Starting phenix.real_space_refine on Tue Jan 14 14:35:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9g_44382/01_2025/9b9g_44382.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.038 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 Ca 8 9.91 5 S 324 5.16 5 C 31366 2.51 5 N 8141 2.21 5 O 8837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 48676 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 13625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1696, 13625 Classifications: {'peptide': 1696} Link IDs: {'PCIS': 1, 'PTRANS': 86, 'TRANS': 1608} Chain breaks: 25 Chain: "B" Number of atoms: 13625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1696, 13625 Classifications: {'peptide': 1696} Link IDs: {'PCIS': 1, 'PTRANS': 86, 'TRANS': 1608} Chain breaks: 25 Chain: "D" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4573 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 5 Chain: "E" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2022 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 238} Chain breaks: 4 Chain: "F" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4573 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 5 Chain: "G" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2022 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 238} Chain breaks: 4 Chain: "H" Number of atoms: 1236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Conformer: "B" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 bond proxies already assigned to first conformer: 1238 Chain: "I" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2866 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 331} Chain breaks: 1 Chain: "J" Number of atoms: 1236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Conformer: "B" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 bond proxies already assigned to first conformer: 1238 Chain: "K" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2890 Classifications: {'peptide': 356} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 334} Chain breaks: 2 Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="CA CA H 204 " occ=0.66 residue: pdb="CA CA J 204 " occ=0.66 Time building chain proxies: 20.30, per 1000 atoms: 0.42 Number of scatterers: 48676 At special positions: 0 Unit cell: (200.703, 276.667, 140.732, 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) Ca 8 19.99 S 324 16.00 O 8837 8.00 N 8141 7.00 C 31366 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: 9.38 Conformation dependent library (CDL) restraints added in 4.9 seconds 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11604 Finding SS restraints... Secondary structure from input PDB file: 318 helices and 15 sheets defined 70.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.522A pdb=" N VAL A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.866A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.711A pdb=" N VAL A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 126 through 146 removed outlier: 3.721A pdb=" N SER A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 169 removed outlier: 3.983A pdb=" N GLN A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.655A pdb=" N LYS A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.555A pdb=" N PHE A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 369 through 385 removed outlier: 3.644A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 414 Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.875A pdb=" N ALA A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 removed outlier: 3.692A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 Processing helix chain 'A' and resid 499 through 513 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 563 through 581 Processing helix chain 'A' and resid 586 through 601 Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.509A pdb=" N ILE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.581A pdb=" N ALA A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 722 through 740 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 788 through 805 Processing helix chain 'A' and resid 817 through 828 removed outlier: 3.657A pdb=" N GLU A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 Processing helix chain 'A' and resid 875 through 883 Processing helix chain 'A' and resid 886 through 907 removed outlier: 3.649A pdb=" N SER A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.918A pdb=" N VAL A 915 " --> pdb=" O ARG A 912 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.516A pdb=" N GLN A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 952 removed outlier: 3.608A pdb=" N LYS A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.793A pdb=" N GLU A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.524A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1022 removed outlier: 3.997A pdb=" N SER A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1072 removed outlier: 3.970A pdb=" N ALA A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS A1061 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1085 removed outlier: 3.773A pdb=" N THR A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A1085 " --> pdb=" O GLN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1093 removed outlier: 4.250A pdb=" N VAL A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 removed outlier: 3.791A pdb=" N ALA A1101 " --> pdb=" O HIS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1157 removed outlier: 3.712A pdb=" N MET A1140 " --> pdb=" O TYR A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 removed outlier: 4.293A pdb=" N MET A1173 " --> pdb=" O LEU A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1202 removed outlier: 3.525A pdb=" N SER A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 3.657A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1223 through 1241 Processing helix chain 'A' and resid 1244 through 1263 removed outlier: 3.511A pdb=" N PHE A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1279 removed outlier: 3.528A pdb=" N ALA A1279 " --> pdb=" O PRO A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1313 removed outlier: 3.758A pdb=" N ILE A1297 " --> pdb=" O THR A1293 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A1300 " --> pdb=" O TYR A1296 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1326 removed outlier: 3.795A pdb=" N ILE A1319 " --> pdb=" O ASP A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1345 Processing helix chain 'A' and resid 1346 through 1361 removed outlier: 3.628A pdb=" N PHE A1350 " --> pdb=" O ILE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1386 removed outlier: 3.582A pdb=" N VAL A1373 " --> pdb=" O THR A1369 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A1386 " --> pdb=" O ALA A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1417 Processing helix chain 'A' and resid 1478 through 1508 removed outlier: 4.151A pdb=" N ARG A1488 " --> pdb=" O TYR A1484 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1534 removed outlier: 3.676A pdb=" N ASN A1523 " --> pdb=" O GLN A1519 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A1524 " --> pdb=" O ALA A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 removed outlier: 4.178A pdb=" N VAL A1544 " --> pdb=" O TRP A1540 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A1545 " --> pdb=" O LYS A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1558 removed outlier: 3.518A pdb=" N ALA A1555 " --> pdb=" O SER A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1561 No H-bonds generated for 'chain 'A' and resid 1559 through 1561' Processing helix chain 'A' and resid 1566 through 1579 removed outlier: 3.510A pdb=" N ASP A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1590 removed outlier: 3.726A pdb=" N ALA A1589 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A1590 " --> pdb=" O VAL A1586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1585 through 1590' Processing helix chain 'A' and resid 1591 through 1593 No H-bonds generated for 'chain 'A' and resid 1591 through 1593' Processing helix chain 'A' and resid 1608 through 1612 removed outlier: 3.971A pdb=" N CYS A1611 " --> pdb=" O HIS A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1621 Processing helix chain 'A' and resid 1622 through 1625 Processing helix chain 'A' and resid 1631 through 1643 Processing helix chain 'A' and resid 1646 through 1653 removed outlier: 3.917A pdb=" N ILE A1650 " --> pdb=" O PRO A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1660 removed outlier: 3.836A pdb=" N ILE A1657 " --> pdb=" O TYR A1653 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A1658 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1664 Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1681 through 1694 Processing helix chain 'A' and resid 1708 through 1723 removed outlier: 3.750A pdb=" N THR A1720 " --> pdb=" O VAL A1716 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY A1721 " --> pdb=" O GLU A1717 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A1722 " --> pdb=" O GLU A1718 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A1723 " --> pdb=" O ILE A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1724 through 1748 removed outlier: 4.193A pdb=" N VAL A1744 " --> pdb=" O LYS A1740 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A1745 " --> pdb=" O ILE A1741 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A1746 " --> pdb=" O THR A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1768 removed outlier: 3.636A pdb=" N LYS A1758 " --> pdb=" O GLY A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1824 Processing helix chain 'A' and resid 1856 through 1876 Processing helix chain 'A' and resid 1916 through 1925 Processing helix chain 'A' and resid 1929 through 1954 removed outlier: 4.130A pdb=" N GLN A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1945 " --> pdb=" O ARG A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2004 Processing helix chain 'A' and resid 2010 through 2028 Processing helix chain 'A' and resid 2030 through 2043 removed outlier: 3.608A pdb=" N MET A2041 " --> pdb=" O LEU A2037 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A2043 " --> pdb=" O THR A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2061 removed outlier: 3.696A pdb=" N LEU A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A2061 " --> pdb=" O LEU A2057 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2081 Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.531A pdb=" N VAL B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 71 through 88 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.604A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.695A pdb=" N TYR B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 341 through 359 removed outlier: 4.081A pdb=" N LEU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.662A pdb=" N LEU B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 414 removed outlier: 3.654A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 Processing helix chain 'B' and resid 451 through 467 removed outlier: 3.516A pdb=" N ALA B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 496 removed outlier: 3.627A pdb=" N PHE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 512 removed outlier: 3.510A pdb=" N LEU B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 563 through 581 Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 633 through 645 removed outlier: 4.056A pdb=" N ILE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.561A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 662 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.919A pdb=" N ALA B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 705 through 719 Processing helix chain 'B' and resid 