Starting phenix.real_space_refine on Sat Mar 7 10:24:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.map" model { file = "/net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7su3_25439/03_2026/7su3_25439.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 241 5.16 5 C 26173 2.51 5 N 7007 2.21 5 O 7745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.04s 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: 41242 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 30378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3802, 30320 Classifications: {'peptide': 3802} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3641} Chain breaks: 15 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'GLU:plan': 17, 'GLN:plan1': 8, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Conformer: "B" Number of residues, atoms: 3802, 30320 Classifications: {'peptide': 3802} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 158, 'TRANS': 3641} Chain breaks: 15 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'GLU:plan': 17, 'GLN:plan1': 8, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 bond proxies already assigned to first conformer: 30875 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 496, 4009 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 27, 'TRANS': 468} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 496, 4009 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 27, 'TRANS': 468} Chain breaks: 1 bond proxies already assigned to first conformer: 4079 Chain: "C" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5354 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 383 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 70 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 70 " occ=0.50 residue: pdb=" N AARG A 257 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 257 " occ=0.50 Time building chain proxies: 14.43, per 1000 atoms: 0.35 Number of scatterers: 41242 At special positions: 0 Unit cell: (179.928, 167.433, 202.419, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 241 16.00 P 76 15.00 O 7745 8.00 N 7007 7.00 C 26173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 2.8 seconds 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9542 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 15 sheets defined 61.3% alpha, 4.7% beta 34 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 26 through 44 removed outlier: 4.144A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.750A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.697A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 120 through 138 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 148 through 162 removed outlier: 4.029A pdb=" N GLU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.641A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 4.075A pdb=" N ILE A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.604A pdb=" N LEU A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.722A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.871A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.546A pdb=" N CYS A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.747A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 386 through 397 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 423 removed outlier: 3.721A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) 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 476 removed outlier: 4.233A pdb=" N LEU A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 491 removed outlier: 4.205A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.547A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.809A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 618 through 631 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 removed outlier: 3.799A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.582A pdb=" N LEU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.706A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (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 723 through 735 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.607A 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: 3.594A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 797 removed outlier: 3.510A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 847 through 863 removed outlier: 4.060A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 875 through 881 Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.617A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.642A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.012A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix removed outlier: 3.739A pdb=" N MET A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1022 through 1041 removed outlier: 3.758A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.822A pdb=" N LYS A1051 " --> pdb=" O GLN A1048 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1052 " --> pdb=" O GLN A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1048 through 1052' Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1091 removed outlier: 3.524A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.631A pdb=" N GLU A1097 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1141 removed outlier: 3.785A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1214 Processing helix chain 'A' and resid 1216 through 1226 removed outlier: 4.512A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1273 Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1284 through 1287 Processing helix chain 'A' and resid 1289 through 1301 Processing helix chain 'A' and resid 1324 through 1352 removed outlier: 4.047A pdb=" N GLU A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1378 Processing helix chain 'A' and resid 1389 through 1406 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.602A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1434 removed outlier: 3.687A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1462 removed outlier: 4.092A pdb=" N ALA A1449 " --> pdb=" O ARG A1445 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.775A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1490 Processing helix chain 'A' and resid 1504 through 1521 removed outlier: 3.953A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.530A pdb=" N LEU A1528 " --> pdb=" O LEU A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1565 through 1574 Processing helix chain 'A' and resid 1574 through 1584 removed outlier: 3.830A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.529A pdb=" N SER A1594 " --> pdb=" O THR A1590 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A1606 " --> pdb=" O ASP A1602 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 3.735A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1630 Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.530A pdb=" N LEU A1646 " --> pdb=" O LYS A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.529A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1691 through 1693 No H-bonds generated for 'chain 'A' and resid 1691 through 1693' Processing helix chain 'A' and resid 1695 through 1699 Processing helix chain 'A' and resid 1705 through 1722 removed outlier: 3.766A pdb=" N GLU A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1753 removed outlier: 3.719A pdb=" N ASN A1738 " --> pdb=" O PRO A1734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.942A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.891A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1807 