Starting phenix.real_space_refine on Sat Oct 31 14:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ot6_70826/10_2026/9ot6_70826.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 282 5.16 5 C 27508 2.51 5 N 7160 2.21 5 O 7728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42678 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1724, 13842 Classifications: {'peptide': 1724} Link IDs: {'PCIS': 1, 'PTRANS': 86, 'TRANS': 1636} Chain breaks: 23 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 811 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 3 Chain: "D" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4676 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Chain breaks: 5 Chain: "E" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2010 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 236} Chain breaks: 4 Restraints were copied for chains: B, H, F, G Time building chain proxies: 28.50, per 1000 atoms: 0.67 Number of scatterers: 42678 At special positions: 0 Unit cell: (197.12, 264.11, 127.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 282 16.00 O 7728 8.00 N 7160 7.00 C 27508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10188 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 16 sheets defined 69.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.550A pdb=" N VAL A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.535A 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 106 removed outlier: 3.713A 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 127 through 146 Processing helix chain 'A' and resid 149 through 169 Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.993A pdb=" N ILE A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.760A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.831A 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 removed outlier: 3.755A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 359 removed outlier: 3.934A pdb=" N LEU A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 removed outlier: 3.596A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 412 removed outlier: 3.554A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 4.054A pdb=" N ALA A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 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 removed outlier: 3.922A pdb=" N PHE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.843A pdb=" N VAL A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) 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: 3.669A pdb=" N ILE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.878A pdb=" N ILE A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 Processing helix chain 'A' and resid 704 through 718 removed outlier: 4.369A pdb=" N ALA A 708 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 741 Processing helix chain 'A' and resid 766 through 769 removed outlier: 4.107A pdb=" N VAL A 769 " --> pdb=" O ASN A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.867A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 806 removed outlier: 3.679A pdb=" N GLN A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 822 removed outlier: 3.873A pdb=" N TYR A 820 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.559A pdb=" N ILE A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 removed outlier: 3.531A pdb=" N VAL A 844 " --> pdb=" O PRO A 840 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 845' Processing helix chain 'A' and resid 858 through 873 Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.944A pdb=" N LYS A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 907 Processing helix chain 'A' and resid 912 through 915 removed outlier: 4.018A pdb=" N VAL A 915 " --> pdb=" O ARG A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 915' Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.744A pdb=" N PHE A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 934 through 952 Processing helix chain 'A' and resid 957 through 974 removed outlier: 3.633A pdb=" N GLU A 961 " --> pdb=" O THR A 957 " (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: 3.671A 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 1021 Processing helix chain 'A' and resid 1046 through 1072 removed outlier: 4.035A pdb=" N ALA A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A1061 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1084 removed outlier: 3.727A pdb=" N THR A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1093 removed outlier: 3.692A pdb=" N TRP A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 removed outlier: 3.789A pdb=" N ILE A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1157 removed outlier: 3.643A pdb=" N MET A1140 " --> pdb=" O TYR A1136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 Processing helix chain 'A' and resid 1185 through 1202 removed outlier: 3.609A pdb=" N SER A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1216 Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1224 through 1241 Processing helix chain 'A' and resid 1244 through 1263 Processing helix chain 'A' and resid 1275 through 1279 removed outlier: 3.708A pdb=" N ALA A1279 " --> pdb=" O PRO A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1309 removed outlier: 3.568A pdb=" N ILE A1299 " --> pdb=" O HIS A1295 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A1300 " --> pdb=" O TYR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1326 Processing helix chain 'A' and resid 1342 through 1345 Processing helix chain 'A' and resid 1346 through 1362 Processing helix chain 'A' and resid 1369 through 1384 Processing helix chain 'A' and resid 1385 through 1387 No H-bonds generated for 'chain 'A' and resid 1385 through 1387' Processing helix chain 'A' and resid 1400 through 1416 Processing helix chain 'A' and resid 1478 through 1508 removed outlier: 3.888A pdb=" N ARG A1488 " --> pdb=" O TYR A1484 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1533 removed outlier: 3.573A pdb=" N GLU A1522 " --> pdb=" O ASP A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 Processing helix chain 'A' and resid 1551 through 1558 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 Processing helix chain 'A' and resid 1580 through 1583 removed outlier: 3.629A pdb=" N VAL A1583 " --> pdb=" O PRO A1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1580 through 1583' Processing helix chain 'A' and resid 1585 through 1590 removed outlier: 3.580A pdb=" N ILE A1590 " --> pdb=" O VAL A1586 " (cutoff:3.500A) 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 1616 through 1622 Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1631 through 1643 Processing helix chain 'A' and resid 1646 through 1653 removed outlier: 3.539A pdb=" N ILE A1650 " --> pdb=" O PRO A1646 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1660 removed outlier: 3.617A pdb=" N ILE A1657 " --> pdb=" O TYR A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1681 through 1695 removed outlier: 4.013A pdb=" N THR A1693 " --> pdb=" O TRP A1689 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A1695 " --> pdb=" O MET A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1720 Processing helix chain 'A' and resid 1725 through 1749 removed outlier: 4.350A pdb=" N VAL A1744 " --> pdb=" O LYS A1740 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER A1745 " --> pdb=" O ILE A1741 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A1746 " --> pdb=" O THR A1742 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A1749 " --> pdb=" O SER A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1768 removed outlier: 3.536A pdb=" N VAL A1768 " --> pdb=" O ALA A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1821 Processing helix chain 'A' and resid 1856 through 1876 Processing helix chain 'A' and resid 1904 through 1913 Processing helix chain 'A' and resid 1915 through 1925 removed outlier: 3.616A pdb=" N TYR A1919 " --> pdb=" O GLY A1915 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1954 removed outlier: 3.598A pdb=" N ALA A1945 " --> pdb=" O ARG A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2004 removed outlier: 3.547A pdb=" N MET A2004 " --> pdb=" O MET A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2028 removed outlier: 3.560A pdb=" N ARG A2028 " --> pdb=" O TYR A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2040 removed outlier: 3.943A pdb=" N VAL A2034 " --> pdb=" O TYR A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2045 removed outlier: 3.962A pdb=" N THR A2044 " --> pdb=" O MET A2041 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY A2045 " --> pdb=" O LEU A2042 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2041 through 2045' Processing helix chain 'A' and resid 2052 through 2060 Processing helix chain 'A' and resid 2066 through 2081 removed outlier: 3.684A pdb=" N CYS A2081 " --> pdb=" O VAL A2077 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.550A pdb=" N VAL B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.535A pdb=" N VAL B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.713A pdb=" N VAL B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 149 through 169 Processing helix chain 'B' and resid 176 through 193 removed outlier: 4.993A pdb=" N ILE B 184 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.760A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.832A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.756A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 359 removed outlier: 3.934A pdb=" N LEU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.595A pdb=" N LEU B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 412 removed outlier: 3.554A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 4.054A pdb=" N ALA B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 Processing helix chain 'B' and resid 479 through 496 Processing helix chain 'B' and resid 499 through 513 Proline residue: B 505 - end of helix removed outlier: 3.922A pdb=" N PHE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.844A pdb=" N VAL B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 601 Processing helix chain 'B' and resid 612 through 627 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.668A pdb=" N ILE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.878A