722 through 740 Processing helix chain 'B' and resid 767 through 769 No H-bonds generated for 'chain 'B' and resid 767 through 769' Processing helix chain 'B' and resid 770 through 779 removed outlier: 4.148A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 806 removed outlier: 3.535A pdb=" N GLN B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 830 removed outlier: 3.776A pdb=" N LYS B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 removed outlier: 3.571A pdb=" N LEU B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 Processing helix chain 'B' and resid 875 through 883 Processing helix chain 'B' and resid 886 through 907 removed outlier: 3.584A pdb=" N SER B 890 " --> pdb=" O ASP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 934 through 952 removed outlier: 4.014A pdb=" N LYS B 942 " --> pdb=" O ALA B 938 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 943 " --> pdb=" O VAL B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 974 removed outlier: 3.880A pdb=" N GLU B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 977 No H-bonds generated for 'chain 'B' and resid 975 through 977' Processing helix chain 'B' and resid 980 through 997 Processing helix chain 'B' and resid 998 through 1001 Processing helix chain 'B' and resid 1005 through 1020 Processing helix chain 'B' and resid 1046 through 1072 removed outlier: 3.900A pdb=" N ALA B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B1061 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B1062 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1085 removed outlier: 3.811A pdb=" N THR B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1093 removed outlier: 4.395A pdb=" N SER B1092 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1109 removed outlier: 3.832A pdb=" N ALA B1101 " --> pdb=" O HIS B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1158 removed outlier: 3.619A pdb=" N MET B1140 " --> pdb=" O TYR B1136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B1158 " --> pdb=" O TYR B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1184 removed outlier: 4.028A pdb=" N MET B1173 " --> pdb=" O LEU B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1202 removed outlier: 3.575A pdb=" N SER B1202 " --> pdb=" O ALA B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1216 removed outlier: 3.581A pdb=" N LEU B1211 " --> pdb=" O ASP B1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'B' and resid 1223 through 1241 Processing helix chain 'B' and resid 1244 through 1263 removed outlier: 3.532A pdb=" N PHE B1248 " --> pdb=" O VAL B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1293 through 1313 removed outlier: 3.747A pdb=" N ILE B1297 " --> pdb=" O THR B1293 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B1300 " --> pdb=" O TYR B1296 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1326 removed outlier: 3.936A pdb=" N ILE B1319 " --> pdb=" O ASP B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1342 through 1345 Processing helix chain 'B' and resid 1346 through 1361 removed outlier: 3.641A pdb=" N PHE B1350 " --> pdb=" O ILE B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1385 removed outlier: 3.769A pdb=" N VAL B1373 " --> pdb=" O THR B1369 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1416 removed outlier: 3.986A pdb=" N ASP B1403 " --> pdb=" O ARG B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1508 removed outlier: 4.131A pdb=" N ARG B1488 " --> pdb=" O TYR B1484 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B1508 " --> pdb=" O ILE B1504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1534 removed outlier: 4.227A pdb=" N GLU B1522 " --> pdb=" O ASP B1518 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B1523 " --> pdb=" O GLN B1519 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B1524 " --> pdb=" O ALA B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1551 Processing helix chain 'B' and resid 1551 through 1558 removed outlier: 3.563A pdb=" N ALA B1555 " --> pdb=" O SER B1551 " (cutoff:3.500A) Processing helix chain 'B' and resid 1559 through 1561 No H-bonds generated for 'chain 'B' and resid 1559 through 1561' Processing helix chain 'B' and resid 1566 through 1579 Processing helix chain 'B' and resid 1589 through 1593 Processing helix chain 'B' and resid 1608 through 1612 removed outlier: 3.562A pdb=" N CYS B1611 " --> pdb=" O HIS B1608 " (cutoff:3.500A) Processing helix chain 'B' and resid 1616 through 1621 Processing helix chain 'B' and resid 1622 through 1625 removed outlier: 3.552A pdb=" N SER B1625 " --> pdb=" O SER B1622 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1622 through 1625' Processing helix chain 'B' and resid 1631 through 1644 Processing helix chain 'B' and resid 1646 through 1653 removed outlier: 3.712A pdb=" N ILE B1650 " --> pdb=" O PRO B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1653 through 1661 removed outlier: 4.177A pdb=" N ILE B1657 " --> pdb=" O TYR B1653 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B1658 " --> pdb=" O ILE B1654 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B1659 " --> pdb=" O PRO B1655 " (cutoff:3.500A) Processing helix chain 'B' and resid 1662 through 1664 No H-bonds generated for 'chain 'B' and resid 1662 through 1664' Processing helix chain 'B' and resid 1667 through 1680 removed outlier: 3.627A pdb=" N GLU B1671 " --> pdb=" O GLY B1667 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B1680 " --> pdb=" O ALA B1676 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1695 Processing helix chain 'B' and resid 1708 through 1720 removed outlier: 3.528A pdb=" N THR B1720 " --> pdb=" O VAL B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1724 through 1749 removed outlier: 4.371A pdb=" N VAL B1744 " --> pdb=" O LYS B1740 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER B1745 " --> pdb=" O ILE B1741 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B1746 " --> pdb=" O THR B1742 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1767 removed outlier: 3.532A pdb=" N LYS B1758 " --> pdb=" O GLY B1754 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1824 Processing helix chain 'B' and resid 1855 through 1876 Processing helix chain 'B' and resid 1916 through 1925 Processing helix chain 'B' and resid 1929 through 1954 removed outlier: 3.656A pdb=" N GLN B1933 " --> pdb=" O THR B1929 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1945 " --> pdb=" O ARG B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1997 through 2004 removed outlier: 3.966A pdb=" N MET B2004 " --> pdb=" O MET B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2028 removed outlier: 3.537A pdb=" N LYS B2014 " --> pdb=" O ALA B2010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2030 through 2043 removed outlier: 3.803A pdb=" N MET B2041 " --> pdb=" O LEU B2037 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B2043 " --> pdb=" O THR B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2052 through 2061 removed outlier: 3.946A pdb=" N LEU B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B2061 " --> pdb=" O LEU B2057 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2080 Processing helix chain 'D' and resid 137 through 153 Processing helix chain 'D' and resid 168 through 194 Processing helix chain 'D' and resid 217 through 232 removed outlier: 4.171A pdb=" N ALA D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.602A pdb=" N ALA D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 273 removed outlier: 4.416A pdb=" N MET D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 340 Processing helix chain 'D' and resid 352 through 375 removed outlier: 4.153A pdb=" N ARG D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 390 Processing helix chain 'D' and resid 396 through 409 removed outlier: 4.011A pdb=" N TRP D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 431 through 442 Processing helix chain 'D' and resid 448 through 460 Processing helix chain 'D' and resid 466 through 486 removed outlier: 3.915A pdb=" N LYS D 471 " --> pdb=" O GLU D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 511 removed outlier: 3.892A pdb=" N GLU D 494 " --> pdb=" O ARG D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 528 Processing helix chain 'D' and resid 530 through 545 removed outlier: 3.727A pdb=" N ALA D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 564 through 579 removed outlier: 3.580A pdb=" N ALA D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 598 through 617 removed outlier: 3.766A pdb=" N ALA D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 708 removed outlier: 3.577A pdb=" N VAL D 705 " --> pdb=" O HIS D 701 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 706 " --> pdb=" O ALA D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 724 Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.523A pdb=" N LEU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 Processing helix chain 'D' and resid 763 through 778 removed outlier: 3.988A pdb=" N MET D 767 " --> pdb=" O HIS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 794 removed outlier: 3.733A pdb=" N LYS D 785 " --> pdb=" O SER D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 810 removed outlier: 3.734A pdb=" N TRP D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 810 " --> pdb=" O GLU D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 829 Processing helix chain 'D' and resid 835 through 839 removed outlier: 3.530A pdb=" N ILE D 838 " --> pdb=" O PRO D 835 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 839 " --> pdb=" O PHE D 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 835 through 839' Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.709A pdb=" N ALA E 28 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 4.156A pdb=" N SER E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 66 Processing helix chain 'E' and resid 68 through 76 removed outlier: 3.971A pdb=" N LEU E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 89 removed outlier: 3.616A pdb=" N LEU E 82 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 176 through 190 removed outlier: 3.542A pdb=" N VAL E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.759A pdb=" N TYR E 194 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 195' Processing helix chain 'E' and resid 196 through 210 removed outlier: 3.523A pdb=" N LEU E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 233 through 248 removed outlier: 3.527A pdb=" N GLY E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 271 Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.522A pdb=" N LEU E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 154 Processing helix chain 'F' and resid 168 through 195 removed outlier: 3.847A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 233 removed outlier: 3.735A pdb=" N ALA F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 245 removed outlier: 3.839A pdb=" N GLY F 238 " --> pdb=" O ASN F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.562A pdb=" N ARG F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR F 260 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.947A pdb=" N TYR F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 342 removed outlier: 4.152A pdb=" N GLU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 375 Processing helix chain 'F' and resid 379 through 390 Processing helix chain 'F' and resid 396 through 410 removed outlier: 3.704A pdb=" N TRP F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 431 through 442 Processing helix chain 'F' and resid 448 through 460 Processing helix chain 'F' and resid 466 through 487 Processing helix chain 'F' and resid 489 through 511 removed outlier: 3.569A pdb=" N GLN F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 