removed outlier: 3.655A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A1797 " --> pdb=" O THR A1793 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A1805 " --> pdb=" O VAL A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1822 removed outlier: 4.078A 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 1852 removed outlier: 4.257A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A1839 " --> pdb=" O ALA A1835 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1893 through 1898 Processing helix chain 'A' and resid 1911 through 1924 removed outlier: 3.591A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1956 removed outlier: 4.000A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1967 removed outlier: 3.575A pdb=" N PHE A1967 " --> pdb=" O GLN A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.983A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2134 removed outlier: 4.474A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.541A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2173 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 2252 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 2284 removed outlier: 3.762A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A2284 " --> pdb=" O VAL A2280 " (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: 3.669A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2356 removed outlier: 3.665A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2368 removed outlier: 3.832A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2375 removed outlier: 3.623A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 removed outlier: 3.648A pdb=" N LEU A2385 " --> pdb=" O ALA A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.958A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A2403 " --> pdb=" O GLU A2399 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.627A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) 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 2459 removed outlier: 3.905A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2464 removed outlier: 3.986A pdb=" N SER A2463 " --> pdb=" O GLU A2460 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A2464 " --> pdb=" O PHE A2461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2460 through 2464' Processing helix chain 'A' and resid 2466 through 2484 Processing helix chain 'A' and resid 2492 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 2516 through 2526 Processing helix chain 'A' and resid 2534 through 2542 removed outlier: 3.664A pdb=" N LEU A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2565 through 2569 removed outlier: 3.513A pdb=" N MET A2568 " --> pdb=" O MET A2565 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2764 removed outlier: 3.710A pdb=" N LYS A2755 " --> pdb=" O GLN A2751 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A2756 " --> pdb=" O LYS A2752 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A2759 " --> pdb=" O LYS A2755 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS A2762 " --> pdb=" O LYS A2758 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2819 Processing helix chain 'A' and resid 2828 through 2847 removed outlier: 3.868A pdb=" N LYS A2835 " --> pdb=" O ASN A2831 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2861 Processing helix chain 'A' and resid 2865 through 2869 Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.713A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2933 removed outlier: 3.722A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2941 removed outlier: 4.437A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.872A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2976 removed outlier: 3.702A pdb=" N GLN A2971 " --> pdb=" O GLU A2967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.543A pdb=" N LYS A2991 " --> pdb=" O THR A2987 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3017 Processing helix chain 'A' and resid 3026 through 3032 removed outlier: 3.908A pdb=" N TRP A3031 " --> pdb=" O ASN A3028 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A3032 " --> pdb=" O LYS A3029 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3040 removed outlier: 3.892A pdb=" N GLU A3038 " --> pdb=" O PRO A3034 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.700A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3073 through 3082 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.756A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3115 Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.742A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 Processing helix chain 'A' and resid 3175 through 3197 Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3251 through 3261 removed outlier: 3.747A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3267 removed outlier: 3.980A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 removed outlier: 3.577A pdb=" N LEU A3273 " --> pdb=" O ARG A3269 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3302 removed outlier: 3.666A pdb=" N THR A3299 " --> pdb=" O GLU A3295 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 3.676A pdb=" N SER A3342 " --> pdb=" O ALA A3338 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3364 removed outlier: 3.829A pdb=" N GLY A3364 " --> pdb=" O LEU A3360 " (cutoff:3.500A) Processing helix chain 'A' and resid 3372 through 3393 Processing helix chain 'A' and resid 3408 through 3426 removed outlier: 4.103A pdb=" N ALA A3412 " --> pdb=" O GLY A3408 " (cutoff:3.500A) Processing helix chain 'A' and resid 3427 through 3430 Processing helix chain 'A' and resid 3433 through 3440 Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 4.309A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3472 removed outlier: 3.703A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A3472 " --> pdb=" O LEU A3468 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 3.908A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.800A pdb=" N VAL A3503 " --> pdb=" O ILE A3499 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3529 through 3537 Processing helix chain 'A' and resid 3547 through 3562 removed outlier: 3.807A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3580 through 3597 removed outlier: 3.544A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3618 removed outlier: 4.304A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3628 through 3637 removed outlier: 3.844A pdb=" N THR A3635 " --> pdb=" O LYS A3631 " (cutoff:3.500A) Processing helix chain 'A' and resid 3638 through 3640 No H-bonds generated for 'chain 'A' and resid 3638 through 3640' Processing helix chain 'A' and resid 3655 through 3671 removed outlier: 4.163A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) Processing helix chain 'A' and resid 3679 through 3684 removed outlier: 3.562A pdb=" N CYS A3683 " --> pdb=" O ASN A3679 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3775 Processing helix chain 'A' and resid 3778 through 3785 removed outlier: 3.673A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.915A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 4.342A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3860 removed outlier: 4.024A pdb=" N MET A3856 " --> pdb=" O VAL A3852 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3876 removed outlier: 3.752A pdb=" N SER A3870 " --> pdb=" O GLU A3866 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3891 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.658A pdb=" N ILE A3913 " --> pdb=" O ALA A3909 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3992 Processing helix chain 'A' and resid 3995 through 4002 removed outlier: 4.018A pdb=" N THR A3999 " --> pdb=" O PRO A3995 " (cutoff:3.500A) Processing helix chain 'A' and resid 4002 through 4008 removed outlier: 3.978A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4024 removed outlier: 4.557A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A4024 " --> pdb=" O MET A4020 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4030 removed outlier: 3.675A pdb=" N GLN A4029 " --> pdb=" O SER A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4082 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.824A pdb=" N VAL A4104 " --> pdb=" O GLU A4100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A4109 " --> pdb=" O LYS A4105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A4110 " --> pdb=" O CYS A4106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A4111 " --> pdb=" O LEU A4107 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 removed outlier: 3.503A pdb=" N GLU A4125 " --> pdb=" O GLU A4122 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.194A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.697A pdb=" N LEU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.820A pdb=" N GLN B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.720A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 377 through 390 Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.595A pdb=" N ALA B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 469 " --> pdb=" O ILE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'C' and resid 29 through 48 removed outlier: 3.785A pdb=" N ARG C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 removed outlier: 3.850A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.964A pdb=" N LEU C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.724A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 219 through 222 removed outlier: 3.607A pdb=" N ASP C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 222' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.525A pdb=" N ARG C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.505A pdb=" N PHE C 355 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 387 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.616A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 492 " --> pdb=" O GLN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.902A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 Processing helix chain 'C' and resid 526 through 537 removed outlier: 3.917A pdb=" N THR C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 596 through 604 Processing helix chain 'C' and resid 610 through 626 Processing helix chain 'C' and resid 628 through 648 removed outlier: 4.172A pdb=" N PHE C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 669 Processing helix chain 'C' and resid 671 through 682 Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 725 through 729 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 1993 through 1994 Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 5.829A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 5.829A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.644A pdb=" N TYR B 88 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.716A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 431 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AB3, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.661A pdb=" N ILE C 540 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 419 through 420 removed outlier: 6.655A pdb=" N GLU B 419 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.642A pdb=" N THR C 78 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG C 130 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 247 through 251 removed outlier: 6.437A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS C 418 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 411 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 341 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) 1997 hydrogen bonds defined for protein. 5881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 15.96 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7270 1.32 - 1.45: 10842 1.45 - 1.58: 23590 1.58 - 1.70: 143 1.70 - 1.83: 382 Bond restraints: 42227 Sorted by residual: bond pdb=" C4 ATP A4201 " pdb=" C5 ATP A4201 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C5 ATP A4201 " pdb=" C6 ATP A4201 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C8 ATP A4201 " pdb=" N7 ATP A4201 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C HIS A1721 " pdb=" N PHE A1722 " ideal model delta sigma weight residual 1.329 1.248 0.081 1.86e-02 2.89e+03 1.87e+01 bond pdb=" C5 ATP A4201 " pdb=" N7 ATP A4201 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.72e+01 ... (remaining 42222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 56580 3.89 - 7.78: 673 7.78 - 11.67: 92 11.67 - 15.56: 13 15.56 - 19.45: 2 Bond angle restraints: 57360 Sorted by residual: angle pdb=" PB ATP A4201 " pdb=" O3B ATP A4201 " pdb=" PG ATP A4201 " ideal model delta sigma weight residual 139.87 120.42 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP A4201 " pdb=" O3A ATP A4201 " pdb=" PB ATP A4201 " ideal model delta sigma weight residual 136.83 120.50 16.33 1.00e+00 1.00e+00 2.67e+02 angle pdb=" C5 ATP A4201 " pdb=" C4 ATP A4201 " pdb=" N3 ATP A4201 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.51e+01 angle pdb=" N3 ATP A4201 " pdb=" C4 ATP A4201 " pdb=" N9 ATP A4201 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 angle pdb=" C VAL A 8 " pdb=" N ARG A 9 " pdb=" CA ARG A 9 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 ... (remaining 57355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 24806 35.98 - 71.97: 791 71.97 - 107.95: 75 107.95 - 143.93: 3 143.93 - 179.91: 3 Dihedral angle restraints: 25678 sinusoidal: 11034 harmonic: 14644 Sorted by residual: dihedral pdb=" CD BARG B 363 " pdb=" NE BARG B 363 " pdb=" CZ BARG B 363 " pdb=" NH1BARG B 363 " ideal model delta sinusoidal sigma weight residual 0.00 179.91 -179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA PHE A3694 " pdb=" C PHE A3694 " pdb=" N LEU A3695 " pdb=" CA LEU A3695 " ideal model delta harmonic sigma weight residual 180.00 133.87 46.13 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA ASP A3563 " pdb=" C ASP A3563 " pdb=" N GLN A3564 " pdb=" CA GLN A3564 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 25675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.980: 6482 0.980 - 1.960: 0 1.960 - 2.941: 0 2.941 - 3.921: 0 3.921 - 4.901: 3 Chirality restraints: 6485 Sorted by residual: chirality pdb=" C2 IHP B 701 " pdb=" C1 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O12 IHP B 701 " both_signs ideal model delta sigma weight residual False -2.52 2.38 -4.90 2.00e-01 2.50e+01 6.01e+02 chirality pdb=" C4 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" C5 IHP B 701 " pdb=" O14 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.48 -2.35 4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C6 IHP B 701 " pdb=" O11 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.77 2.00e-01 2.50e+01 5.69e+02 ... (remaining 6482 not shown) Planarity restraints: 7047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG A 9 " 0.078 2.00e-02 2.50e+03 pdb=" O ARG A 9 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS A 10 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A3893 