pdb=" N ILE B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 662 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 665 " --> pdb=" O GLY B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 Processing helix chain 'B' and resid 704 through 718 removed outlier: 4.370A pdb=" N ALA B 708 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 741 Processing helix chain 'B' and resid 766 through 769 removed outlier: 4.107A pdb=" N VAL B 769 " --> pdb=" O ASN B 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 766 through 769' Processing helix chain 'B' and resid 770 through 779 removed outlier: 3.867A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 806 removed outlier: 3.678A pdb=" N GLN B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 removed outlier: 3.875A pdb=" N TYR B 820 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.559A pdb=" N ILE B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 removed outlier: 3.531A pdb=" N VAL B 844 " --> pdb=" O PRO B 840 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 840 through 845' Processing helix chain 'B' and resid 858 through 873 Processing helix chain 'B' and resid 875 through 884 removed outlier: 3.945A pdb=" N LYS B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 907 Processing helix chain 'B' and resid 912 through 915 removed outlier: 4.017A pdb=" N VAL B 915 " --> pdb=" O ARG B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 915' Processing helix chain 'B' and resid 916 through 921 removed outlier: 3.743A pdb=" N PHE B 920 " --> pdb=" O MET B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 934 through 952 Processing helix chain 'B' and resid 957 through 974 removed outlier: 3.633A pdb=" N GLU B 961 " --> pdb=" O THR B 957 " (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 removed outlier: 3.671A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 Processing helix chain 'B' and resid 1005 through 1021 Processing helix chain 'B' and resid 1046 through 1072 removed outlier: 4.035A pdb=" N ALA B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B1061 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B1062 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1084 removed outlier: 3.728A pdb=" N THR B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1093 removed outlier: 3.692A pdb=" N TRP B1090 " --> pdb=" O LYS B1086 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B1091 " --> pdb=" O HIS B1087 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B1092 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1107 removed outlier: 3.789A pdb=" N ILE B1107 " --> pdb=" O ALA B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1157 removed outlier: 3.642A pdb=" N MET B1140 " --> pdb=" O TYR B1136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B1156 " --> pdb=" O GLU B1152 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B1157 " --> pdb=" O VAL B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1184 Processing helix chain 'B' and resid 1185 through 1202 removed outlier: 3.610A pdb=" N SER B1202 " --> pdb=" O ALA B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1216 Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'B' and resid 1224 through 1241 Processing helix chain 'B' and resid 1244 through 1263 Processing helix chain 'B' and resid 1275 through 1279 removed outlier: 3.708A pdb=" N ALA B1279 " --> pdb=" O PRO B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1309 removed outlier: 3.567A pdb=" N ILE B1299 " --> pdb=" O HIS B1295 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B1300 " --> pdb=" O TYR B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1326 Processing helix chain 'B' and resid 1342 through 1345 Processing helix chain 'B' and resid 1346 through 1362 Processing helix chain 'B' and resid 1369 through 1384 Processing helix chain 'B' and resid 1385 through 1387 No H-bonds generated for 'chain 'B' and resid 1385 through 1387' Processing helix chain 'B' and resid 1400 through 1416 Processing helix chain 'B' and resid 1478 through 1508 removed outlier: 3.887A pdb=" N ARG B1488 " --> pdb=" O TYR B1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B1508 " --> pdb=" O ILE B1504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1533 removed outlier: 3.572A pdb=" N GLU B1522 " --> pdb=" O ASP B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1551 Processing helix chain 'B' and resid 1551 through 1558 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 1580 through 1583 removed outlier: 3.629A pdb=" N VAL B1583 " --> pdb=" O PRO B1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1580 through 1583' Processing helix chain 'B' and resid 1585 through 1590 removed outlier: 3.581A pdb=" N ILE B1590 " --> pdb=" O VAL B1586 " (cutoff:3.500A) Processing helix chain 'B' and resid 1591 through 1593 No H-bonds generated for 'chain 'B' and resid 1591 through 1593' Processing helix chain 'B' and resid 1616 through 1622 Processing helix chain 'B' and resid 1623 through 1625 No H-bonds generated for 'chain 'B' and resid 1623 through 1625' Processing helix chain 'B' and resid 1631 through 1643 Processing helix chain 'B' and resid 1646 through 1653 removed outlier: 3.540A pdb=" N ILE B1650 " --> pdb=" O PRO B1646 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B1653 " --> pdb=" O ALA B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1653 through 1660 removed outlier: 3.618A pdb=" N ILE B1657 " --> pdb=" O TYR B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1667 through 1680 Processing helix chain 'B' and resid 1681 through 1695 removed outlier: 4.012A pdb=" N THR B1693 " --> pdb=" O TRP B1689 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B1694 " --> pdb=" O ASN B1690 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B1695 " --> pdb=" O MET B1691 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1720 Processing helix chain 'B' and resid 1725 through 1749 removed outlier: 4.350A pdb=" N VAL B1744 " --> pdb=" O LYS B1740 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1745 " --> pdb=" O ILE B1741 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B1746 " --> pdb=" O THR B1742 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B1749 " --> pdb=" O SER B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1768 removed outlier: 3.536A pdb=" N VAL B1768 " --> pdb=" O ALA B1764 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1821 Processing helix chain 'B' and resid 1856 through 1876 Processing helix chain 'B' and resid 1904 through 1913 Processing helix chain 'B' and resid 1915 through 1925 removed outlier: 3.618A pdb=" N TYR B1919 " --> pdb=" O GLY B1915 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1954 removed outlier: 3.599A pdb=" N ALA B1945 " --> pdb=" O ARG B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1997 through 2004 removed outlier: 3.548A pdb=" N MET B2004 " --> pdb=" O MET B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2028 removed outlier: 3.560A pdb=" N ARG B2028 " --> pdb=" O TYR B2024 " (cutoff:3.500A) Processing helix chain 'B' and resid 2030 through 2040 removed outlier: 3.943A pdb=" N VAL B2034 " --> pdb=" O TYR B2030 " (cutoff:3.500A) Processing helix chain 'B' and resid 2041 through 2045 removed outlier: 3.963A pdb=" N THR B2044 " --> pdb=" O MET B2041 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B2045 " --> pdb=" O LEU B2042 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2041 through 2045' Processing helix chain 'B' and resid 2052 through 2060 Processing helix chain 'B' and resid 2066 through 2081 removed outlier: 3.685A pdb=" N CYS B2081 " --> pdb=" O VAL B2077 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 154 removed outlier: 3.732A pdb=" N LEU D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 196 Processing helix chain 'D' and resid 217 through 233 removed outlier: 4.510A pdb=" N ALA D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 323 through 341 removed outlier: 3.979A pdb=" N ARG D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 375 removed outlier: 4.035A 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 411 removed outlier: 3.726A 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 443 Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.531A pdb=" N VAL D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 486 Processing helix chain 'D' and resid 490 through 511 removed outlier: 3.625A pdb=" N GLU D 494 " --> pdb=" O ARG D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 528 removed outlier: 3.732A pdb=" N ALA D 518 " --> pdb=" O ASP D 514 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 545 Processing helix chain 'D' and resid 548 through 562 removed outlier: 3.627A pdb=" N GLN D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 579 Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 598 through 617 removed outlier: 3.775A pdb=" N ALA D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 708 Processing helix chain 'D' and resid 711 through 723 Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.627A pdb=" N LEU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 760 removed outlier: 3.616A pdb=" N ARG D 751 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 759 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 778 removed outlier: 3.721A pdb=" N GLN D 776 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 777 " --> pdb=" O ILE D 773 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 778 " --> pdb=" O LEU D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 794 removed outlier: 3.836A pdb=" N LYS D 785 " --> pdb=" O SER D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 810 removed outlier: 3.869A pdb=" N TRP D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA D 810 " --> pdb=" O GLU D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 829 removed outlier: 3.593A pdb=" N ALA D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 36 through 46 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 68 through 77 removed outlier: 3.865A pdb=" N LEU E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.655A pdb=" N LEU E 82 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 91 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.717A pdb=" N LEU E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS E 211 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 221 removed outlier: 4.001A pdb=" N HIS E 219 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 248 removed outlier: 3.886A pdb=" N PHE E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 271 Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.569A pdb=" N LEU E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 154 removed outlier: 3.731A pdb=" N LEU F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 196 Processing helix chain 'F' and resid 217 through 233 removed outlier: 4.511A pdb=" N ALA F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 247 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 323 through 341 removed outlier: 3.979A pdb=" N ARG F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 375 removed outlier: 4.035A pdb=" N ARG F 375 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 390 Processing helix chain 'F' and resid 396 through 411 removed outlier: 3.726A 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 443 Processing helix chain 'F' and resid 448 through 461 removed outlier: 3.532A pdb=" N VAL F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 486 Processing helix chain 'F' and resid 490 through 511 removed outlier: 3.625A pdb=" N GLU F 494 " --> pdb=" O ARG F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 528 removed outlier: 3.732A pdb=" N ALA F 518 " --> pdb=" O ASP F 514 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE F 527 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER F 528 " --> pdb=" O GLN F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 545 Processing helix chain 'F' and resid 548 through 562 removed outlier: 3.627A pdb=" N GLN F 562 " --> pdb=" O LEU F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 579 Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 598 through 617 removed outlier: 3.774A pdb=" N ALA F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 708 Processing helix chain 'F' and resid 711 through 723 Processing helix chain 'F' and resid 729 through 744 removed outlier: 3.627A pdb=" N LEU F 733 " --> pdb=" O SER F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 760 removed outlier: 3.615A pdb=" N ARG F 751 " --> pdb=" O ASP F 747 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 759 " --> pdb=" O GLU F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 778 removed outlier: 3.720A pdb=" N GLN F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 777 " --> pdb=" O ILE F 773 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 778 " --> pdb=" O LEU F 774 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 794 removed outlier: 3.835A pdb=" N LYS F 785 " --> pdb=" O SER F 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 810 removed outlier: 3.869A pdb=" N TRP F 801 " --> pdb=" O ALA F 797 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 829 removed outlier: 3.593A pdb=" N ALA F 829 " --> pdb=" O LEU F 825 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 839 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 36 through 46 Processing helix chain 'G' and resid 52 through 63 Processing helix chain 'G' and resid 68 through 77 removed outlier: 3.866A pdb=" N LEU G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE G 74 " --> pdb=" O GLN G 70 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.656A pdb=" N LEU G 82 " --> pdb=" O PHE G 78 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 176 through 189 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.718A pdb=" N LEU G 200 " --> pdb=" O PRO G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS G 211 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 221 removed outlier: 4.002A pdb=" N HIS G 219 " --> pdb=" O TYR G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 248 removed outlier: 3.886A pdb=" N PHE G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA G 247 " --> pdb=" O GLY G 243 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 271 Processing helix chain 'G' and resid 272 through 284 removed outlier: 3.568A pdb=" N LEU G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.342A pdb=" N PHE A 68 " --> pdb=" O TYR A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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: 6.765A pdb=" N LYS A1808 " --> pdb=" O LEU A1785 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE A1787 " --> pdb=" O LYS A1806 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS A1806 " --> pdb=" O ILE A1787 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A1803 " --> pdb=" O PHE A1849 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A1895 " --> pdb=" O ALA A1888 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA A1888 " --> pdb=" O VAL A1895 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU A1897 " --> pdb=" O VAL A1886 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A1886 " --> pdb=" O GLU A1897 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1964 through 1965 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 70 removed outlier: 6.342A pdb=" N PHE B 68 " --> pdb=" O TYR B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AA7, first strand: chain 'B' and resid 1782 through 1787 removed outlier: 6.765A pdb=" N LYS B1808 " --> pdb=" O LEU B1785 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE B1787 " --> pdb=" O LYS B1806 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS B1806 " --> pdb=" O ILE B1787 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B1803 " --> pdb=" O PHE B1849 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B1895 " --> pdb=" O ALA B1888 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA B1888 " --> pdb=" O VAL B1895 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU B1897 " --> pdb=" O VAL B1886 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B1886 " --> pdb=" O GLU B1897 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1964 through 1965 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.840A pdb=" N LEU C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TRP C 101 " --> pdb=" O HIS C 111 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS C 111 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.840A pdb=" N LEU C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.974A pdb=" N SER E 163 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE E 125 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 161 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 123 through 125 removed outlier: 3.974A pdb=" N SER G 163 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE G 125 " --> pdb=" O VAL G 161 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL G 161 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.841A pdb=" N LEU H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG H 40 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TRP H 101 " --> pdb=" O HIS H 111 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS H 111 " --> pdb=" O TRP H 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.841A pdb=" N LEU H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG H 40 " --> pdb=" O LEU H 49 " (cutoff:3.500A) 2580 hydrogen bonds defined for protein. 7632 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: 9.89 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13627 1.34 - 1.46: 9318 1.46 - 1.58: 20205 1.58 - 1.69: 0 1.69 - 1.81: 440 Bond restraints: 43590 Sorted by residual: bond pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 1.520 1.532 -0.012 8.80e-03 1.29e+04 1.87e+00 bond pdb=" CA VAL B 97 " pdb=" C VAL B 97 " ideal model delta sigma weight residual 1.520 1.532 -0.012 8.80e-03 1.29e+04 1.81e+00 bond pdb=" CA PRO F 134 " pdb=" C PRO F 134 " ideal model delta sigma weight residual 1.514 1.520 -0.006 5.50e-03 3.31e+04 1.09e+00 bond pdb=" CA PRO D 134 " pdb=" C PRO D 134 " ideal model delta sigma weight residual 1.514 1.520 -0.005 5.50e-03 3.31e+04 9.99e-01 bond pdb=" N ILE A 399 " pdb=" CA ILE A 399 " ideal model delta sigma weight residual 1.461 1.472 -0.011 1.17e-02 7.31e+03 9.16e-01 ... (remaining 43585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 58215 1.73 - 3.46: 626 3.46 - 5.20: 104 5.20 - 6.93: 35 6.93 - 8.66: 10 Bond angle restraints: 58990 Sorted by residual: angle pdb=" N VAL E 212 " pdb=" CA VAL E 212 " pdb=" C VAL E 212 " ideal model delta sigma weight residual 113.20 109.60 3.60 9.60e-01 1.09e+00 1.41e+01 angle pdb=" N VAL G 212 " pdb=" CA VAL G 212 " pdb=" C VAL G 212 " ideal model delta sigma weight residual 113.20 109.62 3.58 9.60e-01 1.09e+00 1.39e+01 angle pdb=" N ILE B1297 " pdb=" CA ILE B1297 " pdb=" C ILE B1297 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" N ILE A1297 " pdb=" CA ILE A1297 " pdb=" C ILE A1297 " ideal model delta sigma weight residual 112.96 109.51 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" C TYR H 106 " pdb=" N ASN H 107 " pdb=" CA ASN H 107 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.88e+00 ... (remaining 58985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 24663 17.41 - 34.83: 1309 34.83 - 52.24: 282 52.24 - 69.65: 40 69.65 - 87.07: 30 Dihedral angle restraints: 26324 sinusoidal: 10642 harmonic: 15682 Sorted by residual: dihedral pdb=" CA LEU C 103 " pdb=" C LEU C 103 " pdb=" N ALA C 104 " pdb=" CA ALA C 104 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU H 103 " pdb=" C LEU H 103 " pdb=" N ALA H 104 " pdb=" CA ALA H 104 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PRO B 392 " pdb=" C PRO B 392 " pdb=" N THR B 393 " pdb=" CA THR B 393 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 26321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4504 0.029 - 0.058: 1457 0.058 - 0.087: 466 0.087 - 0.116: 202 0.116 - 0.145: 33 Chirality restraints: 6662 Sorted by residual: chirality pdb=" CA ASN H 107 " pdb=" N ASN H 107 " pdb=" C ASN H 107 " pdb=" CB ASN H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ASN C 107 " pdb=" N ASN C 107 " pdb=" C ASN C 107 " pdb=" CB ASN C 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA LEU E 79 " pdb=" N LEU E 79 " pdb=" C LEU E 79 " pdb=" CB LEU E 79 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 6659 not shown) Planarity restraints: 7438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 159 