527 Processing helix chain 'F' and resid 530 through 545 removed outlier: 3.517A pdb=" N ALA F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 562 Processing helix chain 'F' and resid 564 through 579 removed outlier: 3.621A pdb=" N ALA F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 596 Processing helix chain 'F' and resid 598 through 617 removed outlier: 3.758A pdb=" N ALA F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 710 removed outlier: 3.575A pdb=" N MET F 693 " --> pdb=" O LEU F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 726 removed outlier: 3.917A pdb=" N ALA F 715 " --> pdb=" O LYS F 711 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU F 725 " --> pdb=" O GLU F 721 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F 726 " --> pdb=" O ALA F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 744 removed outlier: 3.748A pdb=" N LEU F 733 " --> pdb=" O SER F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 758 Processing helix chain 'F' and resid 764 through 776 removed outlier: 3.562A pdb=" N GLN F 768 " --> pdb=" O VAL F 764 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 794 Processing helix chain 'F' and resid 797 through 812 removed outlier: 4.156A pdb=" N TRP F 801 " --> pdb=" O ALA F 797 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 829 Processing helix chain 'F' and resid 835 through 839 removed outlier: 3.514A pdb=" N ILE F 839 " --> pdb=" O PHE F 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 24 through 29 removed outlier: 4.463A pdb=" N ALA G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 35 No H-bonds generated for 'chain 'G' and resid 34 through 35' Processing helix chain 'G' and resid 36 through 45 Processing helix chain 'G' and resid 52 through 63 removed outlier: 4.095A pdb=" N VAL G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.780A pdb=" N THR G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.745A pdb=" N LEU G 82 " --> pdb=" O PHE G 78 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 114 Processing helix chain 'G' and resid 176 through 190 removed outlier: 3.550A pdb=" N VAL G 180 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS G 187 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR G 188 " --> pdb=" O LEU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 212 removed outlier: 3.600A pdb=" N LEU G 200 " --> pdb=" O PRO G 196 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 222 removed outlier: 3.942A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.811A pdb=" N MET G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN G 250 " --> pdb=" O PHE G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 271 Processing helix chain 'G' and resid 272 through 285 removed outlier: 3.631A pdb=" N SER G 285 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 39 through 45 Processing helix chain 'H' and resid 46 through 51 removed outlier: 4.172A pdb=" N GLN H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 63 Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.611A pdb=" N GLN H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.666A pdb=" N TYR H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 125 through 141 Processing helix chain 'H' and resid 149 through 158 Processing helix chain 'H' and resid 159 through 166 removed outlier: 6.386A pdb=" N ILE H 162 " --> pdb=" O GLY H 159 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N HIS H 163 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS H 164 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 35 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'I' and resid 57 through 75 Processing helix chain 'I' and resid 94 through 106 Processing helix chain 'I' and resid 125 through 140 Processing helix chain 'I' and resid 153 through 160 Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 171 through 184 Processing helix chain 'I' and resid 208 through 214 removed outlier: 3.874A pdb=" N ILE I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 Processing helix chain 'I' and resid 261 through 273 Processing helix chain 'I' and resid 310 through 314 Processing helix chain 'I' and resid 343 through 347 Processing helix chain 'I' and resid 348 through 370 Proline residue: I 355 - end of helix Processing helix chain 'J' and resid 17 through 31 Processing helix chain 'J' and resid 39 through 45 Processing helix chain 'J' and resid 46 through 51 removed outlier: 4.200A pdb=" N GLN J 51 " --> pdb=" O PRO J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 63 Processing helix chain 'J' and resid 71 through 82 removed outlier: 4.173A pdb=" N PHE J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 Processing helix chain 'J' and resid 108 through 121 Processing helix chain 'J' and resid 125 through 141 Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 159 through 166 removed outlier: 6.376A pdb=" N ILE J 162 " --> pdb=" O GLY J 159 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N HIS J 163 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 35 Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'K' and resid 57 through 75 Processing helix chain 'K' and resid 94 through 106 Processing helix chain 'K' and resid 125 through 140 Processing helix chain 'K' and resid 153 through 160 Processing helix chain 'K' and resid 161 through 170 Processing helix chain 'K' and resid 171 through 184 removed outlier: 3.606A pdb=" N CYS K 184 " --> pdb=" O ASP K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 214 removed outlier: 3.735A pdb=" N ILE K 212 " --> pdb=" O THR K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 233 Processing helix chain 'K' and resid 261 through 273 Processing helix chain 'K' and resid 310 through 314 Processing helix chain 'K' and resid 343 through 347 removed outlier: 3.579A pdb=" N MET K 347 " --> pdb=" O PRO K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 370 Proline residue: K 355 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 540 removed outlier: 7.781A pdb=" N SER A 539 " --> pdb=" O ILE I 331 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN I 333 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1033 Processing sheet with id=AA3, first strand: chain 'A' and resid 1782 through 1787 removed outlier: 6.868A pdb=" N LYS A1808 " --> pdb=" O LEU A1785 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A1787 " --> pdb=" O LYS A1806 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS A1806 " --> pdb=" O ILE A1787 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A1793 " --> pdb=" O LEU A1804 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1782 through 1787 removed outlier: 6.868A pdb=" N LYS A1808 " --> pdb=" O LEU A1785 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A1787 " --> pdb=" O LYS A1806 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS A1806 " --> pdb=" O ILE A1787 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A1846 " --> pdb=" O CYS A1898 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A1895 " --> pdb=" O ALA A1888 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA A1888 " --> pdb=" O VAL A1895 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU A1897 " --> pdb=" O VAL A1886 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A1886 " --> pdb=" O GLU A1897 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1963 through 1965 Processing sheet with id=AA6, first strand: chain 'B' and resid 540 through 541 removed outlier: 7.169A pdb=" N THR B 541 " --> pdb=" O GLN K 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AA8, first strand: chain 'B' and resid 1782 through 1787 removed outlier: 6.789A pdb=" N LYS B1808 " --> pdb=" O LEU B1785 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE B1787 " --> pdb=" O LYS B1806 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LYS B1806 " --> pdb=" O ILE B1787 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B1893 " --> pdb=" O THR B1889 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1903 through 1904 Processing sheet with id=AB1, first strand: chain 'E' and resid 124 through 126 Processing sheet with id=AB2, first strand: chain 'G' and resid 124 through 126 removed outlier: 3.517A pdb=" N PHE G 125 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 78 through 79 removed outlier: 4.158A pdb=" N LEU I 79 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU I 190 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 196 " --> pdb=" O LEU I 278 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE I 277 " --> pdb=" O ILE I 303 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE I 305 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 279 " --> pdb=" O ILE I 305 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU I 302 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 248 through 250 Processing sheet with id=AB5, first strand: chain 'K' and resid 78 through 81 removed outlier: 3.620A pdb=" N LEU K 79 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU K 278 " --> pdb=" O LEU K 196 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE K 277 " --> pdb=" O ILE K 303 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE K 305 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG K 279 " --> pdb=" O ILE K 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 248 through 250 2885 hydrogen bonds defined for protein. 8480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.03 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 15594 1.35 - 1.46: 11336 1.46 - 1.58: 22282 1.58 - 1.70: 0 1.70 - 1.82: 504 Bond restraints: 49716 Sorted by residual: bond pdb=" CB ASN I 251 " pdb=" CG ASN I 251 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" C ILE F 531 " pdb=" N PRO F 532 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.88e+00 bond pdb=" CB GLU A1281 " pdb=" CG GLU A1281 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CA MET A2004 " pdb=" C MET A2004 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.80e-02 3.09e+03 1.65e+00 bond pdb=" CB ASN E 189 " pdb=" CG ASN E 189 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.48e+00 ... (remaining 49711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 66766 3.39 - 6.78: 407 6.78 - 10.17: 72 10.17 - 13.57: 13 13.57 - 16.96: 4 Bond angle restraints: 67262 Sorted by residual: angle pdb=" CA MET D 574 " pdb=" CB MET D 574 " pdb=" CG MET D 574 " ideal model delta sigma weight residual 114.10 123.99 -9.89 2.00e+00 2.50e-01 2.45e+01 angle pdb=" CA LEU A 158 " pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sigma weight residual 116.30 133.26 -16.96 3.50e+00 8.16e-02 2.35e+01 angle pdb=" CA LEU B 139 " pdb=" CB LEU B 139 " pdb=" CG LEU B 139 " ideal model delta sigma weight residual 116.30 132.77 -16.47 3.50e+00 8.16e-02 2.21e+01 angle pdb=" C LEU A 611 " pdb=" N ILE A 612 " pdb=" CA ILE A 612 " ideal model delta sigma weight residual 120.24 123.11 -2.87 6.30e-01 2.52e+00 2.08e+01 angle pdb=" C GLY A 166 " pdb=" N MET A 167 " pdb=" CA MET A 167 " ideal model delta sigma weight residual 122.54 115.53 7.01 1.65e+00 3.67e-01 1.81e+01 ... (remaining 67257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 25850 17.91 - 35.82: 3253 35.82 - 53.72: 780 53.72 - 71.63: 131 71.63 - 89.54: 62 Dihedral angle restraints: 30076 sinusoidal: 12230 harmonic: 17846 Sorted by residual: dihedral pdb=" CA ASP G 115 " pdb=" C ASP G 115 " pdb=" N LYS G 116 " pdb=" CA LYS G 116 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA TYR I 258 " pdb=" C TYR I 258 " pdb=" N PHE I 259 " pdb=" CA PHE I 259 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TYR K 258 " pdb=" C TYR K 258 " pdb=" N PHE K 259 " pdb=" CA PHE K 259 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 30073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 