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A3894 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A3894 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A3894 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASN A 356 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN A 356 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 357 " 0.020 2.00e-02 2.50e+03 ... (remaining 7044 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4905 2.74 - 3.28: 38556 3.28 - 3.82: 68546 3.82 - 4.36: 82726 4.36 - 4.90: 140296 Nonbonded interactions: 335029 Sorted by model distance: nonbonded pdb=" OH TYR A2546 " pdb=" OE2 GLU A2551 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 366 " pdb=" OE2 GLU A 387 " model vdw 2.246 3.040 nonbonded pdb=" O SER A1753 " pdb=" OG SER A1753 " model vdw 2.256 3.040 nonbonded pdb=" O TYR A1560 " pdb=" OG SER A1564 " model vdw 2.264 3.040 nonbonded pdb=" O SER A3731 " pdb=" OG SER A3731 " model vdw 2.280 3.040 ... (remaining 335024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 57.270 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.010 0.120 42227 Z= 0.427 Angle : 1.149 19.446 57360 Z= 0.619 Chirality : 0.122 4.901 6485 Planarity : 0.008 0.095 7047 Dihedral : 17.553 179.913 16136 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.45 % Favored : 90.31 % Rotamer: Outliers : 0.29 % Allowed : 8.47 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.15 % 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: -4.26 (0.09), residues: 4933 helix: -2.50 (0.07), residues: 2859 sheet: -1.46 (0.34), residues: 217 loop : -3.37 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A2899 TYR 0.031 0.003 TYR A3082 PHE 0.050 0.003 PHE A1923 TRP 0.023 0.003 TRP A 813 HIS 0.016 0.002 HIS A3915 Details of bonding type rmsd covalent geometry : bond 0.01018 (42227) covalent geometry : angle 1.14893 (57360) hydrogen bonds : bond 0.13977 ( 2080) hydrogen bonds : angle 6.43531 ( 6049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 469 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.8572 (ttm) cc_final: 0.8336 (ttm) REVERT: A 1353 PRO cc_start: 0.6741 (Cg_endo) cc_final: 0.6512 (Cg_exo) REVERT: A 1378 GLU cc_start: 0.7172 (tp30) cc_final: 0.6902 (tp30) REVERT: A 1719 VAL cc_start: 0.8220 (m) cc_final: 0.7946 (t) REVERT: A 1739 TYR cc_start: 0.7921 (t80) cc_final: 0.7568 (t80) REVERT: A 1814 PHE cc_start: 0.7107 (t80) cc_final: 0.6896 (t80) REVERT: A 2294 ILE cc_start: 0.7266 (mm) cc_final: 0.6648 (mm) REVERT: A 2742 MET cc_start: 0.6837 (mmt) cc_final: 0.6600 (mmt) REVERT: A 2772 TYR cc_start: 0.7332 (m-80) cc_final: 0.7037 (m-80) REVERT: A 3104 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7119 (tp40) REVERT: B 131 PHE cc_start: 0.7922 (t80) cc_final: 0.7566 (t80) REVERT: B 134 MET cc_start: 0.6033 (ppp) cc_final: 0.5094 (ppp) REVERT: B 135 MET cc_start: 0.5262 (tpp) cc_final: 0.4902 (mmm) REVERT: B 530 TYR cc_start: 0.5131 (t80) cc_final: 0.4479 (t80) REVERT: C 14 MET cc_start: 0.4957 (ttm) cc_final: 0.4730 (tmm) REVERT: C 183 PHE cc_start: 0.4564 (t80) cc_final: 0.4136 (t80) outliers start: 9 outliers final: 5 residues processed: 477 average time/residue: 0.2634 time to fit residues: 205.1997 Evaluate side-chains 370 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 365 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 HIS A1175 HIS A1654 GLN A1859 ASN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2183 HIS A2390 HIS A2475 ASN A2574 ASN A2736 GLN A2777 HIS A3384 HIS A3430 ASN A3697 ASN B 68 GLN B 152 ASN C 43 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 547 GLN C 627 ASN C 680 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.125986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100602 restraints weight = 184426.751| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.93 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42227 Z= 0.147 Angle : 0.664 14.436 57360 Z= 0.343 Chirality : 0.042 0.387 6485 Planarity : 0.005 0.080 7047 Dihedral : 13.714 179.914 6183 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 1.00 % Allowed : 10.75 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.11), residues: 4933 helix: -0.66 (0.09), residues: 2876 sheet: -0.97 (0.34), residues: 223 loop : -2.99 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2596 TYR 0.024 0.001 TYR A2288 PHE 0.028 0.001 PHE A1553 TRP 0.016 0.001 TRP A 813 HIS 0.006 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00336 (42227) covalent geometry : angle 0.66411 (57360) hydrogen bonds : bond 0.04298 ( 2080) hydrogen bonds : angle 4.62717 ( 6049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 415 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 1197 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8379 (pp) REVERT: A 1353 PRO cc_start: 0.6876 (Cg_endo) cc_final: 0.6557 (Cg_exo) REVERT: A 1467 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8927 (mp) REVERT: A 1665 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.4929 (p-80) REVERT: A 1739 TYR cc_start: 0.8018 (t80) cc_final: 0.7643 (t80) REVERT: A 1946 ASN cc_start: 0.7730 (t0) cc_final: 0.7527 (t0) REVERT: A 1962 TYR cc_start: 0.6846 (m-80) cc_final: 0.6641 (m-80) REVERT: A 2083 LEU cc_start: 0.7619 (pt) cc_final: 0.7368 (pt) REVERT: A 2294 ILE cc_start: 0.6848 (mm) cc_final: 0.6495 (mm) REVERT: A 2596 ARG cc_start: 0.5265 (ttt90) cc_final: 0.5043 (tpt-90) REVERT: A 2860 ASP cc_start: 0.8251 (t70) cc_final: 0.7910 (t0) REVERT: A 3429 GLU cc_start: 0.6198 (mp0) cc_final: 0.5983 (mp0) REVERT: A 3474 ARG cc_start: 0.6131 (mtp85) cc_final: 0.5888 (mtp85) REVERT: A 3654 MET cc_start: 0.5371 (ptm) cc_final: 0.5074 (ttt) REVERT: A 4019 LYS cc_start: 0.6623 (mtmt) cc_final: 0.6365 (mtmt) REVERT: B 134 MET cc_start: 0.6204 (ppp) cc_final: 0.5539 (ppp) REVERT: B 468 LYS cc_start: 0.7530 (tppt) cc_final: 0.7284 (tppt) REVERT: B 517 ARG cc_start: 0.7024 (tpt170) cc_final: 0.6797 (ttt90) REVERT: B 530 TYR cc_start: 0.4909 (t80) cc_final: 0.4369 (t80) REVERT: C 14 MET cc_start: 0.5041 (ttm) cc_final: 0.4620 (tmm) REVERT: C 183 PHE cc_start: 0.4346 (t80) cc_final: 0.3886 (t80) REVERT: C 611 GLU cc_start: 0.2814 (OUTLIER) cc_final: 0.2250 (pt0) outliers start: 40 outliers final: 18 residues processed: 445 average time/residue: 0.2517 time to fit residues: 186.5919 Evaluate side-chains 382 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 360 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2492 ASP Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 280 optimal weight: 1.9990 chunk 474 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 236 optimal weight: 0.5980 chunk 402 optimal weight: 0.1980 chunk 447 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 466 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 GLN A1071 ASN A1476 HIS A1716 GLN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A3783 GLN A4015 ASN C 627 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100604 restraints weight = 129623.405| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.02 r_work: 0.3099 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 42227 Z= 0.118 Angle : 0.593 9.070 57360 Z= 0.307 Chirality : 0.040 0.246 6485 Planarity : 0.005 0.074 7047 Dihedral : 13.346 179.351 6182 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 1.15 % Allowed : 12.36 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -1.37 (0.12), residues: 4933 helix: 0.19 (0.10), residues: 2908 sheet: -0.69 (0.35), residues: 224 loop : -2.80 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2596 