Starting phenix.real_space_refine on Fri Mar 6 08:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otm_13062/03_2026/7otm_13062.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 30 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 18634 2.51 5 N 4904 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29040 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 28910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3636, 28910 Classifications: {'peptide': 3636} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 158, 'TRANS': 3477} Chain breaks: 16 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 130 Unusual residues: {'2R4': 1} Classifications: {'peptide': 20, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19, None: 1} Not linked: pdbres="UNK A6020 " pdbres="2R4 A6101 " Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 6.35, per 1000 atoms: 0.22 Number of scatterers: 29040 At special positions: 0 Unit cell: (125.184, 152.568, 185.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 5310 8.00 N 4904 7.00 C 18634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 5 sheets defined 71.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.745A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.651A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 53 through 71 removed outlier: 4.075A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.696A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.630A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 127 through 127 No H-bonds generated for 'chain 'A' and resid 127 through 127' Processing helix chain 'A' and resid 128 through 146 removed outlier: 4.019A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.635A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.760A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 4.154A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 4.021A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.040A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 257 through 262 removed outlier: 4.060A pdb=" N ASP A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 308 through 330 Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.246A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.648A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.551A pdb=" N CYS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.877A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 471 through 493 removed outlier: 4.202A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.766A pdb=" N VAL A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 559 through 579 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.705A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.600A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.566A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.692A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.518A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.970A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.842A pdb=" N SER A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.708A pdb=" N VAL A 884 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 921 removed outlier: 3.860A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 removed outlier: 3.817A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.787A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.609A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.748A pdb=" N THR A1006 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1016 removed outlier: 3.643A pdb=" N ILE A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1044 removed outlier: 3.512A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.893A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1072 through 1086 removed outlier: 3.898A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.767A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1146 removed outlier: 6.297A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1216 through 1226 removed outlier: 3.740A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.836A pdb=" N ALA A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1273 removed outlier: 3.852A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.545A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1298 removed outlier: 4.255A pdb=" N LYS A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1325 No H-bonds generated for 'chain 'A' and resid 1323 through 1325' Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.673A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1361 removed outlier: 3.887A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.203A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 4.277A pdb=" N ILE A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A1383 " --> pdb=" O PRO A1379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1378 through 1383' Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.550A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1435 removed outlier: 4.225A pdb=" N VAL A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN A1435 " --> pdb=" O LEU A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 3.723A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1487 " --> pdb=" O LEU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.814A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.875A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 4.503A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1626 Processing helix chain 'A' and resid 1627 through 1633 removed outlier: 3.815A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.692A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.627A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1694 through 1699 Proline residue: A1697 - end of helix No H-bonds generated for 'chain 'A' and resid 1694 through 1699' Processing helix chain 'A' and resid 1706 through 1722 Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.753A pdb=" N ARG A1816 " --> pdb=" O LEU A1812 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 3.675A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 3.768A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 3.717A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1921 removed outlier: 3.662A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 Processing helix chain 'A' and resid 2093 through 2107 removed outlier: 3.791A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 4.211A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 4.141A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 5.521A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2267 through 2269 No H-bonds generated for 'chain 'A' and resid 2267 through 2269' Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.697A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2305 Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.228A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2352 removed outlier: 3.670A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.543A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.811A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2419 through 2425 Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2456 removed outlier: 3.637A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2457 through 2462 removed outlier: 3.602A pdb=" N GLU A2460 " --> pdb=" O PRO A2457 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.815A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2496 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2543 through 2546 Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2821 through 2823 No H-bonds generated for 'chain 'A' and resid 2821 through 2823' Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2864 removed outlier: 3.701A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2871 removed outlier: 4.111A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2899 removed outlier: 3.680A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2934 removed outlier: 3.639A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.612A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A2957 " --> pdb=" O THR A2953 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.847A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.887A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3013 Processing helix chain 'A' and resid 3026 through 3031 removed outlier: 3.596A pdb=" N ILE A3030 " --> pdb=" O ASP A3026 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A3031 " --> pdb=" O LEU A3027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3026 through 3031' Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3071 removed outlier: 3.501A pdb=" N THR A3063 " --> pdb=" O GLN A3059 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3081 Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.756A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3116 Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.676A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 3.912A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3167 removed outlier: 4.175A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3194 Processing helix chain 'A' and resid 3195 through 3197 No H-bonds generated for 'chain 'A' and resid 3195 through 3197' Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.955A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3262 Processing helix chain 'A' and resid 3271 through 3287 removed outlier: 3.641A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3307 removed outlier: 4.377A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 4.151A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3352 removed outlier: 4.050A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A3352 " --> pdb=" O ALA A3349 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3356 Processing helix chain 'A' and resid 3357 through 3364 Processing helix chain 'A' and resid 3369 through 3394 removed outlier: 4.017A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3406 through 3429 Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 3.571A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3465 through 3472 removed outlier: 3.715A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3479 Processing helix chain 'A' and resid 3480 through 3489 removed outlier: 3.512A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.772A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3563 removed outlier: 3.782A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3605 through 3607 No H-bonds generated for 'chain 'A' and resid 3605 through 3607' Processing helix chain 'A' and resid 3608 through 3615 Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.837A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3657 through 3671 removed outlier: 4.518A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3779 through 3784 Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.052A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 3.989A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 4.057A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3878 removed outlier: 3.625A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3890 Processing helix chain 'A' and resid 3893 through 3919 removed outlier: 3.699A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3970 Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.538A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.506A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.537A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4050 removed outlier: 3.525A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4053 No H-bonds generated for 'chain 'A' and resid 4051 through 4053' Processing helix chain 'A' and resid 4055 through 4068 removed outlier: 4.049A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4113 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 6002 through 6016 removed outlier: 3.559A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK A6014 " --> pdb=" O UNK A6010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 5.933A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3727 through 3728 Processing sheet with id=AA5, first strand: chain 'A' and resid 3809 through 3811 removed outlier: 3.518A pdb=" N VAL A3810 " --> pdb=" O VAL A3930 " (cutoff:3.500A) 1599 hydrogen bonds defined for protein. 4710 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: 7.41 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8384 1.33 - 1.45: 4575 1.45 - 1.57: 16377 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 29636 Sorted by residual: bond pdb=" CA PHE A3252 " pdb=" C PHE A3252 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.80e-02 3.09e+03 1.83e+01 bond pdb=" CA ARG A3287 " pdb=" C ARG A3287 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.72e-02 3.38e+03 1.75e+01 bond pdb=" CA THR A3479 " pdb=" C THR A3479 " ideal model delta sigma weight residual 1.523 1.466 0.058 1.80e-02 3.09e+03 1.03e+01 bond pdb=" C02 2R4 A6101 " pdb=" C03 2R4 A6101 " ideal model delta sigma weight residual 1.479 1.418 0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" CA VAL A3728 " pdb=" CB VAL A3728 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.36e-02 5.41e+03 7.14e+00 ... (remaining 29631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 39014 2.50 - 5.01: 916 5.01 - 7.51: 127 7.51 - 10.01: 20 10.01 - 12.52: 4 Bond angle restraints: 40081 Sorted by residual: angle pdb=" C PRO A3735 " pdb=" CA PRO A3735 " pdb=" CB PRO A3735 " ideal model delta sigma weight residual 111.23 123.75 -12.52 1.28e+00 6.10e-01 9.56e+01 angle pdb=" N LEU A2337 " pdb=" CA LEU A2337 " pdb=" C LEU A2337 " ideal model delta sigma weight residual 112.03 120.82 -8.79 1.31e+00 5.83e-01 4.50e+01 angle pdb=" N PRO A3735 " pdb=" CA PRO A3735 " pdb=" C PRO A3735 " ideal model delta sigma weight residual 111.21 101.07 10.14 1.59e+00 3.96e-01 4.07e+01 angle pdb=" N GLY A4024 " pdb=" CA GLY A4024 " pdb=" C GLY A4024 " ideal model delta sigma weight residual 112.50 106.16 6.34 1.16e+00 7.43e-01 2.99e+01 angle pdb=" N ILE A1386 " pdb=" CA ILE A1386 " pdb=" C ILE A1386 " ideal model delta sigma weight residual 112.12 107.55 4.57 8.40e-01 1.42e+00 2.96e+01 ... (remaining 40076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16138 17.98 - 35.96: 1627 35.96 - 53.94: 252 53.94 - 71.93: 45 71.93 - 89.91: 24 Dihedral angle restraints: 18086 sinusoidal: 7329 harmonic: 10757 Sorted by residual: dihedral pdb=" CA GLU A3693 " pdb=" C GLU A3693 " pdb=" N PHE A3694 " pdb=" CA PHE A3694 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA THR A1006 " pdb=" C THR A1006 " pdb=" N VAL A1007 " pdb=" CA VAL A1007 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLN A3037 " pdb=" C GLN A3037 " pdb=" N GLU A3038 " pdb=" CA GLU A3038 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 18083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3621 0.063 - 0.125: 858 0.125 - 0.188: 72 0.188 - 0.251: 10 0.251 - 0.314: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" CA LEU A2337 " pdb=" N LEU A2337 " pdb=" C LEU A2337 " pdb=" CB LEU A2337 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ALA A3730 " pdb=" N ALA A3730 " pdb=" C ALA A3730 " pdb=" CB ALA A3730 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ALA A3406 " pdb=" N ALA A3406 " pdb=" C ALA A3406 " pdb=" CB ALA A3406 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4561 not shown) Planarity restraints: 5087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 2R4 A6101 " -0.043 2.00e-02 2.50e+03 2.45e-02 2.10e+01 pdb=" C06 2R4 A6101 " -0.008 2.00e-02 2.50e+03 pdb=" C07 2R4 A6101 " -0.017 2.00e-02 2.50e+03 pdb=" C08 2R4 A6101 " -0.002 2.00e-02 2.50e+03 pdb=" C09 2R4 A6101 " 0.018 2.00e-02 2.50e+03 pdb=" C10 2R4 A6101 " 0.025 2.00e-02 2.50e+03 pdb=" C11 2R4 A6101 " 0.012 2.00e-02 2.50e+03 pdb=" C13 2R4 A6101 " 0.004 2.00e-02 2.50e+03 pdb=" C14 2R4 A6101 " 0.014 2.00e-02 2.50e+03 pdb=" C15 2R4 A6101 " -0.015 2.00e-02 2.50e+03 pdb=" C16 2R4 A6101 " -0.007 2.00e-02 2.50e+03 pdb=" C17 2R4 A6101 " -0.024 2.00e-02 2.50e+03 pdb=" C18 2R4 A6101 " -0.018 2.00e-02 2.50e+03 pdb=" S12 2R4 A6101 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A4008 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A4009 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A4009 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A4009 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2851 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A2852 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A2852 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2852 " 0.034 5.00e-02 4.00e+02 ... (remaining 5084 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 466 2.64 - 3.20: 29765 3.20 - 3.77: 45517 3.77 - 4.33: 62486 4.33 - 4.90: 99793 Nonbonded interactions: 238027 Sorted by model distance: nonbonded pdb=" O SER A 280 " pdb=" OG SER A 283 " model vdw 2.071 3.040 nonbonded pdb=" O GLU A3361 " pdb=" OG SER A3367 " model vdw 2.086 3.040 nonbonded pdb=" O LYS A3355 " pdb=" NH1 ARG A3358 " model vdw 2.097 3.120 nonbonded pdb=" O GLU A3804 " pdb=" CG GLU A3804 " model vdw 2.099 3.440 nonbonded pdb=" OH TYR A3855 " pdb=" OE1 GLU A4122 " model vdw 2.101 3.040 ... (remaining 238022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.008 0.077 29636 Z= 0.363 Angle : 0.928 12.518 40081 Z= 0.498 Chirality : 0.052 0.314 4564 Planarity : 0.005 0.100 5087 Dihedral : 14.512 89.907 11074 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 0.28 % Allowed : 0.72 % Favored : 99.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3602 helix: -0.50 (0.10), residues: 2298 sheet: -2.39 (0.84), residues: 39 loop : -2.34 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A3708 TYR 0.025 0.002 TYR A3036 PHE 0.030 0.002 PHE A2257 TRP 0.038 0.002 TRP A2479 HIS 0.013 0.002 HIS A3924 Details of bonding type rmsd covalent geometry : bond 0.00842 (29636) covalent geometry : angle 0.92803 (40081) hydrogen bonds : bond 0.10599 ( 1599) hydrogen bonds : angle 5.62152 ( 4710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 356 time to evaluate : 1.073 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: A 96 MET cc_start: 0.5161 (ppp) cc_final: 0.4795 (ppp) REVERT: A 189 MET cc_start: 0.5840 (mmm) cc_final: 0.5184 (mmm) REVERT: A 1009 LEU cc_start: 0.8141 (mm) cc_final: 0.7867 (mm) REVERT: A 1639 LEU cc_start: 0.8331 (mt) cc_final: 0.7927 (mt) REVERT: A 1915 LEU cc_start: 0.8617 (tp) cc_final: 0.8293 (tp) REVERT: A 2237 ILE cc_start: 0.9438 (mm) cc_final: 0.9205 (mm) REVERT: A 2379 MET cc_start: 0.7009 (ptp) cc_final: 0.6797 (ptm) REVERT: A 2577 PHE cc_start: 0.7552 (m-80) cc_final: 0.6745 (m-10) REVERT: A 3644 PHE cc_start: 0.8005 (m-80) cc_final: 0.7253 (m-80) outliers start: 9 outliers final: 1 residues processed: 361 average time/residue: 0.1911 time to fit residues: 110.9008 Evaluate side-chains 254 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3803 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 344 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN A3643 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.121370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.089165 restraints weight = 72940.435| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.53 r_work: 0.3485 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29636 Z= 0.144 Angle : 0.703 10.307 40081 Z= 0.355 Chirality : 0.043 0.249 4564 Planarity : 0.005 0.076 5087 Dihedral : 5.585 57.304 3938 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.84 % Allowed : 9.26 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3602 helix: 0.10 (0.11), residues: 2336 sheet: -1.96 (0.82), residues: 41 loop : -2.17 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.036 0.002 TYR A1881 PHE 0.022 0.002 PHE A2257 TRP 0.018 0.001 TRP A2479 HIS 0.007 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00318 (29636) covalent geometry : angle 0.70268 (40081) hydrogen bonds : bond 0.03915 ( 1599) hydrogen bonds : angle 4.61357 ( 4710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 1.133 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: A 96 MET cc_start: 0.5866 (ppp) cc_final: 0.5555 (ppp) REVERT: A 189 MET cc_start: 0.5562 (mmm) cc_final: 0.4811 (mmm) REVERT: A 340 TYR cc_start: 0.7941 (t80) cc_final: 0.7656 (t80) REVERT: A 713 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8427 (mm-30) REVERT: A 984 TYR cc_start: 0.7808 (m-80) cc_final: 0.7547 (m-80) REVERT: A 996 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 1342 MET cc_start: 0.8981 (tpp) cc_final: 0.8755 (mmt) REVERT: A 1557 GLU cc_start: 0.8511 (pt0) cc_final: 0.8303 (pp20) REVERT: A 1643 MET cc_start: 0.9039 (mpp) cc_final: 0.8749 (mpp) REVERT: A 1863 PHE cc_start: 0.6699 (p90) cc_final: 0.6464 (p90) REVERT: A 1881 TYR cc_start: 0.9068 (m-80) cc_final: 0.8689 (m-80) REVERT: A 2236 GLU cc_start: 0.9373 (pt0) cc_final: 0.9032 (pp20) REVERT: A 2237 ILE cc_start: 0.9497 (mm) cc_final: 0.8931 (mm) REVERT: A 2312 TYR cc_start: 0.6693 (m-10) cc_final: 0.6365 (m-10) REVERT: A 2366 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8876 (mmmt) REVERT: A 3483 MET cc_start: 0.8341 (tpt) cc_final: 0.8015 (tpt) REVERT: A 3643 HIS cc_start: 0.8244 (t70) cc_final: 0.7936 (t70) REVERT: A 3644 PHE cc_start: 0.8882 (m-80) cc_final: 0.8374 (m-80) REVERT: A 3670 MET cc_start: 0.9143 (mpp) cc_final: 0.8894 (mpp) REVERT: A 3729 MET cc_start: 0.8005 (tmm) cc_final: 0.7479 (tmm) REVERT: A 3932 MET cc_start: 0.9019 (mmm) cc_final: 0.8645 (mmm) outliers start: 27 outliers final: 14 residues processed: 318 average time/residue: 0.1841 time to fit residues: 95.5033 Evaluate side-chains 273 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 78 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 GLN ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.119139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.086952 restraints weight = 73669.789| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.56 r_work: 0.3435 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29636 Z= 0.210 Angle : 0.693 7.969 40081 Z= 0.350 Chirality : 0.043 0.296 4564 Planarity : 0.005 0.073 5087 Dihedral : 5.389 53.257 3938 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 1.53 % Allowed : 12.14 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3602 helix: 0.22 (0.11), residues: 2346 sheet: -1.94 (0.79), residues: 41 loop : -2.14 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3746 TYR 0.024 0.002 TYR A3540 PHE 0.018 0.002 PHE A 68 TRP 0.016 0.001 TRP A1632 HIS 0.008 0.001 HIS A3908 Details of bonding type rmsd covalent geometry : bond 0.00486 (29636) covalent geometry : angle 0.69272 (40081) hydrogen bonds : bond 0.03978 ( 1599) hydrogen bonds : angle 4.52540 ( 4710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 1.043 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: A 189 MET cc_start: 0.5580 (mmm) cc_final: 0.4797 (mmm) REVERT: A 340 TYR cc_start: 0.8152 (t80) cc_final: 0.7937 (t80) REVERT: A 620 PHE cc_start: 0.7382 (m-80) cc_final: 0.7121 (m-10) REVERT: A 713 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 937 MET cc_start: 0.9016 (mtm) cc_final: 0.8737 (mtm) REVERT: A 984 TYR cc_start: 0.8125 (m-80) cc_final: 0.7838 (m-80) REVERT: A 996 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 1108 MET cc_start: 0.8939 (tpp) cc_final: 0.8450 (mpp) REVERT: A 1342 MET cc_start: 0.9101 (tpp) cc_final: 0.8758 (mmt) REVERT: A 1557 GLU cc_start: 0.8573 (pt0) cc_final: 0.8359 (pp20) REVERT: A 1643 MET cc_start: 0.9115 (mpp) cc_final: 0.8826 (mpp) REVERT: A 1881 TYR cc_start: 0.9119 (m-80) cc_final: 0.8784 (m-80) REVERT: A 2104 MET cc_start: 0.8407 (tmm) cc_final: 0.8118 (mmt) REVERT: A 2143 ARG cc_start: 0.7174 (mtm180) cc_final: 0.6949 (mpp80) REVERT: A 2220 MET cc_start: 0.8243 (mmm) cc_final: 0.7824 (mtt) REVERT: A 2236 GLU cc_start: 0.9368 (pt0) cc_final: 0.9024 (pp20) REVERT: A 2237 ILE cc_start: 0.9512 (mm) cc_final: 0.8908 (mm) REVERT: A 2312 TYR cc_start: 0.6862 (m-10) cc_final: 0.6540 (m-10) REVERT: A 2396 LEU cc_start: 0.8741 (mm) cc_final: 0.8436 (mm) REVERT: A 2402 LEU cc_start: 0.9001 (tp) cc_final: 0.8780 (pp) REVERT: A 2565 MET cc_start: 0.8131 (tmm) cc_final: 0.7445 (tmm) REVERT: A 2576 MET cc_start: 0.6607 (ppp) cc_final: 0.6304 (ppp) REVERT: A 3173 MET cc_start: 0.9290 (tpt) cc_final: 0.8880 (tpt) REVERT: A 3483 MET cc_start: 0.8447 (tpt) cc_final: 0.8206 (tpt) REVERT: A 3643 HIS cc_start: 0.8228 (t70) cc_final: 0.7904 (t-90) REVERT: A 3644 PHE cc_start: 0.8834 (m-80) cc_final: 0.8430 (m-80) REVERT: A 3729 MET cc_start: 0.8118 (tmm) cc_final: 0.7668 (ttp) REVERT: A 4008 GLU cc_start: 0.7436 (tp30) cc_final: 0.7092 (tp30) outliers start: 49 outliers final: 35 residues processed: 298 average time/residue: 0.1826 time to fit residues: 88.4036 Evaluate side-chains 282 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1403 MET Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1817 GLN Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3181 ASP Chi-restraints excluded: chain A residue 3238 MET Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 310 optimal weight: 0.7980 chunk 256 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 334 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 HIS A2351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.120675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088873 restraints weight = 73365.398| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.80 r_work: 0.3455 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29636 Z= 0.122 Angle : 0.632 8.775 40081 Z= 0.316 Chirality : 0.041 0.273 4564 Planarity : 0.004 0.063 5087 Dihedral : 5.046 49.065 3938 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 2.03 % Allowed : 13.83 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3602 helix: 0.45 (0.11), residues: 2373 sheet: -1.66 (0.80), residues: 41 loop : -2.11 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3708 TYR 0.021 0.001 TYR A1437 PHE 0.018 0.001 PHE A2260 TRP 0.015 0.001 TRP A1632 HIS 0.007 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00271 (29636) covalent geometry : angle 0.63227 (40081) hydrogen bonds : bond 0.03495 ( 1599) hydrogen bonds : angle 4.28199 ( 4710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.5879 (ppp) cc_final: 0.5270 (ppp) REVERT: A 189 MET cc_start: 0.5563 (mmm) cc_final: 0.4696 (mmm) REVERT: A 336 ASN cc_start: 0.9100 (m110) cc_final: 0.8674 (p0) REVERT: A 340 TYR cc_start: 0.8198 (t80) cc_final: 0.7976 (t80) REVERT: A 383 PHE cc_start: 0.8616 (m-80) cc_final: 0.8289 (m-80) REVERT: A 603 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 620 PHE cc_start: 0.7257 (m-80) cc_final: 0.6988 (m-10) REVERT: A 713 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8526 (mm-30) REVERT: A 937 MET cc_start: 0.8969 (mtm) cc_final: 0.8662 (mtm) REVERT: A 959 TYR cc_start: 0.8692 (t80) cc_final: 0.7917 (t80) REVERT: A 996 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 1108 MET cc_start: 0.9104 (tpp) cc_final: 0.8600 (mpp) REVERT: A 1342 MET cc_start: 0.9103 (tpp) cc_final: 0.8728 (mmt) REVERT: A 1402 LEU cc_start: 0.9086 (pp) cc_final: 0.8619 (pp) REVERT: A 1437 TYR cc_start: 0.8081 (m-80) cc_final: 0.7625 (t80) REVERT: A 1557 GLU cc_start: 0.8560 (pt0) cc_final: 0.8310 (pp20) REVERT: A 1643 MET cc_start: 0.9164 (mpp) cc_final: 0.8874 (mpp) REVERT: A 1817 GLN cc_start: 0.8404 (tp40) cc_final: 0.8200 (tp-100) REVERT: A 1881 TYR cc_start: 0.9108 (m-80) cc_final: 0.8774 (m-80) REVERT: A 2220 MET cc_start: 0.8218 (mmm) cc_final: 0.7850 (mtt) REVERT: A 2236 GLU cc_start: 0.9397 (pt0) cc_final: 0.9034 (pp20) REVERT: A 2237 ILE cc_start: 0.9500 (mm) cc_final: 0.8896 (mm) REVERT: A 2301 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: A 2307 MET cc_start: 0.7575 (mmt) cc_final: 0.7225 (mtt) REVERT: A 2312 TYR cc_start: 0.6641 (m-10) cc_final: 0.6290 (m-10) REVERT: A 2366 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8854 (mmmt) REVERT: A 2402 LEU cc_start: 0.8980 (tp) cc_final: 0.8704 (pp) REVERT: A 3454 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8932 (tp) REVERT: A 3643 HIS cc_start: 0.8294 (t70) cc_final: 0.7934 (t-90) REVERT: A 3644 PHE cc_start: 0.8858 (m-80) cc_final: 0.8412 (m-80) REVERT: A 3729 MET cc_start: 0.8205 (tmm) cc_final: 0.7650 (ttp) outliers start: 65 outliers final: 31 residues processed: 328 average time/residue: 0.1783 time to fit residues: 96.3992 Evaluate side-chains 297 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2385 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 264 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 298 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 266 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A1817 GLN A3139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.090386 restraints weight = 74209.612| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.81 r_work: 0.3464 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29636 Z= 0.115 Angle : 0.628 12.747 40081 Z= 0.310 Chirality : 0.040 0.279 4564 Planarity : 0.004 0.063 5087 Dihedral : 4.830 48.448 3938 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 2.25 % Allowed : 14.71 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3602 helix: 0.62 (0.11), residues: 2378 sheet: -1.37 (0.81), residues: 41 loop : -2.09 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3746 TYR 0.019 0.001 TYR A3013 PHE 0.019 0.001 PHE A 68 TRP 0.015 0.001 TRP A1632 HIS 0.007 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00254 (29636) covalent geometry : angle 0.62812 (40081) hydrogen bonds : bond 0.03307 ( 1599) hydrogen bonds : angle 4.15380 ( 4710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5293 (tp) REVERT: A 96 MET cc_start: 0.5835 (ppp) cc_final: 0.5231 (ppp) REVERT: A 189 MET cc_start: 0.5662 (mmm) cc_final: 0.4716 (mmm) REVERT: A 336 ASN cc_start: 0.9116 (m110) cc_final: 0.8592 (p0) REVERT: A 340 TYR cc_start: 0.8291 (t80) cc_final: 0.8049 (t80) REVERT: A 383 PHE cc_start: 0.8642 (m-80) cc_final: 0.8287 (m-80) REVERT: A 453 MET cc_start: 0.8717 (tpt) cc_final: 0.8502 (tpp) REVERT: A 603 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 620 PHE cc_start: 0.7274 (m-80) cc_final: 0.7025 (m-10) REVERT: A 713 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8562 (mm-30) REVERT: A 880 MET cc_start: 0.4430 (mmt) cc_final: 0.3438 (ptt) REVERT: A 959 TYR cc_start: 0.8707 (t80) cc_final: 0.8021 (t80) REVERT: A 996 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8880 (p) REVERT: A 1108 MET cc_start: 0.9114 (tpp) cc_final: 0.8633 (mpp) REVERT: A 1342 MET cc_start: 0.9082 (tpp) cc_final: 0.8733 (mmt) REVERT: A 1402 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 1437 TYR cc_start: 0.7989 (m-80) cc_final: 0.7581 (t80) REVERT: A 1458 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 1557 GLU cc_start: 0.8593 (pt0) cc_final: 0.8325 (pp20) REVERT: A 1643 MET cc_start: 0.8970 (mpp) cc_final: 0.8735 (mpp) REVERT: A 1881 TYR cc_start: 0.9121 (m-80) cc_final: 0.8833 (m-80) REVERT: A 2104 MET cc_start: 0.8255 (tmm) cc_final: 0.8049 (mmt) REVERT: A 2143 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6676 (mmp80) REVERT: A 2220 MET cc_start: 0.8203 (mmm) cc_final: 0.7882 (mtt) REVERT: A 2236 GLU cc_start: 0.9400 (pt0) cc_final: 0.9041 (pp20) REVERT: A 2237 ILE cc_start: 0.9499 (mm) cc_final: 0.8896 (mm) REVERT: A 2301 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: A 2312 TYR cc_start: 0.6649 (m-10) cc_final: 0.6292 (m-10) REVERT: A 2366 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8896 (mmmt) REVERT: A 2565 MET cc_start: 0.7814 (tmm) cc_final: 0.7467 (tmm) REVERT: A 2568 MET cc_start: 0.7973 (mpp) cc_final: 0.7743 (mpp) REVERT: A 3643 HIS cc_start: 0.8307 (t70) cc_final: 0.7938 (t-90) REVERT: A 3644 PHE cc_start: 0.8866 (m-80) cc_final: 0.8411 (m-80) REVERT: A 3729 MET cc_start: 0.8158 (tmm) cc_final: 0.7518 (ttp) REVERT: A 3929 MET cc_start: 0.9027 (mmm) cc_final: 0.8737 (mmm) REVERT: A 3933 GLU cc_start: 0.8679 (pt0) cc_final: 0.8468 (mt-10) outliers start: 72 outliers final: 42 residues processed: 327 average time/residue: 0.1802 time to fit residues: 97.2409 Evaluate side-chains 309 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1403 MET Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1817 GLN Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1896 ILE Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 131 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 354 optimal weight: 0.2980 chunk 253 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 55 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 GLN A3716 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.122137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.090614 restraints weight = 74039.039| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.87 r_work: 0.3475 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29636 Z= 0.113 Angle : 0.635 13.481 40081 Z= 0.309 Chirality : 0.041 0.330 4564 Planarity : 0.004 0.065 5087 Dihedral : 4.693 47.560 3938 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 1.97 % Allowed : 15.93 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3602 helix: 0.72 (0.11), residues: 2374 sheet: -1.18 (0.81), residues: 41 loop : -2.02 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1854 TYR 0.027 0.001 TYR A 103 PHE 0.019 0.001 PHE A2260 TRP 0.017 0.001 TRP A1632 HIS 0.010 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00250 (29636) covalent geometry : angle 0.63504 (40081) hydrogen bonds : bond 0.03219 ( 1599) hydrogen bonds : angle 4.08292 ( 4710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 1.160 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: A 38 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5311 (tp) REVERT: A 96 MET cc_start: 0.5779 (ppp) cc_final: 0.5186 (ppp) REVERT: A 189 MET cc_start: 0.5668 (mmm) cc_final: 0.4702 (mmm) REVERT: A 336 ASN cc_start: 0.8919 (m110) cc_final: 