7262 0.093 - 0.186: 301 0.186 - 0.279: 11 0.279 - 0.372: 0 0.372 - 0.465: 1 Chirality restraints: 7575 Sorted by residual: chirality pdb=" CB ILE I 81 " pdb=" CA ILE I 81 " pdb=" CG1 ILE I 81 " pdb=" CG2 ILE I 81 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CG LEU G 105 " pdb=" CB LEU G 105 " pdb=" CD1 LEU G 105 " pdb=" CD2 LEU G 105 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU F 368 " pdb=" CB LEU F 368 " pdb=" CD1 LEU F 368 " pdb=" CD2 LEU F 368 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 7572 not shown) Planarity restraints: 8519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 96 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PHE K 96 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE K 96 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP K 97 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 256 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C CYS I 256 " 0.051 2.00e-02 2.50e+03 pdb=" O CYS I 256 " -0.020 2.00e-02 2.50e+03 pdb=" N SER I 257 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 96 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C PHE I 96 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE I 96 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP I 97 " -0.017 2.00e-02 2.50e+03 ... (remaining 8516 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 575 2.64 - 3.20: 45561 3.20 - 3.77: 76308 3.77 - 4.33: 94626 4.33 - 4.90: 153689 Nonbonded interactions: 370759 Sorted by model distance: nonbonded pdb=" OH TYR F 278 " pdb=" OE2 GLU F 327 " model vdw 2.073 3.040 nonbonded pdb=" O LEU A 187 " pdb=" OG SER A 191 " model vdw 2.136 3.040 nonbonded pdb=" OG SER K 233 " pdb=" O TYR K 258 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OD1 ASN A 199 " model vdw 2.162 3.040 nonbonded pdb=" O SER B 203 " pdb=" NZ LYS B 207 " model vdw 2.175 3.120 ... (remaining 370754 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 16 through 80 or resid 82 through 170 or resid 201 through \ 204)) selection = (chain 'J' and (resid 16 through 80 or resid 82 through 170 or resid 201 through \ 204)) } ncs_group { reference = (chain 'I' and (resid 11 through 241 or resid 245 through 370)) selection = (chain 'K' and (resid 11 through 291 or resid 300 through 370)) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 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: 1.510 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 84.250 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49716 Z= 0.171 Angle : 0.730 16.958 67262 Z= 0.364 Chirality : 0.042 0.465 7575 Planarity : 0.004 0.057 8519 Dihedral : 16.802 89.539 18472 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.32 % Allowed : 22.70 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5915 helix: 1.42 (0.08), residues: 3850 sheet: -0.13 (0.43), residues: 136 loop : -1.41 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1689 HIS 0.009 0.001 HIS B 622 PHE 0.040 0.001 PHE B 737 TYR 0.031 0.001 TYR A 374 ARG 0.011 0.000 ARG I 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 424 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 HIS cc_start: 0.8776 (m-70) cc_final: 0.8547 (m-70) REVERT: A 322 PHE cc_start: 0.5573 (m-80) cc_final: 0.5325 (m-10) REVERT: A 330 ARG cc_start: 0.9259 (tpt90) cc_final: 0.8961 (ptt90) REVERT: A 445 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: A 634 MET cc_start: 0.9145 (ptp) cc_final: 0.8780 (pmm) REVERT: A 663 LEU cc_start: 0.9446 (mt) cc_final: 0.9245 (tp) REVERT: A 711 ASN cc_start: 0.9502 (t0) cc_final: 0.9194 (m-40) REVERT: A 777 LEU cc_start: 0.9125 (tp) cc_final: 0.8820 (pp) REVERT: A 795 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8588 (t80) REVERT: A 1539 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7900 (pp30) REVERT: A 1713 ASP cc_start: 0.9355 (t0) cc_final: 0.8704 (t0) REVERT: A 1717 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8553 (mm-30) REVERT: A 1723 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8347 (pp) REVERT: A 2000 MET cc_start: 0.7474 (pmm) cc_final: 0.7103 (pmm) REVERT: B 59 MET cc_start: 0.5173 (ppp) cc_final: 0.4767 (ptt) REVERT: B 299 TYR cc_start: 0.8256 (t80) cc_final: 0.7934 (t80) REVERT: B 374 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7462 (t80) REVERT: B 375 LEU cc_start: 0.8701 (tt) cc_final: 0.8267 (mt) REVERT: B 377 MET cc_start: 0.9339 (mpp) cc_final: 0.8911 (mpp) REVERT: B 378 PHE cc_start: 0.8770 (m-10) cc_final: 0.8200 (m-10) REVERT: B 380 MET cc_start: 0.8814 (ptt) cc_final: 0.8453 (ppp) REVERT: B 591 PHE cc_start: 0.9207 (m-10) cc_final: 0.8963 (m-10) REVERT: B 771 ILE cc_start: 0.9246 (pt) cc_final: 0.9004 (mp) REVERT: B 795 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8725 (t80) REVERT: B 870 ASN cc_start: 0.9087 (m-40) cc_final: 0.8865 (m-40) REVERT: B 1051 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8339 (pp20) REVERT: B 1818 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: D 348 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (mm) REVERT: D 569 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8523 (mm) REVERT: E 96 HIS cc_start: 0.5737 (p-80) cc_final: 0.4473 (p-80) REVERT: F 259 MET cc_start: 0.8809 (mmp) cc_final: 0.8296 (mmm) REVERT: F 273 MET cc_start: 0.7011 (mpp) cc_final: 0.6464 (pmm) REVERT: F 369 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8416 (mt) REVERT: F 506 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8044 (tpt-90) REVERT: F 595 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8974 (mm) REVERT: F 750 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8153 (ptt90) REVERT: G 64 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: G 112 GLU cc_start: 0.8561 (tp30) cc_final: 0.8253 (tp30) REVERT: G 181 LEU cc_start: 0.8731 (mp) cc_final: 0.8520 (mm) REVERT: H 44 MET cc_start: -0.1118 (tmm) cc_final: -0.2400 (mtp) REVERT: H 119 MET cc_start: 0.3388 (ptp) cc_final: 0.2055 (tpt) REVERT: H 166 MET cc_start: -0.0433 (mpp) cc_final: -0.2162 (ttm) REVERT: I 84 PRO cc_start: 0.6158 (Cg_endo) cc_final: 0.5874 (Cg_exo) REVERT: I 251 ASN cc_start: -0.1019 (OUTLIER) cc_final: -0.1760 (t0) REVERT: J 44 MET cc_start: 0.1070 (mmm) cc_final: -0.0003 (mtm) REVERT: J 165 LYS cc_start: -0.0048 (OUTLIER) cc_final: -0.1012 (tmtt) REVERT: J 166 MET cc_start: -0.2889 (mtt) cc_final: -0.3862 (mtt) REVERT: K 191 MET cc_start: 0.0795 (mmt) cc_final: 0.0376 (tmm) REVERT: K 329 MET cc_start: 0.3349 (ttt) cc_final: 0.2887 (tpp) outliers start: 123 outliers final: 90 residues processed: 521 average time/residue: 0.4335 time to fit residues: 393.1680 Evaluate side-chains 505 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 399 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1363 ASP Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1710 ASP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 1205 ASP Chi-restraints excluded: chain B residue 1264 PHE Chi-restraints excluded: chain B residue 1273 GLU Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1855 CYS Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1899 ILE Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1950 LEU Chi-restraints excluded: chain B residue 2034 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 731 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 506 ARG Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 750 ARG Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 134 TRP Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 288 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 471 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 546 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 732 ASN A1213 HIS A1519 GLN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1545 ASN A1631 HIS A1685 HIS A1714 GLN A1739 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 HIS B1085 ASN B1138 ASN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS B1223 ASN B1325 GLN B1372 ASN ** B1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1681 GLN B1743 ASN B1870 ASN B1873 GLN B1962 ASN D 188 GLN D 515 HIS D 738 GLN D 763 HIS ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 515 HIS F 608 HIS F 738 GLN F 768 GLN F 809 GLN F 811 GLN G 119 HIS G 166 HIS G 257 GLN I 94 GLN I 327 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.114311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.083760 restraints weight = 299196.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.082840 restraints weight = 161429.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083166 restraints weight = 135201.945| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49716 Z= 0.222 Angle : 0.645 11.974 67262 Z= 0.325 Chirality : 0.041 0.243 7575 Planarity : 0.004 0.063 8519 Dihedral : 6.866 70.425 6745 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.93 % Rotamer: Outliers : 3.78 % Allowed : 20.51 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.11), residues: 5915 helix: 1.58 (0.08), residues: 3921 sheet: -0.20 (0.42), residues: 137 loop : -1.38 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1689 HIS 0.007 0.001 HIS B 622 PHE 0.035 0.002 PHE B 133 TYR 0.032 0.001 TYR A 600 ARG 0.007 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 422 time to evaluate : 6.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 HIS cc_start: 0.8898 (m-70) cc_final: 0.8619 (m-70) REVERT: A 445 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7751 (mpp) REVERT: A 634 MET cc_start: 0.9139 (ptp) cc_final: 0.8744 (pmm) REVERT: A 887 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 1723 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8384 (pp) REVERT: A 2027 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9011 (p) REVERT: B 59 MET cc_start: 0.5466 (ppp) cc_final: 0.5212 (ptt) REVERT: B 87 GLU cc_start: 0.7861 (tp30) cc_final: 0.7649 (tp30) REVERT: B 299 TYR cc_start: 0.8371 (t80) cc_final: 0.8001 (t80) REVERT: B 374 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 375 LEU cc_start: 0.8674 (tt) cc_final: 0.8269 (mt) REVERT: B 378 PHE cc_start: 0.8915 (m-10) cc_final: 0.7994 (m-10) REVERT: B 406 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8945 (tp-100) REVERT: B 591 PHE cc_start: 0.9281 (m-10) cc_final: 0.8969 (m-10) REVERT: B 795 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8703 (t80) REVERT: B 870 ASN cc_start: 0.9150 (m-40) cc_final: 0.8940 (m-40) REVERT: B 1666 MET cc_start: 0.8876 (mmp) cc_final: 0.8606 (mmp) REVERT: B 1818 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: B 1981 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: B 2000 MET cc_start: 0.8616 (tmm) cc_final: 0.8187 (ptt) REVERT: D 569 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8521 (mm) REVERT: E 171 MET cc_start: 0.7931 (tpp) cc_final: 0.7641 (tpp) REVERT: F 176 TYR cc_start: 0.6883 (m-10) cc_final: 0.6656 (m-10) REVERT: F 259 MET cc_start: 0.8963 (mmp) cc_final: 0.8698 (mmm) REVERT: F 273 MET cc_start: 0.7109 (mpp) cc_final: 0.6659 (pmm) REVERT: F 369 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8380 (mt) REVERT: G 64 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: G 106 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9299 (mm) REVERT: H 44 MET cc_start: -0.1318 (tmm) cc_final: -0.2522 (mtp) REVERT: H 119 MET cc_start: 0.3324 (ptp) cc_final: 0.1955 (tpt) REVERT: H 166 MET cc_start: -0.0919 (mpp) cc_final: -0.2613 (ttm) REVERT: J 44 MET cc_start: 0.1069 (mmm) cc_final: 0.0112 (mtm) REVERT: K 85 VAL cc_start: -0.2163 (OUTLIER) cc_final: -0.3243 (m) REVERT: K 191 MET cc_start: 0.0815 (mmt) cc_final: 0.0425 (ttp) REVERT: K 329 MET cc_start: 0.3028 (ttt) cc_final: 0.2556 (tpp) outliers start: 201 outliers final: 122 residues processed: 591 average time/residue: 0.4435 time to fit residues: 455.4902 Evaluate side-chains 529 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 393 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1324 LEU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2035 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1173 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1313 SER Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1363 ASP Chi-restraints excluded: chain B residue 1494 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1776 LEU Chi-restraints excluded: chain B residue 1785 LEU Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1855 CYS Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1942 SER Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 731 ASN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain F residue 837 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 134 TRP Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 427 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 375 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 373 optimal weight: 0.9990 chunk 392 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 591 optimal weight: 6.9990 chunk 406 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 677 ASN A1213 HIS A1223 ASN A1934 GLN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS ** B1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN F 768 GLN I 194 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.114031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.082305 restraints weight = 309151.