TYR 0.019 0.001 TYR A2288 PHE 0.036 0.001 PHE A3554 TRP 0.013 0.001 TRP A1256 HIS 0.006 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00263 (42227) covalent geometry : angle 0.59339 (57360) hydrogen bonds : bond 0.03535 ( 2080) hydrogen bonds : angle 4.24539 ( 6049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 406 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 395 MET cc_start: 0.8757 (ttm) cc_final: 0.8456 (ttm) REVERT: A 878 GLU cc_start: 0.6540 (pt0) cc_final: 0.5756 (tp30) REVERT: A 1197 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8396 (pp) REVERT: A 1353 PRO cc_start: 0.6662 (Cg_endo) cc_final: 0.6259 (Cg_exo) REVERT: A 1359 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7637 (pp) REVERT: A 1467 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8975 (mp) REVERT: A 1665 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.4984 (p-80) REVERT: A 1739 TYR cc_start: 0.8093 (t80) cc_final: 0.7788 (t80) REVERT: A 1812 LEU cc_start: 0.7602 (mt) cc_final: 0.7397 (mt) REVERT: A 1989 ASN cc_start: 0.7525 (m-40) cc_final: 0.7320 (m110) REVERT: A 2083 LEU cc_start: 0.7513 (pt) cc_final: 0.7259 (pt) REVERT: A 2294 ILE cc_start: 0.7044 (mm) cc_final: 0.6533 (mm) REVERT: A 2295 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: A 2860 ASP cc_start: 0.8821 (t70) cc_final: 0.8544 (t0) REVERT: A 3044 MET cc_start: 0.8746 (tmm) cc_final: 0.8520 (ttp) REVERT: A 3654 MET cc_start: 0.5611 (ptm) cc_final: 0.5244 (ttm) REVERT: A 3846 MET cc_start: 0.7622 (mmp) cc_final: 0.7287 (mmp) REVERT: B 134 MET cc_start: 0.6168 (ppp) cc_final: 0.5462 (ppp) REVERT: B 192 ASP cc_start: 0.7389 (m-30) cc_final: 0.7152 (m-30) REVERT: B 468 LYS cc_start: 0.7761 (tppt) cc_final: 0.7382 (tptt) REVERT: B 517 ARG cc_start: 0.7148 (tpt170) cc_final: 0.6871 (ttt90) REVERT: B 521 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4185 (tt) REVERT: B 530 TYR cc_start: 0.4662 (t80) cc_final: 0.4234 (t80) REVERT: C 14 MET cc_start: 0.4953 (ttm) cc_final: 0.4526 (tmm) REVERT: C 183 PHE cc_start: 0.4083 (t80) cc_final: 0.3652 (t80) REVERT: C 320 ILE cc_start: 0.8572 (mt) cc_final: 0.8331 (mt) REVERT: C 611 GLU cc_start: 0.2560 (OUTLIER) cc_final: 0.2124 (pt0) outliers start: 47 outliers final: 24 residues processed: 441 average time/residue: 0.2462 time to fit residues: 182.3227 Evaluate side-chains 390 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 359 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2492 ASP Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 480 optimal weight: 8.9990 chunk 383 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 489 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 358 optimal weight: 0.8980 chunk 386 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 355 optimal weight: 0.5980 chunk 448 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 GLN A1476 HIS A1716 GLN A1974 ASN B 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101504 restraints weight = 166973.728| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.33 r_work: 0.3019 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 42227 Z= 0.120 Angle : 0.578 10.366 57360 Z= 0.298 Chirality : 0.040 0.270 6485 Planarity : 0.004 0.071 7047 Dihedral : 13.272 179.930 6182 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 1.52 % Allowed : 13.27 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.94 (0.12), residues: 4933 helix: 0.55 (0.10), residues: 2904 sheet: -0.57 (0.34), residues: 232 loop : -2.65 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3474 TYR 0.018 0.001 TYR A2288 PHE 0.047 0.001 PHE A1553 TRP 0.012 0.001 TRP A2125 HIS 0.004 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00273 (42227) covalent geometry : angle 0.57760 (57360) hydrogen bonds : bond 0.03393 ( 2080) hydrogen bonds : angle 4.12001 ( 6049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 383 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8460 (p90) REVERT: A 878 GLU cc_start: 0.6656 (pt0) cc_final: 0.5824 (tp30) REVERT: A 1197 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 1353 PRO cc_start: 0.6695 (Cg_endo) cc_final: 0.6290 (Cg_exo) REVERT: A 1359 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7796 (pp) REVERT: A 1467 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9019 (mp) REVERT: A 1526 GLU cc_start: 0.8140 (mp0) cc_final: 0.7912 (mt-10) REVERT: A 1665 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.4902 (p-80) REVERT: A 1739 TYR cc_start: 0.8180 (t80) cc_final: 0.7833 (t80) REVERT: A 1989 ASN cc_start: 0.7696 (m-40) cc_final: 0.7447 (m110) REVERT: A 2083 LEU cc_start: 0.7496 (pt) cc_final: 0.7227 (pt) REVERT: A 2294 ILE cc_start: 0.7094 (mm) cc_final: 0.6609 (mm) REVERT: A 2295 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: A 2860 ASP cc_start: 0.9031 (t70) cc_final: 0.8751 (t0) REVERT: A 2899 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6905 (ptt180) REVERT: A 3044 MET cc_start: 0.8890 (tmm) cc_final: 0.8648 (ttp) REVERT: A 3654 MET cc_start: 0.5568 (ptm) cc_final: 0.5221 (ttm) REVERT: A 4006 VAL cc_start: 0.7917 (p) cc_final: 0.7672 (p) REVERT: A 4101 GLU cc_start: 0.7905 (mp0) cc_final: 0.7640 (mp0) REVERT: B 134 MET cc_start: 0.6194 (ppp) cc_final: 0.5492 (ppp) REVERT: B 445 LYS cc_start: 0.7638 (mmmt) cc_final: 0.6582 (mtpt) REVERT: B 468 LYS cc_start: 0.7777 (tppt) cc_final: 0.7357 (tptt) REVERT: B 517 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6884 (ttt90) REVERT: B 521 LEU cc_start: 0.4557 (OUTLIER) cc_final: 0.4183 (tt) REVERT: B 530 TYR cc_start: 0.4532 (t80) cc_final: 0.4162 (t80) REVERT: C 14 MET cc_start: 0.4991 (ttm) cc_final: 0.4513 (tmm) REVERT: C 20 MET cc_start: 0.3780 (tpt) cc_final: 0.3293 (tpt) REVERT: C 183 PHE cc_start: 0.4087 (t80) cc_final: 0.3611 (t80) REVERT: C 320 ILE cc_start: 0.8582 (mt) cc_final: 0.8352 (mt) REVERT: C 611 GLU cc_start: 0.2498 (OUTLIER) cc_final: 0.2094 (pt0) outliers start: 62 outliers final: 38 residues processed: 430 average time/residue: 0.2445 time to fit residues: 177.4960 Evaluate side-chains 408 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2295 GLN Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2605 MET Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 82 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 267 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 445 optimal weight: 0.0980 chunk 269 optimal weight: 0.0370 chunk 100 optimal weight: 0.6980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A1476 HIS A1716 GLN A1932 GLN C 104 GLN C 619 HIS C 627 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103666 restraints weight = 164679.398| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.17 r_work: 0.3068 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 42227 Z= 0.103 Angle : 0.553 11.698 57360 Z= 0.284 Chirality : 0.039 0.230 6485 Planarity : 0.004 0.067 7047 Dihedral : 13.014 179.588 6182 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.87 % Favored : 93.09 % Rotamer: Outliers : 1.56 % Allowed : 13.83 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.53 (0.12), residues: 4933 helix: 0.90 (0.10), residues: 2892 sheet: -0.37 (0.35), residues: 228 loop : -2.51 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3593 TYR 0.015 0.001 TYR A2288 PHE 0.043 0.001 PHE C 477 TRP 0.013 0.001 TRP A1356 HIS 0.004 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00223 (42227) covalent geometry : angle 0.55335 (57360) hydrogen bonds : bond 0.02998 ( 2080) hydrogen bonds : angle 3.98355 ( 6049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 