEU Chi-restraints excluded: chain C residue 2803 GLU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2835 GLU Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3235 ILE Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3347 CYS Chi-restraints excluded: chain C residue 3438 ILE Chi-restraints excluded: chain C residue 3442 LYS Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3715 ASN Chi-restraints excluded: chain C residue 3731 LEU Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 131 optimal weight: 0.4980 chunk 237 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 273 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27764 Z= 0.155 Angle : 0.551 10.667 37552 Z= 0.280 Chirality : 0.035 0.146 4324 Planarity : 0.004 0.063 4710 Dihedral : 4.581 57.795 3615 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 1.46 % Allowed : 14.35 % Favored : 84.19 % 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: 0.47 (0.16), residues: 3308 helix: 1.02 (0.11), residues: 2234 sheet: -1.40 (0.67), residues: 53 loop : -1.09 (0.22), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C3005 HIS 0.006 0.001 HIS C 772 PHE 0.022 0.001 PHE C3121 TYR 0.010 0.001 TYR C 365 ARG 0.002 0.000 ARG C3502 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 3.271 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: C 309 MET cc_start: 0.8049 (ppp) cc_final: 0.7618 (ppp) REVERT: C 625 MET cc_start: 0.8035 (tpp) cc_final: 0.7716 (tpp) REVERT: C 1587 MET cc_start: 0.8658 (tmm) cc_final: 0.8332 (tmm) REVERT: C 2399 MET cc_start: 0.9138 (ppp) cc_final: 0.8719 (ppp) REVERT: C 2681 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: C 2803 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: C 3158 MET cc_start: 0.8538 (mmm) cc_final: 0.8318 (mmm) REVERT: C 3645 MET cc_start: 0.8228 (mmm) cc_final: 0.7568 (ptp) outliers start: 44 outliers final: 39 residues processed: 177 average time/residue: 0.7238 time to fit residues: 211.4363 Evaluate side-chains 174 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1734 GLU Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2142 SER Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2364 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2803 GLU Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3325 MET Chi-restraints excluded: chain C residue 3442 LYS Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.8980 chunk 320 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 335 optimal weight: 0.0670 chunk 309 optimal weight: 2.9990 chunk 267 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27764 Z= 0.156 Angle : 0.552 9.079 37552 Z= 0.280 Chirality : 0.035 0.149 4324 Planarity : 0.004 0.063 4710 Dihedral : 4.465 56.602 3615 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 1.49 % Allowed : 14.45 % Favored : 84.06 % 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 (0.16), residues: 3308 helix: 1.10 (0.11), residues: 2242 sheet: -1.40 (0.67), residues: 53 loop : -1.06 (0.22), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 964 HIS 0.005 0.001 HIS C2987 PHE 0.021 0.001 PHE C3121 TYR 0.010 0.001 TYR C 365 ARG 0.003 0.000 ARG C1544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 3.252 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: C 309 MET cc_start: 0.8040 (ppp) cc_final: 0.7603 (ppp) REVERT: C 437 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4691 (mp0) REVERT: C 1587 MET cc_start: 0.8671 (tmm) cc_final: 0.8340 (tmm) REVERT: C 2399 MET cc_start: 0.9141 (ppp) cc_final: 0.8728 (ppp) REVERT: C 2681 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: C 3158 MET cc_start: 0.8546 (mmm) cc_final: 0.8263 (mmm) REVERT: C 3645 MET cc_start: 0.8247 (mmm) cc_final: 0.7428 (ptp) outliers start: 45 outliers final: 37 residues processed: 176 average time/residue: 0.7275 time to fit residues: 210.8718 Evaluate side-chains 172 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 928 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1565 HIS Chi-restraints excluded: chain C residue 1652 ASN Chi-restraints excluded: chain C residue 1734 GLU Chi-restraints excluded: chain C residue 1750 ARG Chi-restraints excluded: chain C residue 2142 SER Chi-restraints excluded: chain C residue 2147 GLN Chi-restraints excluded: chain C residue 2354 LEU Chi-restraints excluded: chain C residue 2413 LEU Chi-restraints excluded: chain C residue 2602 LEU Chi-restraints excluded: chain C residue 2641 SER Chi-restraints excluded: chain C residue 2681 GLN Chi-restraints excluded: chain C residue 2804 HIS Chi-restraints excluded: chain C residue 2990 SER Chi-restraints excluded: chain C residue 3173 LEU Chi-restraints excluded: chain C residue 3175 LEU Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3347 CYS Chi-restraints excluded: chain C residue 3442 LYS Chi-restraints excluded: chain C residue 3492 TYR Chi-restraints excluded: chain C residue 3825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2804 HIS ** A2457 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 = 0.3961 r_free = 0.3961 target = 0.061267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.045735 restraints weight = 547735.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.047344 restraints weight = 215680.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.048296 restraints weight = 123295.566| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27764 Z= 0.202 Angle : 0.566 9.465 37552 Z= 0.290 Chirality : 0.036 0.146 4324 Planarity : 0.004 0.062 4710 Dihedral : 4.488 57.088 3615 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 1.42 % Allowed : 14.55 % Favored : 84.03 % 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: 0.52 (0.15), residues: 3308 helix: 1.07 (0.11), residues: 2241 sheet: -1.42 (0.67), residues: 53 loop : -1.10 (0.22), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2882 HIS 0.005 0.001 HIS C 864 PHE 0.020 0.001 PHE C3121 TYR 0.011 0.001 TYR C2251 ARG 0.004 0.000 ARG C1544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7127.48 seconds wall clock time: 125 minutes 19.28 seconds (7519.28 seconds total)