0.8206 (p0) REVERT: A 340 TYR cc_start: 0.8247 (t80) cc_final: 0.7931 (t80) REVERT: A 383 PHE cc_start: 0.8638 (m-80) cc_final: 0.8267 (m-80) REVERT: A 603 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 620 PHE cc_start: 0.7279 (m-80) cc_final: 0.7066 (m-10) REVERT: A 713 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8520 (mm-30) REVERT: A 880 MET cc_start: 0.4436 (mmt) cc_final: 0.3493 (ptt) REVERT: A 959 TYR cc_start: 0.8661 (t80) cc_final: 0.7992 (t80) REVERT: A 996 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 1108 MET cc_start: 0.9103 (tpp) cc_final: 0.8652 (mpp) REVERT: A 1342 MET cc_start: 0.9120 (tpp) cc_final: 0.8756 (mmt) REVERT: A 1402 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8782 (pp) REVERT: A 1437 TYR cc_start: 0.8166 (m-80) cc_final: 0.7949 (t80) REVERT: A 1458 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 1557 GLU cc_start: 0.8516 (pt0) cc_final: 0.8296 (pp20) REVERT: A 1643 MET cc_start: 0.8948 (mpp) cc_final: 0.8711 (mpp) REVERT: A 1817 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7935 (tp40) REVERT: A 1881 TYR cc_start: 0.9174 (m-80) cc_final: 0.8915 (m-80) REVERT: A 2094 MET cc_start: 0.8998 (tmm) cc_final: 0.8618 (tmm) REVERT: A 2104 MET cc_start: 0.8314 (tmm) cc_final: 0.7966 (mmt) REVERT: A 2220 MET cc_start: 0.8160 (mmm) cc_final: 0.7834 (mtt) REVERT: A 2236 GLU cc_start: 0.9398 (pt0) cc_final: 0.9112 (pp20) REVERT: A 2237 ILE cc_start: 0.9489 (mm) cc_final: 0.8901 (mm) REVERT: A 2301 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: A 2312 TYR cc_start: 0.6768 (m-10) cc_final: 0.6405 (m-10) REVERT: A 2366 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8868 (mmmt) REVERT: A 2396 LEU cc_start: 0.8794 (mm) cc_final: 0.8485 (mt) REVERT: A 2565 MET cc_start: 0.7706 (tmm) cc_final: 0.7383 (tmm) REVERT: A 2568 MET cc_start: 0.7963 (mpp) cc_final: 0.7747 (mpp) REVERT: A 3069 MET cc_start: 0.7366 (tpt) cc_final: 0.7137 (tpt) REVERT: A 3643 HIS cc_start: 0.8382 (t70) cc_final: 0.8015 (t-90) REVERT: A 3644 PHE cc_start: 0.8877 (m-80) cc_final: 0.8418 (m-80) REVERT: A 3729 MET cc_start: 0.8128 (tmm) cc_final: 0.7522 (ttp) REVERT: A 3929 MET cc_start: 0.9021 (mmm) cc_final: 0.8723 (mmm) REVERT: A 3932 MET cc_start: 0.8985 (mmm) cc_final: 0.8494 (mmm) REVERT: A 3933 GLU cc_start: 0.8716 (pt0) cc_final: 0.8402 (mt-10) REVERT: A 4008 GLU cc_start: 0.7449 (tp30) cc_final: 0.7043 (tp30) REVERT: A 4048 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8712 (ptmt) outliers start: 63 outliers final: 41 residues processed: 314 average time/residue: 0.1845 time to fit residues: 95.3076 Evaluate side-chains 307 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1817 GLN Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3329 LEU Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3971 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 24 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 236 optimal weight: 0.8980 chunk 283 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 chunk 358 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.122581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.090974 restraints weight = 73916.736| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.91 r_work: 0.3472 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29636 Z= 0.114 Angle : 0.627 14.642 40081 Z= 0.306 Chirality : 0.040 0.288 4564 Planarity : 0.004 0.067 5087 Dihedral : 4.604 47.411 3938 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.13 % Allowed : 16.27 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3602 helix: 0.82 (0.11), residues: 2376 sheet: -1.12 (0.83), residues: 41 loop : -1.97 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3746 TYR 0.033 0.001 TYR A 103 PHE 0.019 0.001 PHE A2260 TRP 0.014 0.001 TRP A1632 HIS 0.011 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00256 (29636) covalent geometry : angle 0.62681 (40081) hydrogen bonds : bond 0.03188 ( 1599) hydrogen bonds : angle 4.04784 ( 4710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 0.824 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: A 38 LEU cc_start: 0.5741 (OUTLIER) cc_final: 0.5175 (tp) REVERT: A 96 MET cc_start: 0.5817 (ppp) cc_final: 0.5204 (ppp) REVERT: A 189 MET cc_start: 0.5625 (mmm) cc_final: 0.4652 (mmm) REVERT: A 336 ASN cc_start: 0.8932 (m110) cc_final: 0.8235 (p0) REVERT: A 340 TYR cc_start: 0.8309 (t80) cc_final: 0.7960 (t80) REVERT: A 603 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 620 PHE cc_start: 0.7257 (m-80) cc_final: 0.7033 (m-10) REVERT: A 632 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: A 880 MET cc_start: 0.4420 (mmt) cc_final: 0.3500 (ptt) REVERT: A 959 TYR cc_start: 0.8667 (t80) cc_final: 0.7967 (t80) REVERT: A 996 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8872 (p) REVERT: A 1108 MET cc_start: 0.9154 (tpp) cc_final: 0.8816 (mpp) REVERT: A 1342 MET cc_start: 0.9031 (tpp) cc_final: 0.8766 (mmt) REVERT: A 1402 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8730 (pp) REVERT: A 1455 CYS cc_start: 0.9389 (m) cc_final: 0.9102 (m) REVERT: A 1458 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 1557 GLU cc_start: 0.8543 (pt0) cc_final: 0.8317 (pp20) REVERT: A 1643 MET cc_start: 0.8958 (mpp) cc_final: 0.8730 (mpp) REVERT: A 1881 TYR cc_start: 0.9189 (m-80) cc_final: 0.8956 (m-80) REVERT: A 2094 MET cc_start: 0.9043 (tmm) cc_final: 0.8681 (tmm) REVERT: A 2104 MET cc_start: 0.8335 (tmm) cc_final: 0.8016 (mmt) REVERT: A 2220 MET cc_start: 0.8109 (mmm) cc_final: 0.7813 (mtt) REVERT: A 2301 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: A 2312 TYR cc_start: 0.6756 (m-10) cc_final: 0.6393 (m-10) REVERT: A 2366 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8880 (mmmt) REVERT: A 2396 LEU cc_start: 0.8799 (mm) cc_final: 0.8514 (mt) REVERT: A 2568 MET cc_start: 0.7961 (mpp) cc_final: 0.7746 (mpp) REVERT: A 2860 ASP cc_start: 0.8592 (t0) cc_final: 0.8301 (t0) REVERT: A 3173 MET cc_start: 0.9293 (mmm) cc_final: 0.8846 (tpt) REVERT: A 3643 HIS cc_start: 0.8393 (t70) cc_final: 0.8017 (t-90) REVERT: A 3644 PHE cc_start: 0.8882 (m-80) cc_final: 0.8415 (m-80) REVERT: A 3729 MET cc_start: 0.8105 (tmm) cc_final: 0.7503 (ttp) REVERT: A 3890 MET cc_start: 0.8747 (ttm) cc_final: 0.8456 (ttm) REVERT: A 3933 GLU cc_start: 0.8694 (pt0) cc_final: 0.8365 (mt-10) REVERT: A 4008 GLU cc_start: 0.7429 (tp30) cc_final: 0.7074 (tp30) outliers start: 68 outliers final: 43 residues processed: 315 average time/residue: 0.1782 time to fit residues: 92.6822 Evaluate side-chains 299 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1896 ILE Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2411 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 203 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 286 optimal weight: 0.2980 chunk 