425 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 MET cc_start: 0.5141 (mtt) cc_final: 0.4923 (mtm) REVERT: A 788 TYR cc_start: 0.8148 (m-80) cc_final: 0.7736 (m-80) REVERT: A 878 GLU cc_start: 0.6599 (pt0) cc_final: 0.5770 (tp30) REVERT: A 958 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: A 1118 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 1197 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 1359 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7761 (pp) REVERT: A 1467 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9013 (mp) REVERT: A 1526 GLU cc_start: 0.8216 (mp0) cc_final: 0.7984 (mt-10) REVERT: A 1640 GLU cc_start: 0.8215 (pm20) cc_final: 0.7921 (pm20) REVERT: A 1665 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.4901 (p-80) REVERT: A 1739 TYR cc_start: 0.8107 (t80) cc_final: 0.7790 (t80) REVERT: A 1985 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7453 (mmtp) REVERT: A 1989 ASN cc_start: 0.7641 (m-40) cc_final: 0.7402 (m110) REVERT: A 2083 LEU cc_start: 0.7334 (pt) cc_final: 0.7055 (pt) REVERT: A 2294 ILE cc_start: 0.7058 (mm) cc_final: 0.6646 (mm) REVERT: A 2860 ASP cc_start: 0.9013 (t70) cc_final: 0.8752 (t0) REVERT: A 3085 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: A 3123 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: A 3654 MET cc_start: 0.5650 (ptm) cc_final: 0.5320 (ttm) REVERT: A 4006 VAL cc_start: 0.7888 (p) cc_final: 0.7669 (p) REVERT: A 4101 GLU cc_start: 0.7894 (mp0) cc_final: 0.7691 (mp0) REVERT: B 134 MET cc_start: 0.6125 (ppp) cc_final: 0.5415 (ppp) REVERT: B 445 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6525 (mtpt) REVERT: B 468 LYS cc_start: 0.7809 (tppt) cc_final: 0.7347 (tptt) REVERT: B 473 TYR cc_start: 0.6980 (t80) cc_final: 0.6587 (t80) REVERT: B 517 ARG cc_start: 0.7177 (tpt170) cc_final: 0.6877 (ttt90) REVERT: B 530 TYR cc_start: 0.4493 (t80) cc_final: 0.4096 (t80) REVERT: C 14 MET cc_start: 0.4853 (ttm) cc_final: 0.4427 (tmm) REVERT: C 40 MET cc_start: 0.7160 (ttp) cc_final: 0.6882 (ttt) REVERT: C 183 PHE cc_start: 0.4118 (t80) cc_final: 0.3649 (t80) REVERT: C 320 ILE cc_start: 0.8549 (mt) cc_final: 0.8309 (mt) REVERT: C 611 GLU cc_start: 0.2372 (OUTLIER) cc_final: 0.1953 (pt0) REVERT: C 625 ASP cc_start: 0.6113 (t0) cc_final: 0.5873 (t0) REVERT: C 670 GLN cc_start: 0.3335 (OUTLIER) cc_final: 0.2393 (pp30) outliers start: 64 outliers final: 33 residues processed: 475 average time/residue: 0.2485 time to fit residues: 197.2701 Evaluate side-chains 417 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3085 GLU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3293 CYS Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 13 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 450 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 403 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 289 ASN A1716 GLN A1946 ASN B 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100844 restraints weight = 171303.025| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.48 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 42227 Z= 0.146 Angle : 0.595 10.503 57360 Z= 0.304 Chirality : 0.041 0.245 6485 Planarity : 0.004 0.067 7047 Dihedral : 13.158 179.966 6182 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.60 % Favored : 92.36 % Rotamer: Outliers : 1.83 % Allowed : 14.29 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: -0.51 (0.12), residues: 4933 helix: 0.89 (0.10), residues: 2898 sheet: -0.41 (0.35), residues: 233 loop : -2.46 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2254 TYR 0.016 0.001 TYR A1945 PHE 0.032 0.001 PHE A3554 TRP 0.012 0.001 TRP A 813 HIS 0.005 0.001 HIS A3915 Details of bonding type rmsd covalent geometry : bond 0.00345 (42227) covalent geometry : angle 0.59464 (57360) hydrogen bonds : bond 0.03479 ( 2080) hydrogen bonds : angle 4.04126 ( 6049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 381 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 878 GLU cc_start: 0.6635 (pt0) cc_final: 0.5929 (tp30) REVERT: A 1118 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: A 1197 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 1467 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 1665 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5022 (p-80) REVERT: A 1739 TYR cc_start: 0.7972 (t80) cc_final: 0.7615 (t80) REVERT: A 1985 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7435 (mmtp) REVERT: A 2083 LEU cc_start: 0.7475 (pt) cc_final: 0.7217 (pt) REVERT: A 2294 ILE cc_start: 0.7000 (mm) cc_final: 0.6577 (mm) REVERT: A 2860 ASP cc_start: 0.8261 (t70) cc_final: 0.8022 (t0) REVERT: A 3123 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: A 3383 GLN cc_start: 0.8266 (tt0) cc_final: 0.7991 (pt0) REVERT: A 4006 VAL cc_start: 0.7770 (p) cc_final: 0.7547 (p) REVERT: B 134 MET cc_start: 0.6032 (ppp) cc_final: 0.5363 (ppp) REVERT: B 468 LYS cc_start: 0.7713 (tppt) cc_final: 0.7285 (tptt) REVERT: B 530 TYR cc_start: 0.4811 (t80) cc_final: 0.4387 (t80) REVERT: C 14 MET cc_start: 0.4792 (ttm) cc_final: 0.4556 (tmm) REVERT: C 40 MET cc_start: 0.7058 (ttp) cc_final: 0.6805 (ttt) REVERT: C 183 PHE cc_start: 0.4500 (t80) cc_final: 0.4121 (t80) REVERT: C 320 ILE cc_start: 0.8383 (mt) cc_final: 0.8146 (mt) REVERT: C 611 GLU cc_start: 0.2857 (OUTLIER) cc_final: 0.2216 (pt0) REVERT: C 625 ASP cc_start: 0.6272 (t0) cc_final: 0.6071 (t0) REVERT: C 670 GLN cc_start: 0.3120 (OUTLIER) cc_final: 0.2324 (pp30) outliers start: 76 outliers final: 50 residues processed: 439 average time/residue: 0.2373 time to fit residues: 176.7011 Evaluate side-chains 417 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 360 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1946 ASN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 687 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 313 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 425 optimal weight: 8.9990 chunk 273 optimal weight: 0.0970 chunk 367 optimal weight: 3.9990 chunk 482 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 244 optimal weight: 0.0040 chunk 412 optimal weight: 0.6980 chunk 404 optimal weight: 0.0870 chunk 314 optimal weight: 0.8980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1716 GLN A1946 ASN A1989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103365 restraints weight = 159525.493| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.05 r_work: 0.3066 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 42227 Z= 0.104 Angle : 0.562 11.774 57360 Z= 0.287 Chirality : 0.039 0.226 6485 Planarity : 0.004 0.064 7047 Dihedral : 12.923 179.550 6182 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.73 % Favored : 93.23 % Rotamer: Outliers : 1.70 % Allowed : 14.58 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.26 (0.12), residues: 4933 helix: 1.10 (0.10), residues: 2911 sheet: -0.26 (0.35), residues: 229 loop : -2.39 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2254 TYR 0.014 0.001 TYR A1945 PHE 0.035 0.001 PHE A3554 TRP 0.011 0.001 TRP A3916 HIS 0.004 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00227 (42227) covalent geometry : angle 0.56179 (57360) hydrogen bonds : bond 0.02987 ( 2080) hydrogen bonds : angle 3.93121 ( 6049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 878 GLU cc_start: 0.6544 (pt0) cc_final: 0.5751 (tp30) REVERT: A 958 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7291 (mtt) REVERT: A 1118 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: A 1197 