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.58e+00 pdb=" C GLN A 159 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 159 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A 160 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 159 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C GLN B 159 " 0.027 2.00e-02 2.50e+03 pdb=" O GLN B 159 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 160 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 262 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ALA F 262 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA F 262 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG F 263 " -0.009 2.00e-02 2.50e+03 ... (remaining 7435 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1672 2.73 - 3.27: 44970 3.27 - 3.81: 69289 3.81 - 4.36: 73938 4.36 - 4.90: 128515 Nonbonded interactions: 318384 Sorted by model distance: nonbonded pdb=" O LEU F 257 " pdb=" OG1 THR F 260 " model vdw 2.183 3.040 nonbonded pdb=" O LEU D 257 " pdb=" OG1 THR D 260 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASN A1372 " pdb=" OH TYR A1485 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN B1372 " pdb=" OH TYR B1485 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 826 " pdb=" OG SER A 830 " model vdw 2.246 3.040 ... (remaining 318379 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 57.820 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.002 0.034 43592 Z= 0.096 Angle : 0.493 8.660 58994 Z= 0.251 Chirality : 0.036 0.145 6662 Planarity : 0.003 0.038 7438 Dihedral : 11.407 87.068 16130 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.57 % Allowed : 8.82 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.12), residues: 5188 helix: 2.32 (0.09), residues: 3380 sheet: 1.23 (0.42), residues: 150 loop : -1.34 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 196 TYR 0.016 0.001 TYR A1484 PHE 0.011 0.001 PHE A 133 TRP 0.008 0.001 TRP A1596 HIS 0.003 0.000 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 (43590) covalent geometry : angle 0.49256 / 0.25 (58990) SS BOND : bond 0.00502 / 0.25 ( 2) SS BOND : angle 2.24273 / 1.15 ( 4) hydrogen bonds : bond 0.13349 / 8.60 ( 2552) hydrogen bonds : angle 4.34812 / 3.11 ( 7632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 556 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8638 (tp) cc_final: 0.8348 (pp) REVERT: A 378 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.5949 (m-10) REVERT: A 397 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8556 (pttt) REVERT: A 654 VAL cc_start: 0.9494 (m) cc_final: 0.9133 (m) REVERT: A 658 ASP cc_start: 0.9309 (t70) cc_final: 0.9102 (m-30) REVERT: A 659 GLN cc_start: 0.9709 (mm-40) cc_final: 0.9444 (mm-40) REVERT: A 719 ASN cc_start: 0.8570 (m-40) cc_final: 0.8126 (p0) REVERT: A 773 VAL cc_start: 0.8929 (m) cc_final: 0.8361 (p) REVERT: A 777 LEU cc_start: 0.9122 (mt) cc_final: 0.8694 (mt) REVERT: A 805 MET cc_start: 0.8646 (mpp) cc_final: 0.8332 (mpp) REVERT: A 860 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: A 902 MET cc_start: 0.8948 (mmm) cc_final: 0.8518 (mmm) REVERT: A 1063 MET cc_start: 0.8322 (tmm) cc_final: 0.7939 (tmm) REVERT: A 1199 MET cc_start: 0.8985 (tmm) cc_final: 0.8359 (tmm) REVERT: A 1258 MET cc_start: 0.8672 (tmt) cc_final: 0.8200 (tmm) REVERT: A 1284 GLN cc_start: 0.8582 (mp10) cc_final: 0.8327 (mp10) REVERT: A 1795 MET cc_start: 0.8473 (pmm) cc_final: 0.8197 (pmm) REVERT: A 1943 MET cc_start: 0.9260 (tpt) cc_final: 0.9010 (tpp) REVERT: A 1964 MET cc_start: 0.8124 (tpt) cc_final: 0.7854 (tpt) REVERT: A 2002 MET cc_start: 0.8555 (ppp) cc_final: 0.8065 (ppp) REVERT: B 40 ARG cc_start: 0.8981 (tpt90) cc_final: 0.8503 (tpp-160) REVERT: B 129 GLU cc_start: 0.8286 (pm20) cc_final: 0.7800 (pm20) REVERT: B 200 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5715 (mmt) REVERT: B 388 MET cc_start: 0.4299 (mmt) cc_final: 0.3972 (mmt) REVERT: B 465 LYS cc_start: 0.9202 (ptmt) cc_final: 0.8995 (pttt) REVERT: B 491 ARG cc_start: 0.8411 (tpm170) cc_final: 0.7981 (tpm170) REVERT: B 492 LEU cc_start: 0.8312 (tp) cc_final: 0.8065 (pp) REVERT: B 617 ILE cc_start: 0.9525 (mm) cc_final: 0.9245 (pt) REVERT: B 659 GLN cc_start: 0.9254 (mm-40) cc_final: 0.9029 (mm-40) REVERT: B 902 MET cc_start: 0.8905 (mmm) cc_final: 0.8692 (mmm) REVERT: B 1063 MET cc_start: 0.8493 (tmm) cc_final: 0.8141 (tmm) REVERT: B 1199 MET cc_start: 0.8832 (tmm) cc_final: 0.8472 (tmm) REVERT: B 1258 MET cc_start: 0.8468 (tmt) cc_final: 0.8201 (tmm) REVERT: B 1964 MET cc_start: 0.8037 (tpt) cc_final: 0.7762 (mmm) REVERT: B 2008 MET cc_start: 0.7904 (mmm) cc_final: 0.7571 (mmt) REVERT: C 22 LEU cc_start: 0.8457 (tt) cc_final: 0.8133 (tt) REVERT: C 38 TRP cc_start: 0.5474 (m-90) cc_final: 0.4965 (t-100) REVERT: C 40 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7193 (mtp85) REVERT: C 41 GLN cc_start: 0.7505 (tt0) cc_final: 0.6349 (tp-100) REVERT: C 84 MET cc_start: 0.3352 (tmm) cc_final: 0.2859 (tmm) REVERT: C 95 TYR cc_start: 0.8165 (m-10) cc_final: 0.7890 (m-10) REVERT: C 105 ARG cc_start: 0.6618 (ttp-170) cc_final: 0.6272 (mtt180) REVERT: D 267 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7272 (mt-10) REVERT: D 333 LEU cc_start: 0.9190 (mm) cc_final: 0.8860 (mm) REVERT: D 338 MET cc_start: 0.8883 (tmm) cc_final: 0.8365 (tmm) REVERT: D 390 MET cc_start: 0.8823 (tpt) cc_final: 0.8532 (tpt) REVERT: D 588 SER cc_start: 0.8732 (m) cc_final: 0.8377 (t) REVERT: E 27 TYR cc_start: 0.6950 (m-10) cc_final: 0.6666 (m-10) REVERT: E 58 HIS cc_start: 0.9175 (m-70) cc_final: 0.8855 (m-70) REVERT: E 112 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8698 (mm-30) REVERT: E 132 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8748 (tptt) REVERT: E 261 ASP cc_start: 0.8029 (m-30) cc_final: 0.7763 (m-30) REVERT: F 338 MET cc_start: 0.9318 (tmm) cc_final: 0.8965 (tmm) REVERT: F 390 MET cc_start: 0.8958 (tpt) cc_final: 0.8701 (tpp) REVERT: F 551 SER cc_start: 0.8886 (m) cc_final: 0.8450 (p) REVERT: F 746 MET cc_start: 0.8045 (mmm) cc_final: 0.7608 (mmm) REVERT: G 58 HIS cc_start: 0.9550 (m-70) cc_final: 0.9335 (m-70) REVERT: G 126 THR cc_start: 0.7663 (p) cc_final: 0.7292 (p) REVERT: G 157 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7363 (mm) REVERT: H 38 TRP cc_start: 0.5606 (m-90) cc_final: 0.4779 (m100) outliers start: 73 outliers final: 27 residues processed: 600 average time/residue: 0.2233 time to fit residues: 226.1880 Evaluate side-chains 451 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 420 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 381 MET Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.3980 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 0.0060 chunk 223 optimal weight: 0.0030 overall best weight: 0.6808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 766 ASN A1029 GLN A1096 GLN ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1170 ASN A1304 GLN A1539 GLN A1690 ASN A1694 ASN B 91 GLN B 169 GLN B 766 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 ASN B1170 ASN B1304 GLN B1539 GLN B1690 ASN B1694 ASN C 83 GLN C 119 GLN D 170 GLN D 545 GLN E 49 GLN E 70 GLN E 166 HIS E 168 GLN F 170 GLN F 515 HIS F 545 GLN G 49 GLN G 70 GLN G 73 GLN G 168 GLN H 83 GLN H 119 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.076717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059275 restraints weight = 237152.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060640 restraints weight = 127857.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061467 restraints weight = 86199.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062090 restraints weight = 67714.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062388 restraints weight = 57334.528| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43592 Z= 0.113 Angle : 0.579 13.219 58994 Z= 0.283 Chirality : 0.037 0.356 6662 Planarity : 0.004 0.050 7438 Dihedral : 4.712 56.394 5828 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 1.97 % Allowed : 11.93 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 5188 helix: 2.27 (0.09), residues: 3462 sheet: 1.58 (0.44), residues: 136 loop : -1.31 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 703 TYR 0.039 0.001 TYR F 176 PHE 0.042 0.001 PHE A 402 TRP 0.009 0.001 TRP B1990 HIS 0.003 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (43590) covalent geometry : angle 0.57877 / 0.28 (58990) SS BOND : bond 0.00107 / 0.05 ( 2) SS BOND : angle 1.03577 / 0.53 ( 4) hydrogen bonds : bond 0.03966 / 2.60 ( 2552) hydrogen bonds : angle 3.71374 / 2.66 ( 7632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 462 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8596 (tp) cc_final: 0.8327 (pp) REVERT: A 194 PHE cc_start: 0.7242 (t80) cc_final: 0.6853 (m-80) REVERT: A 397 LYS cc_start: 0.8986 (ptpp) cc_final: 0.8558 (pttt) REVERT: A 491 ARG cc_start: 0.7936 (tpm170) cc_final: 0.7612 (tpm170) REVERT: A 654 VAL cc_start: 0.9506 (m) cc_final: 0.9110 (m) REVERT: A 659 GLN cc_start: 0.9661 (mm-40) cc_final: 0.9377 (mm-40) REVERT: A 719 ASN cc_start: 0.8388 (m-40) cc_final: 0.8143 (p0) REVERT: A 773 VAL cc_start: 0.8935 (m) cc_final: 0.8348 (p) REVERT: A 777 LEU cc_start: 0.9122 (mt) cc_final: 0.8688 (mt) REVERT: A 902 MET cc_start: 0.8948 (mmm) cc_final: 0.8541 (mmm) REVERT: A 950 MET cc_start: 0.8546 (tmm) cc_final: 0.8276 (tmm) REVERT: A 1199 MET cc_start: 0.8938 (tmm) cc_final: 0.8327 (tmm) REVERT: A 1227 MET cc_start: 0.7556 (tpp) cc_final: 0.7062 (tpt) REVERT: A 1539 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7197 (pp30) REVERT: A 1943 MET cc_start: 0.9261 (tpt) cc_final: 0.9032 (tpp) REVERT: A 1964 MET cc_start: 0.7886 (tpt) cc_final: 0.7665 (tpt) REVERT: A 2002 MET cc_start: 0.8553 (ppp) cc_final: 0.8042 (ppp) REVERT: B 40 ARG cc_start: 0.8914 (tpt90) cc_final: 0.8523 (ttp-170) REVERT: B 129 GLU cc_start: 0.8305 (pm20) cc_final: 0.7842 (pm20) REVERT: B 139 LEU cc_start: 0.8314 (mt) cc_final: 0.7818 (tt) REVERT: B 165 LEU cc_start: 0.9301 (mm) cc_final: 0.9057 (tt) REVERT: B 200 MET cc_start: 0.6140 (tpp) cc_final: 0.5935 (mmp) REVERT: B 374 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 380 MET cc_start: 0.7907 (ppp) cc_final: 0.7568 (ppp) REVERT: B 388 MET cc_start: 0.4235 (mmt) cc_final: 0.4011 (mmt) REVERT: B 491 ARG cc_start: 0.8408 (tpm170) cc_final: 