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081287 restraints weight = 172542.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.081177 restraints weight = 151094.580| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 49716 Z= 0.159 Angle : 0.612 12.799 67262 Z= 0.301 Chirality : 0.040 0.279 7575 Planarity : 0.004 0.063 8519 Dihedral : 6.128 59.657 6660 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 3.57 % Allowed : 21.30 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5915 helix: 1.69 (0.08), residues: 3912 sheet: -0.23 (0.43), residues: 137 loop : -1.27 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1596 HIS 0.006 0.001 HIS B 622 PHE 0.029 0.001 PHE H 96 TYR 0.025 0.001 TYR B1919 ARG 0.006 0.000 ARG B1922 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 443 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 HIS cc_start: 0.8994 (m-70) cc_final: 0.8726 (m-70) REVERT: A 445 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7694 (mpp) REVERT: A 628 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7923 (ttt-90) REVERT: A 634 MET cc_start: 0.9060 (ptp) cc_final: 0.8729 (pmm) REVERT: A 711 ASN cc_start: 0.9507 (t0) cc_final: 0.9208 (m-40) REVERT: A 731 MET cc_start: 0.9567 (ptp) cc_final: 0.9338 (ptp) REVERT: A 777 LEU cc_start: 0.9064 (tp) cc_final: 0.8798 (pp) REVERT: A 795 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8655 (t80) REVERT: A 887 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 1140 MET cc_start: 0.8489 (tpp) cc_final: 0.8277 (tpp) REVERT: A 1539 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7759 (pp30) REVERT: A 1723 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 2027 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 299 TYR cc_start: 0.8481 (t80) cc_final: 0.8122 (t80) REVERT: B 374 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7271 (t80) REVERT: B 375 LEU cc_start: 0.8630 (tt) cc_final: 0.8202 (mt) REVERT: B 377 MET cc_start: 0.9373 (mpp) cc_final: 0.8983 (mpp) REVERT: B 378 PHE cc_start: 0.8826 (m-10) cc_final: 0.7928 (m-10) REVERT: B 380 MET cc_start: 0.8465 (ptt) cc_final: 0.8204 (ppp) REVERT: B 406 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8739 (tp-100) REVERT: B 589 GLU cc_start: 0.9220 (pp20) cc_final: 0.8762 (pm20) REVERT: B 795 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8704 (t80) REVERT: B 1051 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8349 (pp20) REVERT: B 1723 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (pp) REVERT: B 1842 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.6981 (pt) REVERT: B 1981 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: D 542 LEU cc_start: 0.8981 (pp) cc_final: 0.8658 (mt) REVERT: D 569 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8489 (mm) REVERT: E 58 HIS cc_start: 0.8809 (p-80) cc_final: 0.8313 (p-80) REVERT: F 176 TYR cc_start: 0.6957 (m-10) cc_final: 0.6625 (m-10) REVERT: F 259 MET cc_start: 0.9010 (mmp) cc_final: 0.8763 (mmm) REVERT: F 273 MET cc_start: 0.6904 (mpp) cc_final: 0.6460 (pmm) REVERT: F 327 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8636 (mp0) REVERT: F 369 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8493 (mt) REVERT: F 595 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8875 (mm) REVERT: F 704 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: F 706 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7596 (t80) REVERT: F 746 MET cc_start: 0.7594 (pmm) cc_final: 0.7216 (mmm) REVERT: G 26 ASN cc_start: 0.6010 (t0) cc_final: 0.5644 (t0) REVERT: G 64 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: H 44 MET cc_start: -0.1254 (tmm) cc_final: -0.2291 (mtp) REVERT: H 119 MET cc_start: 0.3623 (ptp) cc_final: 0.2325 (tpt) REVERT: H 166 MET cc_start: -0.0899 (mpp) cc_final: -0.2478 (ttm) REVERT: I 251 ASN cc_start: 0.0688 (OUTLIER) cc_final: -0.0334 (t0) REVERT: J 44 MET cc_start: 0.1228 (mmm) cc_final: 0.0281 (mtm) REVERT: J 101 MET cc_start: -0.0808 (tpp) cc_final: -0.1186 (tpt) REVERT: K 85 VAL cc_start: -0.1972 (OUTLIER) cc_final: -0.3584 (m) REVERT: K 191 MET cc_start: 0.0625 (mmt) cc_final: 0.0316 (ttp) REVERT: K 329 MET cc_start: 0.2683 (ttt) cc_final: 0.2354 (tpp) outliers start: 190 outliers final: 105 residues processed: 595 average time/residue: 0.4355 time to fit residues: 451.7394 Evaluate side-chains 528 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 403 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1173 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1363 ASP Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1586 VAL Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1950 LEU Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 775 HIS Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 251 optimal weight: 0.7980 chunk 314 optimal weight: 0.8980 chunk 443 optimal weight: 0.0060 chunk 371 optimal weight: 0.7980 chunk 555 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 HIS ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN G 110 ASN G 119 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.112829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.081579 restraints weight = 287906.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.081444 restraints weight = 161692.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081477 restraints weight = 137022.482| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 49716 Z= 0.148 Angle : 0.618 13.456 67262 Z= 0.299 Chirality : 0.040 0.311 7575 Planarity : 0.004 0.061 8519 Dihedral : 5.836 59.843 6637 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 3.40 % Allowed : 21.41 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 5915 helix: 1.73 (0.08), residues: 3916 sheet: -0.23 (0.43), residues: 135 loop : -1.25 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 676 HIS 0.005 0.001 HIS B 622 PHE 0.037 0.001 PHE G 246 TYR 0.025 0.001 TYR A 374 ARG 0.007 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 440 time to evaluate : 4.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9525 (mp) cc_final: 0.9221 (mp) REVERT: A 162 HIS cc_start: 0.8902 (m-70) cc_final: 0.8628 (m-70) REVERT: A 445 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7887 (mtp) REVERT: A 634 MET cc_start: 0.9050 (ptp) cc_final: 0.8727 (pmm) REVERT: A 711 ASN cc_start: 0.9518 (t0) cc_final: 0.9208 (m-40) REVERT: A 795 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8628 (t80) REVERT: A 887 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 1140 MET cc_start: 0.8446 (tpp) cc_final: 0.8234 (tpp) REVERT: A 1723 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 1916 MET cc_start: 0.7705 (mmm) cc_final: 0.7199 (ptt) REVERT: A 1937 TYR cc_start: 0.8665 (t80) cc_final: 0.8231 (t80) REVERT: A 2027 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 2041 MET cc_start: 0.8957 (mmp) cc_final: 0.8757 (mmp) REVERT: B 141 ASP cc_start: 0.9119 (t0) cc_final: 0.8906 (m-30) REVERT: B 299 TYR cc_start: 0.8355 (t80) cc_final: 0.8030 (t80) REVERT: B 374 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7336 (t80) REVERT: B 375 LEU cc_start: 0.8608 (tt) cc_final: 0.8238 (mt) REVERT: B 377 MET cc_start: 0.9361 (mpp) cc_final: 0.8969 (mpp) REVERT: B 378 PHE cc_start: 0.8774 (m-10) cc_final: 0.7941 (m-10) REVERT: B 380 MET cc_start: 0.8599 (ptt) cc_final: 0.8267 (ppp) REVERT: B 589 GLU cc_start: 0.9236 (pp20) cc_final: 0.8790 (pm20) REVERT: B 795 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8619 (t80) REVERT: B 1723 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (pp) REVERT: B 1818 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 1981 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 2000 MET cc_start: 0.8518 (tmm) cc_final: 0.8094 (ptt) REVERT: D 348 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8065 (mm) REVERT: D 569 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8248 (mm) REVERT: E 96 HIS cc_start: 0.5707 (p-80) cc_final: 0.4441 (p-80) REVERT: E 276 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8790 (tt) REVERT: F 259 MET cc_start: 0.9066 (mmp) cc_final: 0.8742 (mmm) REVERT: F 273 MET cc_start: 0.6993 (mpp) cc_final: 0.6732 (pmm) REVERT: F 327 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8539 (mp0) REVERT: F 369 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8487 (mt) REVERT: F 557 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9084 (mp) REVERT: F 704 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: F 706 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7545 (t80) REVERT: F 746 MET cc_start: 0.7566 (pmm) cc_final: 0.7230 (mmm) REVERT: G 26 ASN cc_start: 0.6004 (t0) cc_final: 0.5225 (t0) REVERT: G 64 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: H 44 MET cc_start: -0.1159 (tmm) cc_final: -0.2325 (mtp) REVERT: H 119 MET cc_start: 0.3382 (ptp) cc_final: 0.2006 (tpp) REVERT: H 166 MET cc_start: -0.0876 (mpp) cc_final: -0.2639 (ttm) REVERT: I 251 ASN cc_start: -0.0508 (OUTLIER) cc_final: -0.1866 (t0) REVERT: J 44 MET cc_start: 0.1165 (mmm) cc_final: 0.0095 (mtm) REVERT: K 85 VAL cc_start: -0.1781 (OUTLIER) cc_final: -0.3062 (m) REVERT: K 191 MET cc_start: 0.0990 (mmt) cc_final: 0.0578 (ttp) REVERT: K 329 MET cc_start: 0.2996 (ttt) cc_final: 0.2498 (tpp) outliers start: 181 outliers final: 104 residues processed: 587 average time/residue: 0.4295 time to fit residues: 440.6646 Evaluate side-chains 530 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 406 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 155 HIS Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 455 optimal weight: 9.9990 chunk 563 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 488 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 596 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 chunk 433 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 768 GLN G 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.113276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082139 restraints weight = 259360.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082031 restraints weight = 145903.