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 1467 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9012 (mp) REVERT: A 1665 HIS cc_start: 0.6773 (OUTLIER) cc_final: 0.4911 (p-80) REVERT: A 1739 TYR cc_start: 0.8123 (t80) cc_final: 0.7814 (t80) REVERT: A 1946 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: A 1989 ASN cc_start: 0.7672 (m-40) cc_final: 0.7428 (m110) REVERT: A 2083 LEU cc_start: 0.7318 (pt) cc_final: 0.7069 (pt) REVERT: A 2294 ILE cc_start: 0.7260 (mm) cc_final: 0.6767 (mm) REVERT: A 2860 ASP cc_start: 0.9046 (t70) cc_final: 0.8785 (t0) REVERT: A 3085 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: A 3383 GLN cc_start: 0.8391 (tt0) cc_final: 0.8139 (pt0) REVERT: A 4006 VAL cc_start: 0.7867 (p) cc_final: 0.7664 (p) REVERT: B 134 MET cc_start: 0.6129 (ppp) cc_final: 0.5509 (ppp) REVERT: B 473 TYR cc_start: 0.6860 (t80) cc_final: 0.6573 (t80) REVERT: B 530 TYR cc_start: 0.4492 (t80) cc_final: 0.4132 (t80) REVERT: C 14 MET cc_start: 0.4810 (ttm) cc_final: 0.4355 (tmm) REVERT: C 24 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.4602 (tp) REVERT: C 40 MET cc_start: 0.7220 (ttp) cc_final: 0.6937 (ttt) REVERT: C 59 PHE cc_start: 0.4782 (p90) cc_final: 0.4462 (p90) REVERT: C 183 PHE cc_start: 0.4109 (t80) cc_final: 0.3605 (t80) REVERT: C 496 HIS cc_start: 0.7125 (t-90) cc_final: 0.6618 (t70) REVERT: C 611 GLU cc_start: 0.2288 (OUTLIER) cc_final: 0.1844 (pt0) REVERT: C 670 GLN cc_start: 0.3408 (OUTLIER) cc_final: 0.2405 (pp30) outliers start: 70 outliers final: 50 residues processed: 451 average time/residue: 0.2410 time to fit residues: 184.7292 Evaluate side-chains 437 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 376 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain A residue 1946 ASN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3085 GLU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 687 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 238 optimal weight: 0.0010 chunk 19 optimal weight: 5.9990 chunk 444 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 373 optimal weight: 0.9990 chunk 352 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100825 restraints weight = 147773.533| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.67 r_work: 0.3038 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 42227 Z= 0.145 Angle : 0.597 14.002 57360 Z= 0.304 Chirality : 0.041 0.224 6485 Planarity : 0.004 0.065 7047 Dihedral : 13.048 179.976 6182 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.54 % Favored : 92.42 % Rotamer: Outliers : 1.74 % Allowed : 14.83 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.32 (0.12), residues: 4933 helix: 1.05 (0.10), residues: 2903 sheet: -0.29 (0.35), residues: 233 loop : -2.39 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3380 TYR 0.016 0.001 TYR A2288 PHE 0.030 0.002 PHE A3554 TRP 0.011 0.001 TRP A 813 HIS 0.005 0.001 HIS A3915 Details of bonding type rmsd covalent geometry : bond 0.00342 (42227) covalent geometry : angle 0.59670 (57360) hydrogen bonds : bond 0.03409 ( 2080) hydrogen bonds : angle 3.99889 ( 6049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 371 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 GLU cc_start: 0.6565 (pt0) cc_final: 0.5769 (tp30) REVERT: A 1118 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 1197 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8459 (pp) REVERT: A 1467 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9029 (mp) REVERT: A 1665 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.4963 (p-80) REVERT: A 1739 TYR cc_start: 0.8150 (t80) cc_final: 0.7797 (t80) REVERT: A 1989 ASN cc_start: 0.7640 (m-40) cc_final: 0.7384 (m110) REVERT: A 2083 LEU cc_start: 0.7418 (pt) cc_final: 0.7164 (pt) REVERT: A 2294 ILE cc_start: 0.7299 (mm) cc_final: 0.6776 (mm) REVERT: A 2860 ASP cc_start: 0.8980 (t70) cc_final: 0.8726 (t0) REVERT: A 3085 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: A 3123 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 3383 GLN cc_start: 0.8417 (tt0) cc_final: 0.8171 (pt0) REVERT: A 3588 TRP cc_start: 0.7267 (t60) cc_final: 0.6792 (t60) REVERT: A 4006 VAL cc_start: 0.7859 (p) cc_final: 0.7643 (p) REVERT: B 134 MET cc_start: 0.6064 (ppp) cc_final: 0.5378 (ppp) REVERT: B 473 TYR cc_start: 0.6969 (t80) cc_final: 0.6462 (t80) REVERT: B 530 TYR cc_start: 0.4573 (t80) cc_final: 0.4272 (t80) REVERT: C 14 MET cc_start: 0.4965 (ttm) cc_final: 0.4482 (tmm) REVERT: C 24 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.4603 (tp) REVERT: C 40 MET cc_start: 0.7217 (ttp) cc_final: 0.6970 (ttt) REVERT: C 183 PHE cc_start: 0.4136 (t80) cc_final: 0.3715 (t80) REVERT: C 496 HIS cc_start: 0.7121 (t-90) cc_final: 0.6578 (t70) REVERT: C 611 GLU cc_start: 0.2406 (OUTLIER) cc_final: 0.1894 (pt0) REVERT: C 670 GLN cc_start: 0.3302 (OUTLIER) cc_final: 0.2324 (pp30) outliers start: 72 outliers final: 52 residues processed: 430 average time/residue: 0.2427 time to fit residues: 177.4176 Evaluate side-chains 424 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 363 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain A residue 1946 ASN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3085 GLU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 687 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 154 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 418 optimal weight: 6.9990 chunk 291 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1716 GLN A1946 ASN B 152 ASN B 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101686 restraints weight = 145927.199| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.68 r_work: 0.3064 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 42227 Z= 0.117 Angle : 0.579 14.165 57360 Z= 0.294 Chirality : 0.040 0.219 6485 Planarity : 0.004 0.064 7047 Dihedral : 12.978 179.823 6182 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.01 % Favored : 92.95 % Rotamer: Outliers : 1.68 % Allowed : 15.01 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.22 (0.12), residues: 4933 helix: 1.12 (0.10), residues: 2912 sheet: -0.23 (0.35), residues: 237 loop : -2.36 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3380 TYR 0.022 0.001 TYR A1945 PHE 0.034 0.001 PHE A3554 TRP 0.010 0.001 TRP A 813 HIS 0.003 0.001 HIS A3549 Details of bonding type rmsd covalent geometry : bond 0.00268 (42227) covalent geometry : angle 0.57947 (57360) hydrogen bonds : bond 0.03192 ( 2080) hydrogen bonds : angle 3.95766 ( 6049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 380 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 MET cc_start: 0.4895 (mtt) cc_final: 0.4628 (mtm) REVERT: A 878 GLU cc_start: 0.6547 (pt0) cc_final: 0.5783 (tp30) REVERT: A 958 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7800 (mtp) REVERT: A 1118 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 1197 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8443 (pp) REVERT: A 1467 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9019 (mp) REVERT: A 1640 GLU cc_start: 0.8238 (pm20) cc_final: 0.8002 (pm20) REVERT: A 1665 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.4849 (p-80) REVERT: A 1739 TYR cc_start: 0.8125 (t80) cc_final: 0.7784 (t80) REVERT: A 1946 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7391 (m110) REVERT: A 1989 ASN cc_start: 0.7605 (m-40) cc_final: 0.7365 (m110) REVERT: A 2083 LEU cc_start: 0.7283 (pt) cc_final: 0.7044 (pt) REVERT: A 2294 ILE cc_start: 0.7260 (mm) cc_final: 0.6771 (mm) REVERT: A 2860 ASP cc_start: 0.8962 (t70) cc_final: 0.8708 (t0) REVERT: A 3085 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: A 3123 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 3383 GLN cc_start: 0.8425 (tt0) cc_final: 0.8194 (pt0) REVERT: A 3588 TRP cc_start: 0.7260 (t60) cc_final: 0.6663 (t60) REVERT: A 4006 VAL cc_start: 0.7845 (p) cc_final: 0.7634 (p) REVERT: B 76 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 134 MET cc_start: 0.6066 (ppp) cc_final: 0.5426 (ppp) REVERT: B 473 TYR cc_start: 0.6913 (t80) cc_final: 0.6570 (t80) REVERT: B 530 TYR cc_start: 0.4581 (t80) cc_final: 0.4260 (t80) REVERT: C 14 MET cc_start: 0.4941 (ttm) cc_final: 0.4484 (tmm) REVERT: C 24 ILE cc_start: 0.5155 (OUTLIER) cc_final: 0.4473 (tp) REVERT: C 40 MET cc_start: 0.7206 (ttp) cc_final: 0.6927 (ttt) REVERT: C 183 PHE cc_start: 0.4215 (t80) cc_final: 0.3772 (t80) REVERT: C 496 HIS cc_start: 0.7131 (t-90) cc_final: 0.6638 (t70) REVERT: C 611 GLU cc_start: 0.2433 (OUTLIER) cc_final: 0.1920 (pt0) REVERT: C 670 GLN cc_start: 0.3333 (OUTLIER) cc_final: 0.2366 (pp30) outliers start: 69 outliers final: 55 residues processed: 435 average time/residue: 0.2399 time to fit residues: 177.0734 Evaluate side-chains 438 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 371 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1876 ILE Chi-restraints excluded: chain A residue 1946 ASN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3085 GLU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 476 optimal weight: 0.8980 chunk 498 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 364 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 188 optimal weight: 0.0270 chunk 214 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A1946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102722 restraints weight = 165010.618| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.24 r_work: 0.3041 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 42227 Z= 0.111 Angle : 0.573 14.257 57360 Z= 0.291 Chirality : 0.040 0.297 6485 Planarity : 0.004 0.064 7047 Dihedral : 12.905 179.866 6182 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.03 % Favored : 92.93 % Rotamer: Outliers : 1.70 % Allowed : 15.01 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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 (0.12), residues: 4933 helix: 1.19 (0.10), residues: 2910 sheet: -0.19 (0.35), residues: 237 loop : -2.33 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3380 TYR 0.014 0.001 TYR A2288 PHE 0.033 0.001 PHE A3554 TRP 0.009 0.001 TRP A3916 HIS 0.003 0.001 HIS A3501 Details of bonding type rmsd covalent geometry : bond 0.00252 (42227) covalent geometry : angle 0.57256 (57360) hydrogen bonds : bond 0.03106 ( 2080) hydrogen bonds : angle 3.92759 ( 6049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9866 Ramachandran restraints generated. 4933 Oldfield, 0 Emsley, 4933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 380 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 MET cc_start: 0.5064 (mtt) cc_final: 0.4834 (mtm) REVERT: A 878 GLU cc_start: 0.6580 (pt0) cc_final: 0.5784 (tp30) REVERT: A 1118 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: A 1467 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9022 (mp) REVERT: A 1640 GLU cc_start: 0.8250 (pm20) cc_final: 0.7992 (pm20) REVERT: A 1665 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.4949 (p-80) REVERT: A 1739 TYR cc_start: 0.8165 (t80) cc_final: 0.7825 (t80) REVERT: A 1927 MET cc_start: 0.6018 (mtm) cc_final: 0.5028 (mmt) REVERT: A 1946 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7322 (m110) REVERT: A 1989 ASN cc_start: 0.7656 (m-40) cc_final: 0.7392 (m110) REVERT: A 2294 ILE cc_start: 0.7255 (mm) cc_final: 0.6792 (mm) REVERT: A 2860 ASP cc_start: 0.9053 (t70) cc_final: 0.8789 (t0) REVERT: A 3085 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: A 3123 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: A 3383 GLN cc_start: 0.8423 (tt0) cc_final: 0.8182 (pt0) REVERT: A 3588 TRP cc_start: 0.7321 (t60) cc_final: 0.6763 (t60) REVERT: A 4006 VAL cc_start: 0.7839 (p) cc_final: 0.7634 (p) REVERT: B 76 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 131 PHE cc_start: 0.8256 (t80) cc_final: 0.7863 (t80) REVERT: B 134 MET cc_start: 0.6154 (ppp) cc_final: 0.5537 (ppp) REVERT: B 236 SER cc_start: 0.6424 (t) cc_final: 0.5661 (m) REVERT: B 473 TYR cc_start: 0.6864 (t80) cc_final: 0.6586 (t80) REVERT: B 530 TYR cc_start: 0.4552 (t80) cc_final: 0.4220 (t80) REVERT: C 14 MET cc_start: 0.4981 (ttm) cc_final: 0.4492 (tmm) REVERT: C 24 ILE cc_start: 0.5145 (OUTLIER) cc_final: 0.4510 (tp) REVERT: C 40 MET cc_start: 0.7237 (ttp) cc_final: 0.6963 (ttt) REVERT: C 183 PHE cc_start: 0.4261 (t80) cc_final: 0.3819 (t80) REVERT: C 496 HIS cc_start: 0.7171 (t-90) cc_final: 0.6722 (t70) REVERT: C 611 GLU cc_start: 0.2399 (OUTLIER) cc_final: 0.1880 (pt0) REVERT: C 670 GLN cc_start: 0.3316 (OUTLIER) cc_final: 0.2352 (pp30) outliers start: 70 outliers final: 55 residues processed: 436 average time/residue: 0.2326 time to fit residues: 173.1322 Evaluate side-chains 440 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 375 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1467 ILE Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1665 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1746 PHE Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1866 GLN Chi-restraints excluded: chain A residue 1946 ASN Chi-restraints excluded: chain A residue 1962 TYR Chi-restraints excluded: chain A residue 2086 ASP Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2443 MET Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 3085 GLU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3312 VAL Chi-restraints excluded: chain A residue 3487 ILE Chi-restraints excluded: chain A residue 3510 GLN Chi-restraints excluded: chain A residue 3578 LEU Chi-restraints excluded: chain A residue 3583 LEU Chi-restraints excluded: chain A residue 3895 GLU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 670 GLN Chi-restraints excluded: chain C residue 687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 411 optimal weight: 0.0470 chunk 247 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 289 optimal weight: 0.5980 chunk 445 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 367 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 434 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1721 HIS A1946 ASN A2574 ASN A3951 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103671 restraints weight = 182008.757| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.81 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 42227 Z= 0.106 Angle : 0.565 14.283 57360 Z= 0.287 Chirality : 0.039 0.284 6485 Planarity : 0.004 0.064 7047 Dihedral : 12.825 179.866 6182 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.13 % Rotamer: Outliers : 1.70 % Allowed : 15.10 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.04 (0.13), residues: 4933 helix: 1.28 (0.10), residues: 2903 sheet: -0.15 (0.35), residues: 233 loop : -2.29 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3380 TYR 0.017 0.001 TYR A1945 PHE 0.033 0.001 PHE A3554 TRP 0.009 0.001 TRP A3916 HIS 0.003 0.001 HIS A3501 Details of bonding type rmsd covalent geometry : bond 0.00237 (42227) covalent geometry : angle 0.56495 (57360) hydrogen bonds : bond 0.02991 ( 2080) hydrogen bonds : angle 3.88940 ( 6049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10356.52 seconds wall clock time: 178 minutes 31.11 seconds (10711.11 seconds total)