0.7920 (tpm170) REVERT: B 492 LEU cc_start: 0.8273 (tp) cc_final: 0.7997 (pp) REVERT: B 617 ILE cc_start: 0.9515 (mm) cc_final: 0.9229 (pt) REVERT: B 659 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8973 (mm-40) REVERT: B 902 MET cc_start: 0.8932 (mmm) cc_final: 0.8708 (mmm) REVERT: B 1063 MET cc_start: 0.8419 (tmm) cc_final: 0.8032 (tmm) REVERT: B 1588 GLU cc_start: 0.7946 (mp0) cc_final: 0.7353 (mp0) REVERT: B 1964 MET cc_start: 0.7807 (tpt) cc_final: 0.7601 (mmm) REVERT: B 2008 MET cc_start: 0.7703 (mmm) cc_final: 0.7368 (mmt) REVERT: C 1 MET cc_start: 0.7588 (tmm) cc_final: 0.6267 (tpp) REVERT: C 22 LEU cc_start: 0.8316 (tt) cc_final: 0.7875 (tt) REVERT: C 38 TRP cc_start: 0.5978 (m-90) cc_final: 0.5168 (t-100) REVERT: C 40 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7154 (ttt-90) REVERT: C 41 GLN cc_start: 0.7652 (tt0) cc_final: 0.6519 (tp-100) REVERT: C 84 MET cc_start: 0.3758 (tmm) cc_final: 0.3210 (tmm) REVERT: C 95 TYR cc_start: 0.8228 (m-10) cc_final: 0.7967 (m-10) REVERT: D 267 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7264 (mt-10) REVERT: D 333 LEU cc_start: 0.9188 (mm) cc_final: 0.8870 (mm) REVERT: D 338 MET cc_start: 0.9244 (tmm) cc_final: 0.8721 (tmm) REVERT: D 387 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: D 390 MET cc_start: 0.8890 (tpt) cc_final: 0.8528 (tpt) REVERT: D 440 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8055 (mm) REVERT: D 588 SER cc_start: 0.8768 (m) cc_final: 0.8447 (t) REVERT: D 614 LYS cc_start: 0.9483 (tttp) cc_final: 0.9214 (ptmm) REVERT: E 26 ASN cc_start: 0.8436 (p0) cc_final: 0.8199 (p0) REVERT: E 27 TYR cc_start: 0.6899 (m-10) cc_final: 0.6648 (m-10) REVERT: E 261 ASP cc_start: 0.8314 (m-30) cc_final: 0.8029 (m-30) REVERT: F 192 ARG cc_start: 0.8020 (tpt90) cc_final: 0.7209 (ptm160) REVERT: F 387 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: F 390 MET cc_start: 0.8940 (tpt) cc_final: 0.8572 (tpp) REVERT: F 551 SER cc_start: 0.8891 (m) cc_final: 0.8475 (p) REVERT: F 557 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7139 (tp) REVERT: F 735 MET cc_start: 0.9009 (tpp) cc_final: 0.8678 (tpt) REVERT: G 64 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5770 (t80) REVERT: G 157 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7359 (mm) REVERT: G 262 ASP cc_start: 0.8646 (m-30) cc_final: 0.8407 (m-30) REVERT: H 38 TRP cc_start: 0.6096 (m-90) cc_final: 0.5682 (m-90) outliers start: 92 outliers final: 38 residues processed: 532 average time/residue: 0.2160 time to fit residues: 196.4710 Evaluate side-chains 458 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 412 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET 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 1800 LYS Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1539 GLN Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 1950 LEU Chi-restraints excluded: chain B residue 2000 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 157 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [263, 169, 412, 275, 153, 19, 161, 78, 399, 494, 232] chunk 263 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 412 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 399 optimal weight: 4.9990 chunk 494 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 969 GLN ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1539 GLN A1694 ASN B 169 GLN B 501 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1539 GLN B1694 ASN E 166 HIS F 730 HIS G 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057149 restraints weight = 237998.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058489 restraints weight = 129332.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059337 restraints weight = 88365.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.059894 restraints weight = 68799.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.060232 restraints weight = 58526.406| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43592 Z= 0.142 Angle : 0.575 11.063 58994 Z= 0.284 Chirality : 0.038 0.268 6662 Planarity : 0.004 0.100 7438 Dihedral : 4.533 54.681 5808 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 2.49 % Allowed : 12.55 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.12), residues: 5188 helix: 2.31 (0.09), residues: 3446 sheet: 1.93 (0.46), residues: 116 loop : -1.37 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 529 TYR 0.036 0.001 TYR F 176 PHE 0.039 0.001 PHE A 402 TRP 0.018 0.001 TRP A1540 HIS 0.004 0.001 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (43590) covalent geometry : angle 0.57374 / 0.28 (58990) SS BOND : bond 0.01019 / 0.49 ( 2) SS BOND : angle 4.04196 / 1.60 ( 4) hydrogen bonds : bond 0.04038 / 2.63 ( 2552) hydrogen bonds : angle 3.71486 / 2.66 ( 7632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 428 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8670 (mp) cc_final: 0.8466 (mp) REVERT: A 378 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: A 397 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8644 (pttt) REVERT: A 659 GLN cc_start: 0.9673 (mm-40) cc_final: 0.9401 (mm-40) REVERT: A 719 ASN cc_start: 0.8511 (m-40) cc_final: 0.8187 (p0) REVERT: A 773 VAL cc_start: 0.8945 (m) cc_final: 0.8338 (p) REVERT: A 777 LEU cc_start: 0.9113 (mt) cc_final: 0.8691 (mt) REVERT: A 902 MET cc_start: 0.8952 (mmm) cc_final: 0.8623 (mmm) REVERT: A 950 MET cc_start: 0.8602 (tmm) cc_final: 0.8337 (tmm) REVERT: A 1199 MET cc_start: 0.8921 (tmm) cc_final: 0.8402 (tmm) REVERT: A 1227 MET cc_start: 0.7762 (tpp) cc_final: 0.7256 (tpt) REVERT: A 1284 GLN cc_start: 0.8570 (mp10) cc_final: 0.8315 (mp10) REVERT: A 1943 MET cc_start: 0.9213 (tpt) cc_final: 0.8984 (tpp) REVERT: A 1964 MET cc_start: 0.7800 (tpt) cc_final: 0.7562 (tpt) REVERT: A 2002 MET cc_start: 0.8624 (ppp) cc_final: 0.8111 (ppp) REVERT: A 2065 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8013 (ttt) REVERT: B 40 ARG cc_start: 0.8884 (tpt90) cc_final: 0.8594 (ttp-170) REVERT: B 139 LEU cc_start: 0.8321 (mt) cc_final: 0.7815 (tt) REVERT: B 165 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9058 (tt) REVERT: B 324 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 380 MET cc_start: 0.8085 (ppp) cc_final: 0.7780 (ppp) REVERT: B 491 ARG cc_start: 0.8414 (tpm170) cc_final: 0.7908 (tpm170) REVERT: B 492 LEU cc_start: 0.8234 (tp) cc_final: 0.7969 (pp) REVERT: B 617 ILE cc_start: 0.9507 (mm) cc_final: 0.9183 (pt) REVERT: B 655 LEU cc_start: 0.9448 (pt) cc_final: 0.9099 (pt) REVERT: B 659 GLN cc_start: 0.9347 (mm-40) cc_final: 0.8986 (mm-40) REVERT: B 902 MET cc_start: 0.8922 (mmm) cc_final: 0.8718 (mmm) REVERT: B 1063 MET cc_start: 0.8418 (tmm) cc_final: 0.8167 (tmm) REVERT: B 1539 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6784 (pp30) REVERT: B 2008 MET cc_start: 0.7675 (mmm) cc_final: 0.7420 (mmt) REVERT: C 1 MET cc_start: 0.7557 (tmm) cc_final: 0.7006 (tpt) REVERT: C 22 LEU cc_start: 0.8410 (tt) cc_final: 0.7684 (tt) REVERT: C 38 TRP cc_start: 0.6095 (m-90) cc_final: 0.5094 (t-100) REVERT: C 41 GLN cc_start: 0.7584 (tt0) cc_final: 0.6374 (tp-100) REVERT: C 84 MET cc_start: 0.3644 (tmm) cc_final: 0.3150 (tmm) REVERT: C 95 TYR cc_start: 0.8229 (m-10) cc_final: 0.7806 (m-10) REVERT: D 267 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 333 LEU cc_start: 0.9248 (mm) cc_final: 0.8922 (mm) REVERT: D 338 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9043 (tmm) REVERT: D 387 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: D 440 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 588 SER cc_start: 0.8814 (m) cc_final: 0.8459 (t) REVERT: D 614 LYS cc_start: 0.9466 (tttp) cc_final: 0.9195 (ptmm) REVERT: E 26 ASN cc_start: 0.8380 (p0) cc_final: 0.8150 (p0) REVERT: E 27 TYR cc_start: 0.6945 (m-10) cc_final: 0.6708 (m-10) REVERT: F 267 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7554 (mp0) REVERT: F 387 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: F 390 MET cc_start: 0.9007 (tpt) cc_final: 0.8712 (tpp) REVERT: F 735 MET cc_start: 0.9137 (tpp) cc_final: 0.8844 (tpt) REVERT: G 64 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5957 (t80) REVERT: G 157 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7427 (mm) REVERT: G 262 ASP cc_start: 0.8642 (m-30) cc_final: 0.8374 (m-30) REVERT: H 8 GLU cc_start: 0.6648 (pm20) cc_final: 0.6102 (mp0) REVERT: H 38 TRP cc_start: 0.6087 (m-90) cc_final: 0.5796 (m-90) outliers start: 116 outliers final: 62 residues processed: 515 average time/residue: 0.2153 time to fit residues: 191.1039 Evaluate side-chains 473 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 400 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1694 ASN Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1539 GLN Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1694 ASN Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1916 MET Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 2000 MET Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 64 TYR Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [523, 98, 242, 529, 19, 507, 6, 96, 26, 129, 47] chunk 523 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 529 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 507 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1539 GLN B1694 ASN E 166 HIS F 188 GLN G 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.074968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057363 restraints weight = 236593.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.058708 restraints weight = 129481.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.059580 restraints weight = 88665.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.060117 restraints weight = 68922.