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.081421 restraints weight = 143499.843| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49716 Z= 0.189 Angle : 0.624 13.914 67262 Z= 0.304 Chirality : 0.040 0.343 7575 Planarity : 0.004 0.059 8519 Dihedral : 5.714 59.667 6628 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.72 % Favored : 95.26 % Rotamer: Outliers : 3.93 % Allowed : 21.19 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 5915 helix: 1.75 (0.08), residues: 3932 sheet: -0.23 (0.41), residues: 150 loop : -1.26 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 676 HIS 0.012 0.001 HIS E 58 PHE 0.033 0.001 PHE G 178 TYR 0.016 0.001 TYR A 99 ARG 0.004 0.000 ARG G 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 418 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9543 (mt) cc_final: 0.9206 (mm) REVERT: A 162 HIS cc_start: 0.8889 (m-70) cc_final: 0.8622 (m-70) REVERT: A 377 MET cc_start: 0.9231 (mpp) cc_final: 0.9016 (mpp) REVERT: A 445 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: A 628 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7965 (ttt180) REVERT: A 634 MET cc_start: 0.9195 (ptp) cc_final: 0.8829 (pmm) REVERT: A 711 ASN cc_start: 0.9523 (t0) cc_final: 0.9213 (m-40) REVERT: A 777 LEU cc_start: 0.9098 (tp) cc_final: 0.8759 (pp) REVERT: A 795 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8641 (t80) REVERT: A 887 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (t80) REVERT: A 1140 MET cc_start: 0.8657 (tpp) cc_final: 0.8443 (tpp) REVERT: A 1723 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8353 (pp) REVERT: A 1916 MET cc_start: 0.7796 (mmm) cc_final: 0.7221 (ptt) REVERT: A 2027 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 59 MET cc_start: 0.4520 (ptt) cc_final: 0.4023 (ppp) REVERT: B 299 TYR cc_start: 0.8335 (t80) cc_final: 0.8021 (t80) REVERT: B 374 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7276 (t80) REVERT: B 375 LEU cc_start: 0.8675 (tt) cc_final: 0.8326 (mt) REVERT: B 377 MET cc_start: 0.9347 (mpp) cc_final: 0.9003 (mpp) REVERT: B 378 PHE cc_start: 0.8820 (m-10) cc_final: 0.7977 (m-10) REVERT: B 380 MET cc_start: 0.8644 (ptt) cc_final: 0.8313 (ppp) REVERT: B 406 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8808 (tp-100) REVERT: B 589 GLU cc_start: 0.9298 (pp20) cc_final: 0.8816 (pm20) REVERT: B 731 MET cc_start: 0.9235 (pmm) cc_final: 0.9007 (pmm) REVERT: B 795 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8665 (t80) REVERT: B 1051 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8383 (pp20) REVERT: B 1723 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 1818 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: B 1981 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: B 2017 MET cc_start: 0.8768 (mmm) cc_final: 0.8528 (mmm) REVERT: D 273 MET cc_start: 0.8203 (pmm) cc_final: 0.7910 (pmm) REVERT: D 348 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7933 (mm) REVERT: D 569 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 96 HIS cc_start: 0.5796 (p-80) cc_final: 0.4596 (p-80) REVERT: E 276 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8857 (tt) REVERT: F 259 MET cc_start: 0.9068 (mmp) cc_final: 0.8767 (mmm) REVERT: F 273 MET cc_start: 0.7052 (mpp) cc_final: 0.6759 (pmm) REVERT: F 327 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8566 (mp0) REVERT: F 352 LYS cc_start: 0.3290 (OUTLIER) cc_final: 0.2766 (mtmm) REVERT: F 369 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8449 (mt) REVERT: F 557 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9112 (mp) REVERT: F 704 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: F 706 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7631 (t80) REVERT: F 746 MET cc_start: 0.7694 (pmm) cc_final: 0.7333 (mmm) REVERT: G 26 ASN cc_start: 0.6020 (t0) cc_final: 0.5229 (t0) REVERT: G 64 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: G 106 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9289 (mm) REVERT: H 44 MET cc_start: -0.1178 (tmm) cc_final: -0.2341 (mtp) REVERT: H 119 MET cc_start: 0.3324 (ptp) cc_final: 0.1973 (tpp) REVERT: H 166 MET cc_start: -0.0870 (mpp) cc_final: -0.2567 (ttm) REVERT: I 191 MET cc_start: -0.3548 (OUTLIER) cc_final: -0.4346 (tpp) REVERT: I 251 ASN cc_start: -0.0352 (OUTLIER) cc_final: -0.1740 (t0) REVERT: J 44 MET cc_start: 0.1137 (mmm) cc_final: 0.0060 (mtm) REVERT: K 85 VAL cc_start: -0.1699 (OUTLIER) cc_final: -0.2988 (m) REVERT: K 329 MET cc_start: 0.2923 (ttt) cc_final: 0.2441 (tpp) outliers start: 209 outliers final: 139 residues processed: 592 average time/residue: 0.4366 time to fit residues: 449.8608 Evaluate side-chains 553 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 390 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1324 LEU Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1363 ASP Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2035 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1173 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1363 ASP Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1661 LEU Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain F residue 837 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 276 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 379 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 349 optimal weight: 0.4980 chunk 245 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 chunk 538 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1934 GLN ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN F 768 GLN G 189 ASN ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.112797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.081518 restraints weight = 313644.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.081910 restraints weight = 161652.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081837 restraints weight = 136999.212| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 49716 Z= 0.148 Angle : 0.629 14.942 67262 Z= 0.300 Chirality : 0.040 0.304 7575 Planarity : 0.004 0.059 8519 Dihedral : 5.641 57.992 6628 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.59 % Rotamer: Outliers : 3.68 % Allowed : 21.65 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 5915 helix: 1.75 (0.08), residues: 3935 sheet: -0.14 (0.41), residues: 150 loop : -1.19 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1689 HIS 0.005 0.001 HIS B 622 PHE 0.025 0.001 PHE B 679 TYR 0.014 0.001 TYR A 99 ARG 0.008 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 428 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9529 (mt) cc_final: 0.9181 (mm) REVERT: A 162 HIS cc_start: 0.8894 (m-70) cc_final: 0.8623 (m-70) REVERT: A 445 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: A 634 MET cc_start: 0.9097 (ptp) cc_final: 0.8772 (pmm) REVERT: A 711 ASN cc_start: 0.9521 (t0) cc_final: 0.9209 (m-40) REVERT: A 777 LEU cc_start: 0.9062 (tp) cc_final: 0.8731 (pp) REVERT: A 795 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8617 (t80) REVERT: A 887 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 1102 MET cc_start: 0.8628 (tpt) cc_final: 0.8388 (tpp) REVERT: A 1140 MET cc_start: 0.8553 (tpp) cc_final: 0.8329 (tpp) REVERT: A 1723 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 1916 MET cc_start: 0.7831 (mmm) cc_final: 0.7286 (ptt) REVERT: A 2027 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8896 (p) REVERT: B 141 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: B 158 LEU cc_start: 0.9588 (mt) cc_final: 0.9272 (pp) REVERT: B 299 TYR cc_start: 0.8338 (t80) cc_final: 0.8014 (t80) REVERT: B 374 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7231 (t80) REVERT: B 375 LEU cc_start: 0.8658 (tt) cc_final: 0.8335 (mt) REVERT: B 377 MET cc_start: 0.9330 (mpp) cc_final: 0.8988 (mpp) REVERT: B 378 PHE cc_start: 0.8739 (m-10) cc_final: 0.7917 (m-10) REVERT: B 380 MET cc_start: 0.8594 (ptt) cc_final: 0.8266 (ppp) REVERT: B 406 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8560 (tp-100) REVERT: B 589 GLU cc_start: 0.9223 (pp20) cc_final: 0.8817 (pm20) REVERT: B 795 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8684 (t80) REVERT: B 797 ASP cc_start: 0.9249 (m-30) cc_final: 0.9045 (m-30) REVERT: B 1051 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8318 (pp20) REVERT: B 1723 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 1818 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: B 1981 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: B 2017 MET cc_start: 0.8762 (mmm) cc_final: 0.8547 (mmm) REVERT: D 273 MET cc_start: 0.8267 (pmm) cc_final: 0.7920 (pmm) REVERT: D 348 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (mm) REVERT: D 569 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8540 (mm) REVERT: E 16 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: E 96 HIS cc_start: 0.5916 (p-80) cc_final: 0.4677 (p-80) REVERT: E 276 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8814 (tt) REVERT: F 259 MET cc_start: 0.9047 (mmp) cc_final: 0.8684 (mmm) REVERT: F 260 THR cc_start: 0.9173 (p) cc_final: 0.8957 (t) REVERT: F 273 MET cc_start: 0.7022 (mpp) cc_final: 0.6803 (pmm) REVERT: F 327 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8542 (mp0) REVERT: F 369 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8470 (mt) REVERT: F 557 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9088 (mp) REVERT: F 706 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7523 (t80) REVERT: F 746 MET cc_start: 0.7574 (pmm) cc_final: 0.7271 (mmm) REVERT: G 26 ASN cc_start: 0.6144 (t0) cc_final: 0.5278 (t0) REVERT: G 64 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: G 110 ASN cc_start: 0.9561 (m-40) cc_final: 0.9360 (m110) REVERT: H 44 MET cc_start: -0.1199 (tmm) cc_final: -0.2344 (mtp) REVERT: H 119 MET cc_start: 0.3309 (ptp) cc_final: 0.1916 (tpp) REVERT: H 166 MET cc_start: -0.0867 (mpp) cc_final: -0.2593 (ttm) REVERT: I 191 MET cc_start: -0.3572 (OUTLIER) cc_final: -0.3773 (tpt) REVERT: I 251 ASN cc_start: -0.0668 (OUTLIER) cc_final: -0.2001 (t0) REVERT: J 44 MET cc_start: 0.1093 (mmm) cc_final: 0.0017 (mtm) REVERT: K 329 MET cc_start: 0.2932 (ttt) cc_final: 0.2442 (tpp) outliers start: 196 outliers final: 118 residues processed: 592 average time/residue: 0.4373 time to fit residues: 449.5810 Evaluate side-chains 540 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 400 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1950 LEU Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 404 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 180 optimal weight: 0.0970 chunk 443 optimal weight: 0.0870 chunk 167 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 HIS A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.110646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.079502 restraints weight = 261211.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.077876 restraints weight = 175374.