77 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1624 GLN A1817 GLN A2233 HIS ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.091593 restraints weight = 74015.083| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.90 r_work: 0.3467 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29636 Z= 0.124 Angle : 0.639 15.559 40081 Z= 0.312 Chirality : 0.041 0.249 4564 Planarity : 0.004 0.062 5087 Dihedral : 4.580 47.583 3938 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.00 % Allowed : 16.93 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3602 helix: 0.87 (0.11), residues: 2373 sheet: -1.15 (0.88), residues: 33 loop : -2.02 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1854 TYR 0.026 0.001 TYR A 103 PHE 0.019 0.001 PHE A2260 TRP 0.019 0.001 TRP A2196 HIS 0.006 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00286 (29636) covalent geometry : angle 0.63869 (40081) hydrogen bonds : bond 0.03231 ( 1599) hydrogen bonds : angle 4.05187 ( 4710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 1.115 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: A 38 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5233 (tp) REVERT: A 96 MET cc_start: 0.5755 (ppp) cc_final: 0.5144 (ppp) REVERT: A 189 MET cc_start: 0.5725 (mmm) cc_final: 0.4711 (mmm) REVERT: A 336 ASN cc_start: 0.8904 (m110) cc_final: 0.8217 (p0) REVERT: A 340 TYR cc_start: 0.8308 (t80) cc_final: 0.7921 (t80) REVERT: A 603 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8343 (tp) REVERT: A 620 PHE cc_start: 0.7240 (m-80) cc_final: 0.7002 (m-10) REVERT: A 632 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 959 TYR cc_start: 0.8633 (t80) cc_final: 0.7957 (t80) REVERT: A 996 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 1108 MET cc_start: 0.9141 (tpp) cc_final: 0.8809 (mpp) REVERT: A 1342 MET cc_start: 0.9023 (tpp) cc_final: 0.8745 (mmt) REVERT: A 1402 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8701 (pp) REVERT: A 1437 TYR cc_start: 0.7955 (m-80) cc_final: 0.7634 (t80) REVERT: A 1455 CYS cc_start: 0.9379 (m) cc_final: 0.9087 (m) REVERT: A 1458 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 1643 MET cc_start: 0.8924 (mpp) cc_final: 0.8630 (mpp) REVERT: A 1825 LEU cc_start: 0.9346 (tp) cc_final: 0.9086 (mt) REVERT: A 2094 MET cc_start: 0.9060 (tmm) cc_final: 0.8680 (tmm) REVERT: A 2104 MET cc_start: 0.8315 (tmm) cc_final: 0.8003 (mmt) REVERT: A 2129 LEU cc_start: 0.9505 (pp) cc_final: 0.9156 (mp) REVERT: A 2220 MET cc_start: 0.8085 (mmm) cc_final: 0.7780 (mtt) REVERT: A 2239 LYS cc_start: 0.9230 (mttm) cc_final: 0.8947 (mptt) REVERT: A 2301 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: A 2312 TYR cc_start: 0.6546 (m-10) cc_final: 0.6180 (m-10) REVERT: A 2366 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8786 (mmmt) REVERT: A 2396 LEU cc_start: 0.8872 (mm) cc_final: 0.8598 (mt) REVERT: A 2411 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 2565 MET cc_start: 0.7802 (tmm) cc_final: 0.6624 (tmm) REVERT: A 2568 MET cc_start: 0.7837 (mpp) cc_final: 0.7168 (mpp) REVERT: A 2860 ASP cc_start: 0.8579 (t0) cc_final: 0.8293 (t0) REVERT: A 3173 MET cc_start: 0.9260 (mmm) cc_final: 0.8844 (tpt) REVERT: A 3643 HIS cc_start: 0.8347 (t70) cc_final: 0.7981 (t-90) REVERT: A 3644 PHE cc_start: 0.8867 (m-80) cc_final: 0.8406 (m-80) REVERT: A 3729 MET cc_start: 0.8263 (tmm) cc_final: 0.7631 (ttp) REVERT: A 4008 GLU cc_start: 0.7401 (tp30) cc_final: 0.7025 (tp30) outliers start: 64 outliers final: 46 residues processed: 312 average time/residue: 0.1807 time to fit residues: 93.1126 Evaluate side-chains 305 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1896 ILE Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2411 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2789 SER Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 276 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 314 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 285 optimal weight: 0.6980 chunk 194 optimal weight: 20.0000 chunk 254 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 613 HIS ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 GLN A2233 HIS ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.122413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.090910 restraints weight = 74234.431| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.50 r_work: 0.3449 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29636 Z= 0.130 Angle : 0.650 16.484 40081 Z= 0.317 Chirality : 0.041 0.232 4564 Planarity : 0.004 0.060 5087 Dihedral : 4.569 47.101 3938 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.91 % Allowed : 17.30 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3602 helix: 0.90 (0.11), residues: 2367 sheet: -1.60 (0.79), residues: 43 loop : -2.04 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A3746 TYR 0.036 0.001 TYR A1881 PHE 0.038 0.001 PHE A1605 TRP 0.014 0.001 TRP A2196 HIS 0.009 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00299 (29636) covalent geometry : angle 0.64950 (40081) hydrogen bonds : bond 0.03258 ( 1599) hydrogen bonds : angle 4.07220 ( 4710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 1.164 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: A 38 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5228 (tp) REVERT: A 96 MET cc_start: 0.5777 (ppp) cc_final: 0.5187 (ppp) REVERT: A 189 MET cc_start: 0.5814 (mmm) cc_final: 0.4778 (mmm) REVERT: A 336 ASN cc_start: 0.8923 (m110) cc_final: 0.8233 (p0) REVERT: A 340 TYR cc_start: 0.8324 (t80) cc_final: 0.7925 (t80) REVERT: A 603 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 620 PHE cc_start: 0.7243 (m-80) cc_final: 0.6984 (m-10) REVERT: A 632 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 959 TYR cc_start: 0.8664 (t80) cc_final: 0.7977 (t80) REVERT: A 996 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8849 (p) REVERT: A 1108 MET cc_start: 0.9147 (tpp) cc_final: 0.8815 (mpp) REVERT: A 1119 LYS cc_start: 0.8829 (tppt) cc_final: 0.8425 (tppt) REVERT: A 1342 MET cc_start: 0.9040 (tpp) cc_final: 0.8743 (mmt) REVERT: A 1402 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 1437 TYR cc_start: 0.7877 (m-80) cc_final: 0.7610 (t80) REVERT: A 1455 CYS cc_start: 0.9383 (m) cc_final: 0.9091 (m) REVERT: A 1458 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 1583 MET cc_start: 0.9017 (mtt) cc_final: 0.8583 (mtp) REVERT: A 1643 MET cc_start: 0.8920 (mpp) cc_final: 0.8620 (mpp) REVERT: A 1825 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9068 (mt) REVERT: A 1880 MET cc_start: 0.8544 (mtt) cc_final: 0.8128 (mpp) REVERT: A 2094 MET cc_start: 0.9085 (tmm) cc_final: 0.8717 (tmm) REVERT: A 2155 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8499 (tm-30) REVERT: A 2220 MET cc_start: 0.8137 (mmm) cc_final: 0.7894 (mtt) REVERT: A 2239 LYS cc_start: 0.9237 (mttm) cc_final: 0.8959 (mptt) REVERT: A 2301 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: A 2312 TYR cc_start: 0.6570 (m-10) cc_final: 0.6203 (m-10) REVERT: A 2366 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8848 (mmmt) REVERT: A 2565 MET cc_start: 0.7785 (tmm) cc_final: 0.6968 (tmm) REVERT: A 2568 MET cc_start: 0.7895 (mpp) cc_final: 0.7522 (mpp) REVERT: A 2860 ASP cc_start: 0.8563 (t0) cc_final: 0.8281 (t0) REVERT: A 3111 MET cc_start: 0.8722 (mtm) cc_final: 0.8470 (mtm) REVERT: A 3173 MET cc_start: 0.9272 (mmm) cc_final: 0.8827 (tpt) REVERT: A 3613 MET cc_start: 0.8302 (ppp) cc_final: 0.8099 (ppp) REVERT: A 3643 HIS cc_start: 0.8356 (t70) cc_final: 0.7971 (t-90) REVERT: A 3644 PHE cc_start: 0.8896 (m-80) cc_final: 0.8443 (m-80) REVERT: A 3729 MET cc_start: 0.8271 (tmm) cc_final: 0.7661 (ttp) REVERT: A 4008 GLU cc_start: 0.7427 (tp30) cc_final: 0.6855 (tp30) outliers start: 61 outliers final: 49 residues processed: 298 average time/residue: 0.1852 time to fit residues: 90.3491 Evaluate side-chains 310 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1817 GLN Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1896 ILE Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2789 SER Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 359 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 331 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 360 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 244 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS A1624 GLN ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2233 HIS ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.122353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.090263 restraints weight = 73783.942| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.58 r_work: 0.3463 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29636 Z= 0.122 Angle : 0.654 15.416 40081 Z= 0.319 Chirality : 0.041 0.246 4564 Planarity : 0.004 0.060 5087 Dihedral : 4.539 46.466 3938 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.81 % Allowed : 17.58 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3602 helix: 0.94 (0.11), residues: 2366 sheet: -1.55 (0.81), residues: 43 loop : -2.02 (0.19), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3746 TYR 0.039 0.001 TYR A1881 PHE 0.026 0.001 PHE A1605 TRP 0.014 0.001 TRP A2245 HIS 0.011 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00277 (29636) covalent geometry : angle 0.65435 (40081) hydrogen bonds : bond 0.03221 ( 1599) hydrogen bonds : angle 4.05984 ( 4710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5184 (tp) REVERT: A 96 MET cc_start: 0.5781 (ppp) cc_final: 0.5188 (ppp) REVERT: A 189 MET cc_start: 0.6019 (mmm) cc_final: 0.4889 (mmm) REVERT: A 336 ASN cc_start: 0.8898 (m110) cc_final: 0.8189 (p0) REVERT: A 340 TYR cc_start: 0.8339 (t80) cc_final: 0.7894 (t80) REVERT: A 620 PHE cc_start: 0.7237 (m-80) cc_final: 0.6958 (m-10) REVERT: A 632 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 880 MET cc_start: 0.4204 (mmt) cc_final: 0.3170 (ptp) REVERT: A 959 TYR cc_start: 0.8650 (t80) cc_final: 0.7972 (t80) REVERT: A 996 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 1108 MET cc_start: 0.9152 (tpp) cc_final: 0.8826 (mpp) REVERT: A 1342 MET cc_start: 0.9036 (tpp) cc_final: 0.8746 (mmt) REVERT: A 1402 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8724 (pp) REVERT: A 1455 CYS cc_start: 0.9403 (m) cc_final: 0.9110 (m) REVERT: A 1458 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 1643 MET cc_start: 0.8900 (mpp) cc_final: 0.8604 (mpp) REVERT: A 1825 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 1880 MET cc_start: 0.8539 (mtt) cc_final: 0.8114 (mpp) REVERT: A 2094 MET cc_start: 0.9097 (tmm) cc_final: 0.8740 (tmm) REVERT: A 2155 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8530 (tm-30) REVERT: A 2220 MET cc_start: 0.8159 (mmm) cc_final: 0.7899 (mtt) REVERT: A 2301 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: A 2312 TYR cc_start: 0.6802 (m-10) cc_final: 0.6404 (m-10) REVERT: A 2366 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8847 (mmmt) REVERT: A 2565 MET cc_start: 0.7798 (tmm) cc_final: 0.6979 (tmm) REVERT: A 2568 MET cc_start: 0.7882 (mpp) cc_final: 0.7508 (mpp) REVERT: A 2860 ASP cc_start: 0.8585 (t0) cc_final: 0.8303 (t0) REVERT: A 3111 MET cc_start: 0.8669 (mtm) cc_final: 0.8414 (mtm) REVERT: A 3613 MET cc_start: 0.8288 (ppp) cc_final: 0.8077 (ppp) REVERT: A 3643 HIS cc_start: 0.8441 (t70) cc_final: 0.8056 (t-90) REVERT: A 3644 PHE cc_start: 0.8929 (m-80) cc_final: 0.8495 (m-80) REVERT: A 3729 MET cc_start: 0.8271 (tmm) cc_final: 0.7853 (ttp) REVERT: A 4008 GLU cc_start: 0.7340 (tp30) cc_final: 0.6828 (tp30) outliers start: 58 outliers final: 50 residues processed: 294 average time/residue: 0.1831 time to fit residues: 88.0330 Evaluate side-chains 305 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1896 ILE Chi-restraints excluded: chain A residue 1984 LEU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2241 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2365 ASN Chi-restraints excluded: chain A residue 2370 SER Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 3358 ARG Chi-restraints excluded: chain A residue 3522 THR Chi-restraints excluded: chain A residue 3640 PHE Chi-restraints excluded: chain A residue 3696 ARG Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3800 LEU Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4018 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 312 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 267 optimal weight: 0.0030 chunk 297 optimal weight: 0.0370 chunk 346 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 GLN A2233 HIS ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.092261 restraints weight = 74372.009| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 4.02 r_work: 0.3458 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29636 Z= 0.118 Angle : 0.645 15.448 40081 Z= 0.315 Chirality : 0.041 0.227 4564 Planarity : 0.004 0.058 5087 Dihedral : 4.505 46.528 3938 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.88 % Allowed : 17.71 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3602 helix: 0.99 (0.11), residues: 2355 sheet: -1.54 (0.81), residues: 43 loop : -1.94 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3746 TYR 0.038 0.001 TYR A1881 PHE 0.024 0.001 PHE A1605 TRP 0.014 0.001 TRP A2245 HIS 0.014 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00270 (29636) covalent geometry : angle 0.64452 (40081) hydrogen bonds : bond 0.03188 ( 1599) hydrogen bonds : angle 4.04473 ( 4710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8830.56 seconds wall clock time: 151 minutes 17.08 seconds (9077.08 seconds total)