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060486 restraints weight = 58892.542| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 43592 Z= 0.110 Angle : 0.568 10.932 58994 Z= 0.276 Chirality : 0.037 0.406 6662 Planarity : 0.004 0.078 7438 Dihedral : 4.488 53.273 5806 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 2.47 % Allowed : 13.18 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 5188 helix: 2.33 (0.09), residues: 3450 sheet: 1.78 (0.45), residues: 116 loop : -1.41 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.037 0.001 TYR F 176 PHE 0.042 0.001 PHE A 402 TRP 0.018 0.001 TRP B1540 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (43590) covalent geometry : angle 0.56758 / 0.28 (58990) SS BOND : bond 0.01006 / 0.53 ( 2) SS BOND : angle 3.70899 / 1.88 ( 4) hydrogen bonds : bond 0.03611 / 2.36 ( 2552) hydrogen bonds : angle 3.59965 / 2.58 ( 7632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 429 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8647 (tp) cc_final: 0.8395 (pp) REVERT: A 76 ASP cc_start: 0.7678 (m-30) cc_final: 0.7178 (t0) REVERT: A 378 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: A 397 LYS cc_start: 0.9087 (ptpp) cc_final: 0.8747 (pttt) REVERT: A 659 GLN cc_start: 0.9660 (mm-40) cc_final: 0.9421 (mm-40) REVERT: A 719 ASN cc_start: 0.8517 (m-40) cc_final: 0.8206 (p0) REVERT: A 773 VAL cc_start: 0.8932 (m) cc_final: 0.8313 (p) REVERT: A 777 LEU cc_start: 0.9086 (mt) cc_final: 0.8612 (mt) REVERT: A 902 MET cc_start: 0.8959 (mmm) cc_final: 0.8598 (mmm) REVERT: A 950 MET cc_start: 0.8653 (tmm) cc_final: 0.8382 (tmm) REVERT: A 1199 MET cc_start: 0.8933 (tmm) cc_final: 0.8387 (tmm) REVERT: A 1227 MET cc_start: 0.7727 (tpp) cc_final: 0.7247 (tpt) REVERT: A 1284 GLN cc_start: 0.8565 (mp10) cc_final: 0.8305 (mp10) REVERT: A 1691 MET cc_start: 0.8793 (mtm) cc_final: 0.8571 (mtm) REVERT: A 1943 MET cc_start: 0.9187 (tpt) cc_final: 0.8949 (tpp) REVERT: A 1964 MET cc_start: 0.7740 (tpt) cc_final: 0.7492 (tpt) REVERT: A 2002 MET cc_start: 0.8642 (ppp) cc_final: 0.8151 (ppp) REVERT: A 2065 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: B 40 ARG cc_start: 0.8872 (tpt90) cc_final: 0.8622 (ttp-170) REVERT: B 129 GLU cc_start: 0.8574 (pm20) cc_final: 0.8009 (pm20) REVERT: B 165 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9089 (tt) REVERT: B 324 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 378 PHE cc_start: 0.5364 (OUTLIER) cc_final: 0.5083 (m-10) REVERT: B 456 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8137 (pp20) REVERT: B 491 ARG cc_start: 0.8419 (tpm170) cc_final: 0.7910 (tpm170) REVERT: B 492 LEU cc_start: 0.8182 (tp) cc_final: 0.7907 (pp) REVERT: B 617 ILE cc_start: 0.9506 (mm) cc_final: 0.9215 (pt) REVERT: B 634 MET cc_start: 0.7903 (mpp) cc_final: 0.7468 (mmm) REVERT: B 655 LEU cc_start: 0.9425 (pt) cc_final: 0.8794 (tt) REVERT: B 659 GLN cc_start: 0.9367 (mm-40) cc_final: 0.8926 (mm-40) REVERT: B 902 MET cc_start: 0.8903 (mmm) cc_final: 0.8693 (mmm) REVERT: B 1063 MET cc_start: 0.8390 (tmm) cc_final: 0.7938 (tmm) REVERT: B 1964 MET cc_start: 0.7554 (mmm) cc_final: 0.7204 (mmm) REVERT: C 1 MET cc_start: 0.7526 (tmm) cc_final: 0.6474 (tpp) REVERT: C 40 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7237 (ttt90) REVERT: C 41 GLN cc_start: 0.7542 (tt0) cc_final: 0.6365 (tp-100) REVERT: D 267 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7509 (mt-10) REVERT: D 333 LEU cc_start: 0.9252 (mm) cc_final: 0.8932 (mm) REVERT: D 338 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9069 (tmm) REVERT: D 387 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: D 440 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8226 (mm) REVERT: D 588 SER cc_start: 0.8809 (m) cc_final: 0.8480 (t) REVERT: D 614 LYS cc_start: 0.9468 (tttp) cc_final: 0.9196 (ptmm) REVERT: E 27 TYR cc_start: 0.6945 (m-10) cc_final: 0.6673 (m-10) REVERT: F 192 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7253 (ptm160) REVERT: F 267 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7618 (mp0) REVERT: F 387 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: F 767 MET cc_start: 0.8326 (ptt) cc_final: 0.8103 (ptt) REVERT: G 157 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7476 (mm) REVERT: G 262 ASP cc_start: 0.8654 (m-30) cc_final: 0.8365 (m-30) REVERT: H 38 TRP cc_start: 0.5986 (m-90) cc_final: 0.5761 (m-90) REVERT: H 116 GLN cc_start: 0.6888 (pm20) cc_final: 0.6540 (pm20) outliers start: 115 outliers final: 57 residues processed: 510 average time/residue: 0.2127 time to fit residues: 186.6167 Evaluate side-chains 476 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 408 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1540 TRP Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1920 PHE Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1694 ASN Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 2000 MET Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 381 MET Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [85, 340, 146, 16, 303, 436, 21, 388, 321, 280, 212] chunk 85 optimal weight: 0.0020 chunk 340 optimal weight: 0.0270 chunk 146 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 303 optimal weight: 0.1980 chunk 436 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 1.0450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 169 GLN B 967 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1170 ASN B1694 ASN E 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.074708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.057124 restraints weight = 237227.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.058487 restraints weight = 129703.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059348 restraints weight = 88137.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059916 restraints weight = 69061.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060228 restraints weight = 59082.900| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 43592 Z= 0.108 Angle : 0.566 11.068 58994 Z= 0.273 Chirality : 0.037 0.352 6662 Planarity : 0.004 0.066 7438 Dihedral : 4.492 56.910 5806 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 2.17 % Allowed : 13.99 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.12), residues: 5188 helix: 2.34 (0.09), residues: 3450 sheet: 1.78 (0.44), residues: 118 loop : -1.43 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 382 TYR 0.037 0.001 TYR F 176 PHE 0.044 0.001 PHE A 402 TRP 0.019 0.001 TRP F 279 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (43590) covalent geometry : angle 0.56574 / 0.27 (58990) SS BOND : bond 0.00285 / 0.15 ( 2) SS BOND : angle 2.76567 / 1.43 ( 4) hydrogen bonds : bond 0.03484 / 2.28 ( 2552) hydrogen bonds : angle 3.55580 / 2.55 ( 7632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 425 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8645 (tp) cc_final: 0.8409 (pp) REVERT: A 76 ASP cc_start: 0.7754 (m-30) cc_final: 0.7256 (t0) REVERT: A 377 MET cc_start: 0.8420 (mmt) cc_final: 0.8193 (ppp) REVERT: A 397 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8762 (pttt) REVERT: A 659 GLN cc_start: 0.9670 (mm-40) cc_final: 0.9419 (mm-40) REVERT: A 719 ASN cc_start: 0.8521 (m-40) cc_final: 0.8205 (p0) REVERT: A 773 VAL cc_start: 0.8939 (m) cc_final: 0.8324 (p) REVERT: A 777 LEU cc_start: 0.8963 (mt) cc_final: 0.8582 (mt) REVERT: A 902 MET cc_start: 0.8929 (mmm) cc_final: 0.8563 (mmm) REVERT: A 950 MET cc_start: 0.8662 (tmm) cc_final: 0.8404 (tmm) REVERT: A 1199 MET cc_start: 0.8928 (tmm) cc_final: 0.8387 (tmm) REVERT: A 1227 MET cc_start: 0.7716 (tpp) cc_final: 0.7257 (tpt) REVERT: A 1284 GLN cc_start: 0.8575 (mp10) cc_final: 0.8318 (mp10) REVERT: A 1943 MET cc_start: 0.9154 (tpt) cc_final: 0.8948 (tpp) REVERT: A 1964 MET cc_start: 0.7703 (tpt) cc_final: 0.7450 (tpt) REVERT: A 2002 MET cc_start: 0.8671 (ppp) cc_final: 0.8179 (ppp) REVERT: A 2065 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7971 (ttt) REVERT: B 40 ARG cc_start: 0.8867 (tpt90) cc_final: 0.8657 (ttp-170) REVERT: B 129 GLU cc_start: 0.8617 (pm20) cc_final: 0.7974 (pm20) REVERT: B 188 ILE cc_start: 0.8021 (mt) cc_final: 0.7777 (pt) REVERT: B 456 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: B 491 ARG cc_start: 0.8423 (tpm170) cc_final: 0.8124 (tpm170) REVERT: B 492 LEU cc_start: 0.8177 (tp) cc_final: 0.7885 (pp) REVERT: B 617 ILE cc_start: 0.9503 (mm) cc_final: 0.9217 (pt) REVERT: B 634 MET cc_start: 0.7916 (mpp) cc_final: 0.7521 (mmm) REVERT: B 655 LEU cc_start: 0.9416 (pt) cc_final: 0.8760 (tt) REVERT: B 659 GLN cc_start: 0.9376 (mm-40) cc_final: 0.8925 (mm-40) REVERT: B 902 MET cc_start: 0.8908 (mmm) cc_final: 0.8685 (mmm) REVERT: B 1063 MET cc_start: 0.8408 (tmm) cc_final: 0.7941 (tmm) REVERT: B 1964 MET cc_start: 0.7491 (mmm) cc_final: 0.7189 (mmm) REVERT: C 1 MET cc_start: 0.7511 (tmm) cc_final: 0.6578 (tpp) REVERT: C 22 LEU cc_start: 0.8403 (tt) cc_final: 0.8000 (tt) REVERT: C 38 TRP cc_start: 0.6178 (m-90) cc_final: 0.5640 (t-100) REVERT: C 41 GLN cc_start: 0.7493 (tt0) cc_final: 0.6307 (tp-100) REVERT: C 95 TYR cc_start: 0.8214 (m-10) cc_final: 0.7952 (m-10) REVERT: D 267 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 333 LEU cc_start: 0.9261 (mm) cc_final: 0.8937 (mm) REVERT: D 338 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9075 (tmm) REVERT: D 387 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: D 440 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8243 (mm) REVERT: D 588 SER cc_start: 0.8821 (m) cc_final: 0.8487 (t) REVERT: D 614 LYS cc_start: 0.9462 (tttp) cc_final: 0.9179 (ptmm) REVERT: E 27 TYR cc_start: 0.6893 (m-10) cc_final: 0.6682 (m-10) REVERT: F 267 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7643 (mp0) REVERT: F 767 MET cc_start: 0.8313 (ptt) cc_final: 0.8098 (ptt) REVERT: G 157 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7514 (mm) REVERT: G 262 ASP cc_start: 0.8659 (m-30) cc_final: 0.8354 (m-30) REVERT: H 38 TRP cc_start: 0.6047 (m-90) cc_final: 0.5350 (m100) REVERT: H 95 TYR cc_start: 0.8239 (m-10) cc_final: 0.7849 (m-10) outliers start: 101 outliers final: 58 residues processed: 498 average time/residue: 0.2171 time to fit residues: 186.4712 Evaluate side-chains 475 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 411 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1297 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 381 MET Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 12 TRP Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [508, 103, 226, 95, 459, 402, 211, 157, 186, 106, 374] chunk 508 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 459 optimal weight: 2.9990 chunk 402 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 186 optimal weight: 0.0010 chunk 106 optimal weight: 4.9990 chunk 374 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1694 ASN E 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.075042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057536 restraints weight = 237256.