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.078602 restraints weight = 115125.078| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 49716 Z= 0.224 Angle : 0.659 14.660 67262 Z= 0.322 Chirality : 0.041 0.278 7575 Planarity : 0.004 0.059 8519 Dihedral : 5.603 58.171 6622 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.98 % Rotamer: Outliers : 3.85 % Allowed : 21.73 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.11), residues: 5915 helix: 1.73 (0.08), residues: 3936 sheet: -0.15 (0.40), residues: 150 loop : -1.24 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1689 HIS 0.005 0.001 HIS B 622 PHE 0.023 0.001 PHE B 798 TYR 0.029 0.001 TYR A 99 ARG 0.009 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 404 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9502 (mt) cc_final: 0.9141 (mm) REVERT: A 162 HIS cc_start: 0.8863 (m-70) cc_final: 0.8581 (m-70) REVERT: A 634 MET cc_start: 0.9078 (ptp) cc_final: 0.8752 (pmm) REVERT: A 711 ASN cc_start: 0.9508 (t0) cc_final: 0.9204 (m-40) REVERT: A 795 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8667 (t80) REVERT: A 887 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 933 MET cc_start: 0.6037 (mmm) cc_final: 0.5590 (tpp) REVERT: A 1723 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8280 (pp) REVERT: A 1916 MET cc_start: 0.7822 (mmm) cc_final: 0.7379 (ptt) REVERT: A 2000 MET cc_start: 0.7522 (pmm) cc_final: 0.7319 (pmm) REVERT: A 2027 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 141 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: B 204 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8282 (pt) REVERT: B 299 TYR cc_start: 0.8352 (t80) cc_final: 0.8015 (t80) REVERT: B 366 TYR cc_start: 0.4140 (m-80) cc_final: 0.3888 (m-80) REVERT: B 374 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7286 (t80) REVERT: B 375 LEU cc_start: 0.8683 (tt) cc_final: 0.8382 (mt) REVERT: B 377 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8964 (mpp) REVERT: B 378 PHE cc_start: 0.8785 (m-10) cc_final: 0.7954 (m-10) REVERT: B 380 MET cc_start: 0.8630 (ptt) cc_final: 0.8292 (ppp) REVERT: B 406 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8565 (tp-100) REVERT: B 444 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8914 (mt) REVERT: B 589 GLU cc_start: 0.9279 (pp20) cc_final: 0.8777 (pm20) REVERT: B 591 PHE cc_start: 0.9163 (m-10) cc_final: 0.8791 (m-10) REVERT: B 795 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8635 (t80) REVERT: B 917 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 1723 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8481 (pp) REVERT: B 1818 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: B 1981 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: D 273 MET cc_start: 0.8249 (pmm) cc_final: 0.7954 (pmm) REVERT: D 348 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8080 (mm) REVERT: D 569 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8448 (mm) REVERT: E 16 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.5008 (m-80) REVERT: E 276 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8730 (tt) REVERT: F 259 MET cc_start: 0.9064 (mmp) cc_final: 0.8738 (mmm) REVERT: F 260 THR cc_start: 0.9189 (p) cc_final: 0.8970 (t) REVERT: F 273 MET cc_start: 0.7083 (mpp) cc_final: 0.6822 (pmm) REVERT: F 327 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8514 (mp0) REVERT: F 352 LYS cc_start: 0.3208 (OUTLIER) cc_final: 0.1838 (mtmm) REVERT: F 369 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8490 (mt) REVERT: G 26 ASN cc_start: 0.6265 (t0) cc_final: 0.5452 (t0) REVERT: H 44 MET cc_start: -0.1606 (tmm) cc_final: -0.2718 (mtp) REVERT: H 119 MET cc_start: 0.3606 (ptp) cc_final: 0.2090 (tpp) REVERT: H 166 MET cc_start: -0.0852 (mpp) cc_final: -0.2562 (ttm) REVERT: I 191 MET cc_start: -0.4137 (OUTLIER) cc_final: -0.4736 (tpt) REVERT: I 251 ASN cc_start: -0.0215 (OUTLIER) cc_final: -0.1701 (t0) REVERT: J 44 MET cc_start: 0.1165 (mmm) cc_final: 0.0123 (mtm) REVERT: K 329 MET cc_start: 0.2970 (ttt) cc_final: 0.2502 (tpp) outliers start: 205 outliers final: 137 residues processed: 580 average time/residue: 0.4507 time to fit residues: 453.3778 Evaluate side-chains 549 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 389 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1615 THR Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1963 ILE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2035 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 815 TRP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 917 PHE Chi-restraints excluded: chain B residue 935 CYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1494 SER Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 731 ASN Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain F residue 837 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 288 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 519 optimal weight: 8.9990 chunk 576 optimal weight: 5.9990 chunk 278 optimal weight: 0.0370 chunk 136 optimal weight: 0.2980 chunk 386 optimal weight: 0.4980 chunk 438 optimal weight: 0.5980 chunk 418 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 544 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 681 GLN A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS B1659 GLN D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.113998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.082613 restraints weight = 271436.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.081785 restraints weight = 155093.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081892 restraints weight = 125912.352| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 49716 Z= 0.154 Angle : 0.662 14.525 67262 Z= 0.315 Chirality : 0.040 0.315 7575 Planarity : 0.004 0.059 8519 Dihedral : 5.521 59.107 6620 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 22.74 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 5915 helix: 1.77 (0.08), residues: 3933 sheet: -0.02 (0.41), residues: 153 loop : -1.23 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1689 HIS 0.005 0.001 HIS B 622 PHE 0.030 0.001 PHE B 798 TYR 0.024 0.001 TYR A 374 ARG 0.016 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 423 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9529 (mt) cc_final: 0.9174 (mm) REVERT: A 162 HIS cc_start: 0.8866 (m-70) cc_final: 0.8593 (m-70) REVERT: A 322 PHE cc_start: 0.5519 (m-80) cc_final: 0.5208 (m-10) REVERT: A 330 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.9038 (ptt90) REVERT: A 634 MET cc_start: 0.9112 (ptp) cc_final: 0.8800 (pmm) REVERT: A 680 GLN cc_start: 0.9724 (tp-100) cc_final: 0.9457 (pt0) REVERT: A 711 ASN cc_start: 0.9522 (t0) cc_final: 0.9181 (m-40) REVERT: A 777 LEU cc_start: 0.9065 (tp) cc_final: 0.8741 (pp) REVERT: A 795 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8669 (t80) REVERT: A 887 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 933 MET cc_start: 0.5792 (mmm) cc_final: 0.5444 (tpp) REVERT: A 1723 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 1916 MET cc_start: 0.7905 (mmm) cc_final: 0.7360 (ptt) REVERT: A 2027 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8920 (p) REVERT: B 101 LEU cc_start: 0.9628 (mt) cc_final: 0.9224 (tp) REVERT: B 141 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: B 204 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8275 (pt) REVERT: B 299 TYR cc_start: 0.8341 (t80) cc_final: 0.8022 (t80) REVERT: B 366 TYR cc_start: 0.4249 (m-80) cc_final: 0.3954 (m-80) REVERT: B 374 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7431 (t80) REVERT: B 375 LEU cc_start: 0.8722 (tt) cc_final: 0.8381 (mt) REVERT: B 377 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8968 (mpp) REVERT: B 378 PHE cc_start: 0.8866 (m-10) cc_final: 0.8108 (m-10) REVERT: B 380 MET cc_start: 0.8563 (ptt) cc_final: 0.8259 (ppp) REVERT: B 406 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8646 (tp-100) REVERT: B 444 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8958 (mt) REVERT: B 589 GLU cc_start: 0.9350 (pp20) cc_final: 0.8863 (pm20) REVERT: B 795 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8678 (t80) REVERT: B 797 ASP cc_start: 0.9273 (m-30) cc_final: 0.9061 (m-30) REVERT: B 917 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8434 (t80) REVERT: B 1051 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8361 (pp20) REVERT: B 1723 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8487 (pp) REVERT: B 1818 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: B 1981 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: D 273 MET cc_start: 0.8275 (pmm) cc_final: 0.7966 (pmm) REVERT: D 348 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (mm) REVERT: D 569 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8568 (mm) REVERT: D 784 GLU cc_start: 0.8338 (tp30) cc_final: 0.8085 (tp30) REVERT: E 16 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.4913 (m-80) REVERT: E 96 HIS cc_start: 0.5825 (p-80) cc_final: 0.4567 (p-80) REVERT: E 276 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8815 (tt) REVERT: F 259 MET cc_start: 0.9070 (mmp) cc_final: 0.8726 (mmm) REVERT: F 327 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8492 (mp0) REVERT: F 369 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8456 (mt) REVERT: F 573 ASP cc_start: 0.9329 (t70) cc_final: 0.8958 (m-30) REVERT: F 706 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7479 (t80) REVERT: G 26 ASN cc_start: 0.6283 (t0) cc_final: 0.5404 (t0) REVERT: H 44 MET cc_start: -0.1260 (tmm) cc_final: -0.2376 (mtp) REVERT: H 119 MET cc_start: 0.3538 (ptp) cc_final: 0.2003 (tpp) REVERT: H 166 MET cc_start: -0.0791 (mpp) cc_final: -0.2571 (ttm) REVERT: I 191 MET cc_start: -0.4059 (OUTLIER) cc_final: -0.4692 (tpt) REVERT: I 251 ASN cc_start: -0.0130 (OUTLIER) cc_final: -0.1659 (t0) REVERT: J 44 MET cc_start: 0.1225 (mmm) cc_final: 0.0161 (mtm) REVERT: K 329 MET cc_start: 0.3066 (ttt) cc_final: 0.2562 (tpp) outliers start: 158 outliers final: 109 residues processed: 553 average time/residue: 0.4393 time to fit residues: 423.5673 Evaluate side-chains 539 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 406 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1204 LYS Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2031 MET Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 917 PHE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1494 SER Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1715 LEU Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1899 ILE Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 437 optimal weight: 1.9990 chunk 478 optimal weight: 6.9990 chunk 96 optimal weight: 0.0170 chunk 39 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 517 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 ASN ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.111937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.081295 restraints weight = 267786.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.080568 restraints weight = 171179.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.081222 restraints weight = 124076.491| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 49716 Z= 0.160 Angle : 0.666 14.418 67262 Z= 0.316 Chirality : 0.040 0.348 7575 Planarity : 0.004 0.060 8519 Dihedral : 5.385 57.974 6613 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.47 % Rotamer: Outliers : 2.94 % Allowed : 22.66 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 5915 helix: 1.77 (0.08), residues: 3937 sheet: 0.07 (0.41), residues: 153 loop : -1.21 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1689 HIS 0.007 0.001 HIS D 775 PHE 0.030 0.001 PHE B 798 TYR 0.022 0.001 TYR A 374 ARG 0.008 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 413 time to evaluate : 4.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.9534 (mt) cc_final: 0.9183 (mm) REVERT: A 162 HIS cc_start: 0.8923 (m-70) cc_final: 0.8643 (m-70) REVERT: A 322 PHE cc_start: 0.5532 (m-80) cc_final: 0.5247 (m-10) REVERT: A 330 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.9073 (ptt90) REVERT: A 634 MET cc_start: 0.9103 (ptp) cc_final: 0.8781 (pmm) REVERT: A 711 ASN cc_start: 0.9528 (t0) cc_final: 0.9199 (m-40) REVERT: A 731 MET cc_start: 0.9521 (ptp) cc_final: 0.9275 (ptp) REVERT: A 777 LEU cc_start: 0.9032 (tp) cc_final: 0.8748 (pp) REVERT: A 795 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8651 (t80) REVERT: A 887 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7542 (t80) REVERT: A 1723 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8231 (pp) REVERT: A 1916 MET cc_start: 0.7829 (mmm) cc_final: 0.7403 (ptt) REVERT: A 2000 MET cc_start: 0.7534 (pmm) cc_final: 0.7152 (pmm) REVERT: A 2027 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8806 (p) REVERT: B 141 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: B 167 MET cc_start: 0.7745 (pmm) cc_final: 0.7359 (pmm) REVERT: B 204 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8233 (pt) REVERT: B 299 TYR cc_start: 0.8322 (t80) cc_final: 0.7988 (t80) REVERT: B 366 TYR cc_start: 0.4314 (m-80) cc_final: 0.4003 (m-80) REVERT: B 374 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7100 (t80) REVERT: B 375 LEU cc_start: 0.8653 (tt) cc_final: 0.8337 (mt) REVERT: B 378 PHE cc_start: 0.8836 (m-10) cc_final: 0.8094 (m-10) REVERT: B 380 MET cc_start: 0.8576 (ptt) cc_final: 0.8297 (ppp) REVERT: B 406 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8557 (tp-100) REVERT: B 444 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8999 (mt) REVERT: B 589 GLU cc_start: 0.9344 (pp20) cc_final: 0.8861 (pm20) REVERT: B 795 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8596 (t80) REVERT: B 797 ASP cc_start: 0.9238 (m-30) cc_final: 0.9033 (m-30) REVERT: B 917 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 1051 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8367 (pp20) REVERT: B 1723 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8515 (pp) REVERT: B 1818 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: B 1981 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 2019 MET cc_start: 0.8199 (mtp) cc_final: 0.7987 (ttt) REVERT: D 273 MET cc_start: 0.8326 (pmm) cc_final: 0.8088 (pmm) REVERT: D 348 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (mm) REVERT: D 569 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8385 (mm) REVERT: E 16 PHE cc_start: 0.5292 (OUTLIER) cc_final: 0.4925 (m-80) REVERT: E 96 HIS cc_start: 0.5888 (p-80) cc_final: 0.4597 (p-80) REVERT: E 276 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8683 (tt) REVERT: F 256 ASN cc_start: 0.9438 (p0) cc_final: 0.8909 (m110) REVERT: F 259 MET cc_start: 0.9061 (mmp) cc_final: 0.8724 (mmm) REVERT: F 273 MET cc_start: 0.7475 (pmm) cc_final: 0.5459 (mmt) REVERT: F 327 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8459 (mp0) REVERT: F 369 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8407 (mt) REVERT: F 706 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7444 (t80) REVERT: F 746 MET cc_start: 0.7494 (pmm) cc_final: 0.7124 (mmm) REVERT: G 26 ASN cc_start: 0.6329 (t0) cc_final: 0.5515 (t0) REVERT: G 63 PHE cc_start: 0.8997 (m-80) cc_final: 0.8743 (m-10) REVERT: H 44 MET cc_start: -0.1287 (tmm) cc_final: -0.2328 (mtp) REVERT: H 119 MET cc_start: 0.3576 (ptp) cc_final: 0.2104 (tpp) REVERT: H 166 MET cc_start: -0.0777 (mpp) cc_final: -0.2544 (ttm) REVERT: I 191 MET cc_start: -0.4151 (OUTLIER) cc_final: -0.4690 (tpt) REVERT: I 251 ASN cc_start: 0.0246 (OUTLIER) cc_final: -0.1328 (t0) REVERT: J 44 MET cc_start: 0.1313 (mmm) cc_final: 0.0305 (mtm) REVERT: K 329 MET cc_start: 0.3024 (ttt) cc_final: 0.2575 (tpp) outliers start: 156 outliers final: 118 residues processed: 541 average time/residue: 0.4394 time to fit residues: 416.5476 Evaluate side-chains 542 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 401 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2031 MET Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 917 PHE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1494 SER Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1715 LEU Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1899 ILE Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2031 MET Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 767 MET Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 288 TYR Chi-restraints excluded: chain K residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 591 optimal weight: 4.9990 chunk 432 optimal weight: 20.0000 chunk 444 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 560 optimal weight: 0.9990 chunk 519 optimal weight: 20.0000 chunk 510 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 296 optimal weight: 0.0050 chunk 98 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.111958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.081838 restraints weight = 280285.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.081211 restraints weight = 159906.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.081159 restraints weight = 137794.792| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 49716 Z= 0.156 Angle : 0.675 15.258 67262 Z= 0.319 Chirality : 0.040 0.375 7575 Planarity : 0.004 0.060 8519 Dihedral : 5.332 57.867 6611 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 2.66 % Allowed : 23.04 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 5915 helix: 1.78 (0.08), residues: 3938 sheet: 0.11 (0.42), residues: 153 loop : -1.19 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1689 HIS 0.006 0.000 HIS B 622 PHE 0.035 0.001 PHE B 798 TYR 0.023 0.001 TYR A 374 ARG 0.007 0.000 ARG B1399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11830 Ramachandran restraints generated. 5915 Oldfield, 0 Emsley, 5915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 420 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8840 (pt0) cc_final: 0.8571 (pt0) REVERT: A 158 LEU cc_start: 0.9544 (mt) cc_final: 0.9177 (mm) REVERT: A 162 HIS cc_start: 0.8915 (m-70) cc_final: 0.8654 (m-70) REVERT: A 322 PHE cc_start: 0.5569 (m-80) cc_final: 0.5316 (m-10) REVERT: A 330 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.9055 (ptt90) REVERT: A 634 MET cc_start: 0.9095 (ptp) cc_final: 0.8770 (pmm) REVERT: A 676 TRP cc_start: 0.8919 (t-100) cc_final: 0.8370 (t60) REVERT: A 711 ASN cc_start: 0.9516 (t0) cc_final: 0.9186 (m-40) REVERT: A 777 LEU cc_start: 0.9002 (tp) cc_final: 0.8704 (pp) REVERT: A 795 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8686 (t80) REVERT: A 887 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 1723 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8091 (pp) REVERT: A 1916 MET cc_start: 0.7883 (mmm) cc_final: 0.7446 (ptt) REVERT: A 2000 MET cc_start: 0.7545 (pmm) cc_final: 0.7151 (pmm) REVERT: A 2027 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8820 (p) REVERT: B 59 MET cc_start: 0.4715 (ppp) cc_final: 0.3454 (pmm) REVERT: B 141 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: B 167 MET cc_start: 0.7647 (pmm) cc_final: 0.7302 (pmm) REVERT: B 299 TYR cc_start: 0.8315 (t80) cc_final: 0.8007 (t80) REVERT: B 366 TYR cc_start: 0.4358 (m-80) cc_final: 0.4019 (m-80) REVERT: B 374 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7037 (t80) REVERT: B 375 LEU cc_start: 0.8608 (tt) cc_final: 0.8280 (mt) REVERT: B 378 PHE cc_start: 0.8760 (m-10) cc_final: 0.8102 (m-10) REVERT: B 380 MET cc_start: 0.8569 (ptt) cc_final: 0.8282 (ppp) REVERT: B 406 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8539 (tp-100) REVERT: B 444 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8970 (mt) REVERT: B 589 GLU cc_start: 0.9332 (pp20) cc_final: 0.8861 (pm20) REVERT: B 795 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8676 (t80) REVERT: B 797 ASP cc_start: 0.9274 (m-30) cc_final: 0.9063 (m-30) REVERT: B 917 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8447 (t80) REVERT: B 1051 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8314 (pp20) REVERT: B 1723 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 1818 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: B 1981 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 2019 MET cc_start: 0.8500 (mtp) cc_final: 0.8265 (ttt) REVERT: D 273 MET cc_start: 0.8305 (pmm) cc_final: 0.8024 (pmm) REVERT: D 348 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8016 (mm) REVERT: D 569 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8512 (mm) REVERT: E 16 PHE cc_start: 0.5232 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: E 96 HIS cc_start: 0.5912 (p-80) cc_final: 0.4644 (p-80) REVERT: E 276 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8782 (tt) REVERT: F 256 ASN cc_start: 0.9460 (p0) cc_final: 0.8946 (m110) REVERT: F 259 MET cc_start: 0.9079 (mmp) cc_final: 0.8741 (mmm) REVERT: F 273 MET cc_start: 0.7445 (pmm) cc_final: 0.5418 (mmt) REVERT: F 327 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8448 (mp0) REVERT: F 369 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8476 (mt) REVERT: F 706 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7469 (t80) REVERT: F 746 MET cc_start: 0.7632 (pmm) cc_final: 0.7106 (mmm) REVERT: G 26 ASN cc_start: 0.6374 (t0) cc_final: 0.5547 (t0) REVERT: H 44 MET cc_start: -0.1254 (tmm) cc_final: -0.2380 (mtp) REVERT: H 119 MET cc_start: 0.3319 (ptp) cc_final: 0.1951 (tpp) REVERT: H 166 MET cc_start: -0.0761 (mpp) cc_final: -0.2610 (ttm) REVERT: I 191 MET cc_start: -0.4078 (OUTLIER) cc_final: -0.4673 (tpt) REVERT: I 251 ASN cc_start: -0.0537 (OUTLIER) cc_final: -0.2089 (t0) REVERT: J 44 MET cc_start: 0.1300 (mmm) cc_final: 0.0201 (mtm) REVERT: K 329 MET cc_start: 0.3145 (ttt) cc_final: 0.2709 (ttm) outliers start: 141 outliers final: 106 residues processed: 538 average time/residue: 0.4389 time to fit residues: 410.5538 Evaluate side-chains 536 residues out of total 5348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 408 time to evaluate : 4.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1611 CYS Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1767 GLU Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 LEU Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2031 MET Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 917 PHE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1322 SER Chi-restraints excluded: chain B residue 1332 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1494 SER Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1708 ILE Chi-restraints excluded: chain B residue 1715 LEU Chi-restraints excluded: chain B residue 1723 LEU Chi-restraints excluded: chain B residue 1809 VAL Chi-restraints excluded: chain B residue 1818 GLU Chi-restraints excluded: chain B residue 1860 LEU Chi-restraints excluded: chain B residue 1899 ILE Chi-restraints excluded: chain B residue 1939 PHE Chi-restraints excluded: chain B residue 1981 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 508 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 776 GLN Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 175 CYS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 579 TYR Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 709 ILE Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain F residue 800 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 288 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 291 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 387 optimal weight: 5.9990 chunk 209 optimal weight: 0.0040 chunk 260 optimal weight: 1.9990 chunk 404 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A1213 HIS ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 HIS D 776 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.111500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081603 restraints weight = 270619.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.080706 restraints weight = 165381.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.080678 restraints weight = 144170.794| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49716 Z= 0.169 Angle : 0.678 14.931 67262 Z= 0.321 Chirality : 0.041 0.371 7575 Planarity : 0.004 0.060 8519 Dihedral : 5.283 58.283 6609 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 2.67 % Allowed : 23.09 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 5915 helix: 1.82 (0.08), residues: 3932 sheet: 0.09 (0.42), residues: 153 loop : -1.16 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1689 HIS 0.007 0.001 HIS B 622 PHE 0.029 0.001 PHE F 319 TYR 0.040 0.001 TYR A 144 ARG 0.007 0.000 ARG K 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19210.63 seconds wall clock time: 331 minutes 32.67 seconds (19892.67 seconds total)