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.058829 restraints weight = 129616.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.059698 restraints weight = 87948.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060272 restraints weight = 68585.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060616 restraints weight = 58645.934| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 43592 Z= 0.101 Angle : 0.570 12.716 58994 Z= 0.273 Chirality : 0.037 0.295 6662 Planarity : 0.003 0.055 7438 Dihedral : 4.326 57.586 5796 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 1.87 % Allowed : 14.55 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.12), residues: 5188 helix: 2.38 (0.09), residues: 3450 sheet: 1.67 (0.44), residues: 118 loop : -1.42 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 105 TYR 0.036 0.001 TYR F 176 PHE 0.046 0.001 PHE A 402 TRP 0.019 0.001 TRP F 279 HIS 0.003 0.000 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (43590) covalent geometry : angle 0.57022 / 0.27 (58990) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 1.92405 / 0.97 ( 4) hydrogen bonds : bond 0.03272 / 2.15 ( 2552) hydrogen bonds : angle 3.50292 / 2.51 ( 7632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 422 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8655 (tp) cc_final: 0.8435 (pp) REVERT: A 76 ASP cc_start: 0.7732 (m-30) cc_final: 0.7322 (t0) REVERT: A 194 PHE cc_start: 0.7346 (t80) cc_final: 0.6953 (m-80) REVERT: A 374 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7364 (t80) REVERT: A 397 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8768 (pmtt) REVERT: A 659 GLN cc_start: 0.9656 (mm-40) cc_final: 0.9422 (mm-40) REVERT: A 719 ASN cc_start: 0.8502 (m-40) cc_final: 0.8207 (p0) REVERT: A 777 LEU cc_start: 0.8976 (mt) cc_final: 0.8631 (mt) REVERT: A 902 MET cc_start: 0.8936 (mmm) cc_final: 0.8569 (mmm) REVERT: A 950 MET cc_start: 0.8670 (tmm) cc_final: 0.8390 (tmm) REVERT: A 1199 MET cc_start: 0.8925 (tmm) cc_final: 0.8373 (tmm) REVERT: A 1227 MET cc_start: 0.7694 (tpp) cc_final: 0.7263 (tpt) REVERT: A 1284 GLN cc_start: 0.8595 (mp10) cc_final: 0.8367 (mp10) REVERT: A 1943 MET cc_start: 0.9126 (tpt) cc_final: 0.8844 (tpp) REVERT: A 1964 MET cc_start: 0.7723 (tpt) cc_final: 0.7471 (tpt) REVERT: A 2002 MET cc_start: 0.8679 (ppp) cc_final: 0.8180 (ppp) REVERT: A 2065 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7982 (ttt) REVERT: B 456 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: B 491 ARG cc_start: 0.8434 (tpm170) cc_final: 0.8113 (tpm170) REVERT: B 492 LEU cc_start: 0.8194 (tp) cc_final: 0.7868 (pp) REVERT: B 617 ILE cc_start: 0.9501 (mm) cc_final: 0.9214 (pt) REVERT: B 634 MET cc_start: 0.7966 (mpp) cc_final: 0.7614 (mmm) REVERT: B 655 LEU cc_start: 0.9412 (pt) cc_final: 0.8745 (tt) REVERT: B 659 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8925 (mm-40) REVERT: B 902 MET cc_start: 0.8924 (mmm) cc_final: 0.8695 (mmm) REVERT: B 1063 MET cc_start: 0.8414 (tmm) cc_final: 0.7940 (tmm) REVERT: B 1927 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: B 1964 MET cc_start: 0.7524 (mmm) cc_final: 0.7294 (mmm) REVERT: C 1 MET cc_start: 0.7473 (tmm) cc_final: 0.6566 (tpp) REVERT: C 22 LEU cc_start: 0.8411 (tt) cc_final: 0.8023 (tt) REVERT: C 38 TRP cc_start: 0.6399 (m-90) cc_final: 0.5518 (t-100) REVERT: C 40 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7272 (ttt90) REVERT: C 41 GLN cc_start: 0.7534 (tt0) cc_final: 0.6407 (tp-100) REVERT: C 84 MET cc_start: 0.3341 (tmm) cc_final: 0.2444 (tpp) REVERT: D 267 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 333 LEU cc_start: 0.9270 (mm) cc_final: 0.8943 (mm) REVERT: D 338 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9063 (tmm) REVERT: D 387 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: D 440 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8220 (mm) REVERT: D 588 SER cc_start: 0.8783 (m) cc_final: 0.8451 (t) REVERT: D 614 LYS cc_start: 0.9468 (tttp) cc_final: 0.9186 (ptmm) REVERT: E 27 TYR cc_start: 0.6910 (m-10) cc_final: 0.6694 (m-10) REVERT: F 267 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7642 (mp0) REVERT: F 268 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8632 (mp) REVERT: F 387 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: G 63 PHE cc_start: 0.8901 (m-10) cc_final: 0.8652 (m-10) REVERT: G 157 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7563 (mm) REVERT: G 262 ASP cc_start: 0.8662 (m-30) cc_final: 0.8355 (m-30) REVERT: H 38 TRP cc_start: 0.6071 (m-90) cc_final: 0.5347 (m100) REVERT: H 95 TYR cc_start: 0.8243 (m-10) cc_final: 0.7869 (m-10) outliers start: 87 outliers final: 59 residues processed: 477 average time/residue: 0.2112 time to fit residues: 173.6398 Evaluate side-chains 471 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 402 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1297 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 1920 PHE Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 381 MET Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 12 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [410, 210, 222, 108, 441, 343, 193, 90, 151, 153, 318] chunk 410 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 441 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1539 GLN B 169 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 763 HIS D 811 GLN E 166 HIS E 168 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.073883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056261 restraints weight = 237026.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057610 restraints weight = 130702.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058456 restraints weight = 89350.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.058959 restraints weight = 69829.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059331 restraints weight = 60102.370| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43592 Z= 0.121 Angle : 0.588 11.948 58994 Z= 0.285 Chirality : 0.038 0.218 6662 Planarity : 0.004 0.075 7438 Dihedral : 4.288 52.973 5796 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 2.08 % Allowed : 14.68 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.12), residues: 5188 helix: 2.37 (0.09), residues: 3438 sheet: 2.05 (0.44), residues: 112 loop : -1.43 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 382 TYR 0.037 0.001 TYR F 176 PHE 0.048 0.001 PHE A 402 TRP 0.019 0.001 TRP F 279 HIS 0.004 0.001 HIS B1097 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (43590) covalent geometry : angle 0.58777 / 0.28 (58990) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 1.83290 / 0.92 ( 4) hydrogen bonds : bond 0.03571 / 2.34 ( 2552) hydrogen bonds : angle 3.56436 / 2.56 ( 7632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 416 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7772 (m-30) cc_final: 0.7365 (t0) REVERT: A 374 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7826 (t80) REVERT: A 397 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8761 (pmtt) REVERT: A 508 ARG cc_start: 0.9059 (ptp-170) cc_final: 0.8859 (ptp-170) REVERT: A 659 GLN cc_start: 0.9668 (mm-40) cc_final: 0.9432 (mm-40) REVERT: A 719 ASN cc_start: 0.8535 (m-40) cc_final: 0.8240 (p0) REVERT: A 777 LEU cc_start: 0.8937 (mt) cc_final: 0.8598 (mt) REVERT: A 902 MET cc_start: 0.8966 (mmm) cc_final: 0.8642 (mmm) REVERT: A 950 MET cc_start: 0.8730 (tmm) cc_final: 0.8442 (tmm) REVERT: A 1199 MET cc_start: 0.8946 (tmm) cc_final: 0.8404 (tmm) REVERT: A 1227 MET cc_start: 0.7772 (tpp) cc_final: 0.7338 (tpt) REVERT: A 1284 GLN cc_start: 0.8592 (mp10) cc_final: 0.8334 (mp10) REVERT: A 1866 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (t0) REVERT: A 1943 MET cc_start: 0.9148 (tpt) cc_final: 0.8874 (tpp) REVERT: A 1964 MET cc_start: 0.7743 (tpt) cc_final: 0.7442 (mmm) REVERT: A 2002 MET cc_start: 0.8704 (ppp) cc_final: 0.8239 (ppp) REVERT: A 2065 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7997 (ttt) REVERT: B 188 ILE cc_start: 0.7992 (mt) cc_final: 0.7755 (pt) REVERT: B 374 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 380 MET cc_start: 0.8040 (ppp) cc_final: 0.7600 (ppp) REVERT: B 456 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: B 491 ARG cc_start: 0.8413 (tpm170) cc_final: 0.7967 (tpm170) REVERT: B 492 LEU cc_start: 0.8186 (tp) cc_final: 0.7852 (pp) REVERT: B 634 MET cc_start: 0.8035 (mpp) cc_final: 0.7734 (mmm) REVERT: B 902 MET cc_start: 0.8962 (mmm) cc_final: 0.8726 (mmm) REVERT: B 1063 MET cc_start: 0.8470 (tmm) cc_final: 0.7975 (tmm) REVERT: B 1199 MET cc_start: 0.8860 (tmm) cc_final: 0.8641 (tmm) REVERT: C 1 MET cc_start: 0.7548 (tmm) cc_final: 0.6745 (tpp) REVERT: C 22 LEU cc_start: 0.8454 (tt) cc_final: 0.8132 (tt) REVERT: C 38 TRP cc_start: 0.6531 (m-90) cc_final: 0.5700 (t-100) REVERT: C 40 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7268 (ttt90) REVERT: C 41 GLN cc_start: 0.7512 (tt0) cc_final: 0.6360 (tp-100) REVERT: C 84 MET cc_start: 0.3435 (tmm) cc_final: 0.2726 (tmm) REVERT: D 267 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 338 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9051 (tmm) REVERT: D 387 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: D 440 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8344 (mm) REVERT: D 486 ASP cc_start: 0.8323 (m-30) cc_final: 0.7944 (t0) REVERT: D 588 SER cc_start: 0.8803 (m) cc_final: 0.8471 (t) REVERT: D 614 LYS cc_start: 0.9480 (tttp) cc_final: 0.9189 (ptmm) REVERT: E 27 TYR cc_start: 0.6988 (m-10) cc_final: 0.6750 (m-10) REVERT: F 267 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7684 (mp0) REVERT: F 387 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: G 157 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7598 (mm) REVERT: G 262 ASP cc_start: 0.8704 (m-30) cc_final: 0.8391 (m-30) REVERT: H 38 TRP cc_start: 0.6130 (m-90) cc_final: 0.5816 (m-90) outliers start: 97 outliers final: 58 residues processed: 486 average time/residue: 0.2128 time to fit residues: 177.6217 Evaluate side-chains 466 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 398 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [51, 384, 412, 426, 499, 464, 420, 508, 230, 69, 172] chunk 51 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 chunk 412 optimal weight: 0.9990 chunk 426 optimal weight: 3.9990 chunk 499 optimal weight: 6.9990 chunk 464 optimal weight: 0.5980 chunk 420 optimal weight: 20.0000 chunk 508 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1694 ASN E 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.074245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056618 restraints weight = 237702.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.057982 restraints weight = 129900.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.058846 restraints weight = 88530.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059357 restraints weight = 69276.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.059722 restraints weight = 59678.574| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 43592 Z= 0.106 Angle : 0.594 12.937 58994 Z= 0.284 Chirality : 0.037 0.380 6662 Planarity : 0.003 0.051 7438 Dihedral : 4.184 52.613 5794 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 1.65 % Allowed : 15.24 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.12), residues: 5188 helix: 2.39 (0.09), residues: 3436 sheet: 2.08 (0.44), residues: 112 loop : -1.43 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 192 TYR 0.039 0.001 TYR F 176 PHE 0.051 0.001 PHE A 402 TRP 0.019 0.001 TRP F 279 HIS 0.003 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (43590) covalent geometry : angle 0.59364 / 0.28 (58990) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 1.74971 / 0.85 ( 4) hydrogen bonds : bond 0.03309 / 2.17 ( 2552) hydrogen bonds : angle 3.49427 / 2.51 ( 7632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 410 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8805 (tp) cc_final: 0.8563 (pp) REVERT: A 76 ASP cc_start: 0.7751 (m-30) cc_final: 0.7327 (t0) REVERT: A 194 PHE cc_start: 0.7469 (t80) cc_final: 0.7032 (m-80) REVERT: A 374 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (t80) REVERT: A 397 LYS cc_start: 0.9219 (ptpp) cc_final: 0.9011 (pttp) REVERT: A 508 ARG cc_start: 0.9049 (ptp-170) cc_final: 0.8844 (ptp-170) REVERT: A 659 GLN cc_start: 0.9663 (mm-40) cc_final: 0.9441 (mm-40) REVERT: A 719 ASN cc_start: 0.8532 (m-40) cc_final: 0.8233 (p0) REVERT: A 777 LEU cc_start: 0.8961 (mt) cc_final: 0.8622 (mt) REVERT: A 902 MET cc_start: 0.8941 (mmm) cc_final: 0.8583 (mmm) REVERT: A 950 MET cc_start: 0.8720 (tmm) cc_final: 0.8429 (tmm) REVERT: A 1199 MET cc_start: 0.8929 (tmm) cc_final: 0.8385 (tmm) REVERT: A 1227 MET cc_start: 0.7674 (tpp) cc_final: 0.7270 (tpt) REVERT: A 1284 GLN cc_start: 0.8585 (mp10) cc_final: 0.8325 (mp10) REVERT: A 1943 MET cc_start: 0.9100 (tpt) cc_final: 0.8838 (tpp) REVERT: A 1964 MET cc_start: 0.7746 (tpt) cc_final: 0.7504 (mmm) REVERT: A 2002 MET cc_start: 0.8699 (ppp) cc_final: 0.8216 (ppp) REVERT: A 2065 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8030 (ttt) REVERT: B 374 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6889 (t80) REVERT: B 456 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: B 492 LEU cc_start: 0.8206 (tp) cc_final: 0.7849 (pp) REVERT: B 634 MET cc_start: 0.7986 (mpp) cc_final: 0.7751 (mmm) REVERT: B 902 MET cc_start: 0.8945 (mmm) cc_final: 0.8707 (mmm) REVERT: B 1063 MET cc_start: 0.8463 (tmm) cc_final: 0.7985 (tmm) REVERT: B 1199 MET cc_start: 0.8805 (tmm) cc_final: 0.8577 (tmm) REVERT: C 1 MET cc_start: 0.7462 (tmm) cc_final: 0.6815 (tpt) REVERT: C 22 LEU cc_start: 0.8450 (tt) cc_final: 0.8134 (tt) REVERT: C 38 TRP cc_start: 0.6570 (m-90) cc_final: 0.5714 (t-100) REVERT: C 40 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7268 (ttt90) REVERT: C 41 GLN cc_start: 0.7497 (tt0) cc_final: 0.6350 (tp-100) REVERT: C 84 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.2642 (tmm) REVERT: D 267 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 338 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9055 (tmm) REVERT: D 387 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: D 486 ASP cc_start: 0.8268 (m-30) cc_final: 0.7882 (t0) REVERT: D 588 SER cc_start: 0.8801 (m) cc_final: 0.8459 (t) REVERT: D 614 LYS cc_start: 0.9473 (tttp) cc_final: 0.9188 (ptmm) REVERT: E 27 TYR cc_start: 0.6976 (m-10) cc_final: 0.6711 (m-10) REVERT: F 192 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7306 (ptm160) REVERT: F 267 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7723 (mp0) REVERT: F 387 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: G 63 PHE cc_start: 0.8905 (m-10) cc_final: 0.8619 (m-10) REVERT: G 157 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7646 (mm) REVERT: G 262 ASP cc_start: 0.8668 (m-30) cc_final: 0.8344 (m-30) REVERT: H 38 TRP cc_start: 0.6115 (m-90) cc_final: 0.5541 (m100) REVERT: H 95 TYR cc_start: 0.8257 (m-10) cc_final: 0.8034 (m-10) outliers start: 77 outliers final: 57 residues processed: 467 average time/residue: 0.2132 time to fit residues: 171.2968 Evaluate side-chains 466 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 400 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1297 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1694 ASN Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [298, 165, 300, 144, 353, 224, 61, 267, 302, 292, 341] chunk 298 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 267 optimal weight: 0.5980 chunk 302 optimal weight: 0.0770 chunk 292 optimal weight: 0.6980 chunk 341 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1694 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.074659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057066 restraints weight = 236087.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058439 restraints weight = 128659.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059334 restraints weight = 88107.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.059738 restraints weight = 69086.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060164 restraints weight = 60882.250| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 43592 Z= 0.100 Angle : 0.595 12.242 58994 Z= 0.282 Chirality : 0.037 0.346 6662 Planarity : 0.003 0.051 7438 Dihedral : 4.086 53.764 5788 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 1.67 % Allowed : 15.30 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.12), residues: 5188 helix: 2.40 (0.09), residues: 3440 sheet: 2.09 (0.44), residues: 112 loop : -1.41 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 40 TYR 0.039 0.001 TYR F 176 PHE 0.050 0.001 PHE A 402 TRP 0.020 0.001 TRP F 279 HIS 0.003 0.000 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (43590) covalent geometry : angle 0.59440 / 0.28 (58990) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 1.60586 / 0.78 ( 4) hydrogen bonds : bond 0.03096 / 2.03 ( 2552) hydrogen bonds : angle 3.42601 / 2.46 ( 7632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 410 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8802 (tp) cc_final: 0.8561 (pp) REVERT: A 76 ASP cc_start: 0.7731 (m-30) cc_final: 0.7280 (t0) REVERT: A 374 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7908 (t80) REVERT: A 397 LYS cc_start: 0.9199 (ptpp) cc_final: 0.8865 (pmtt) REVERT: A 508 ARG cc_start: 0.9056 (ptp-170) cc_final: 0.8850 (ptp-170) REVERT: A 659 GLN cc_start: 0.9684 (mm-40) cc_final: 0.9453 (mm-40) REVERT: A 719 ASN cc_start: 0.8556 (m-40) cc_final: 0.8221 (p0) REVERT: A 777 LEU cc_start: 0.8969 (mt) cc_final: 0.8626 (mt) REVERT: A 902 MET cc_start: 0.9000 (mmm) cc_final: 0.8606 (mmm) REVERT: A 950 MET cc_start: 0.8757 (tmm) cc_final: 0.8484 (tmm) REVERT: A 1199 MET cc_start: 0.8965 (tmm) cc_final: 0.8413 (tmm) REVERT: A 1227 MET cc_start: 0.7602 (tpp) cc_final: 0.7242 (tpt) REVERT: A 1284 GLN cc_start: 0.8628 (mp10) cc_final: 0.8360 (mp10) REVERT: A 1381 THR cc_start: 0.9060 (t) cc_final: 0.8858 (t) REVERT: A 1943 MET cc_start: 0.9138 (tpt) cc_final: 0.8863 (tpp) REVERT: A 1964 MET cc_start: 0.7813 (tpt) cc_final: 0.7540 (tpt) REVERT: A 2002 MET cc_start: 0.8693 (ppp) cc_final: 0.8197 (ppp) REVERT: A 2065 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: B 374 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6948 (t80) REVERT: B 456 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: B 492 LEU cc_start: 0.8199 (tp) cc_final: 0.7836 (pp) REVERT: B 634 MET cc_start: 0.8066 (mpp) cc_final: 0.7854 (mmm) REVERT: B 902 MET cc_start: 0.9030 (mmm) cc_final: 0.8776 (mmm) REVERT: B 1063 MET cc_start: 0.8463 (tmm) cc_final: 0.7980 (tmm) REVERT: B 1199 MET cc_start: 0.8820 (tmm) cc_final: 0.8527 (tmm) REVERT: B 1258 MET cc_start: 0.8737 (tmm) cc_final: 0.8495 (tmm) REVERT: C 1 MET cc_start: 0.7550 (tmm) cc_final: 0.6910 (tpt) REVERT: C 22 LEU cc_start: 0.8451 (tt) cc_final: 0.8164 (tt) REVERT: C 38 TRP cc_start: 0.6593 (m-90) cc_final: 0.5673 (t-100) REVERT: C 40 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7340 (ttt90) REVERT: C 41 GLN cc_start: 0.7532 (tt0) cc_final: 0.6386 (tp-100) REVERT: C 84 MET cc_start: 0.3404 (OUTLIER) cc_final: 0.2626 (tmm) REVERT: D 267 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7618 (mt-10) REVERT: D 338 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9044 (tmm) REVERT: D 486 ASP cc_start: 0.8222 (m-30) cc_final: 0.7869 (t0) REVERT: D 588 SER cc_start: 0.8749 (m) cc_final: 0.8420 (t) REVERT: D 614 LYS cc_start: 0.9500 (tttp) cc_final: 0.9200 (ptmm) REVERT: E 27 TYR cc_start: 0.6977 (m-10) cc_final: 0.6726 (m-10) REVERT: F 153 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8632 (pp20) REVERT: F 192 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7292 (ptm160) REVERT: F 267 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7717 (mp0) REVERT: F 387 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: G 63 PHE cc_start: 0.8919 (m-10) cc_final: 0.8626 (m-10) REVERT: G 157 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7711 (mm) REVERT: G 262 ASP cc_start: 0.8759 (m-30) cc_final: 0.8393 (m-30) REVERT: H 38 TRP cc_start: 0.6163 (m-90) cc_final: 0.5683 (m100) REVERT: H 40 ARG cc_start: 0.9100 (ttm-80) cc_final: 0.8630 (ttm-80) REVERT: H 95 TYR cc_start: 0.8259 (m-10) cc_final: 0.7780 (m-10) REVERT: H 102 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7031 (tp) outliers start: 78 outliers final: 52 residues processed: 465 average time/residue: 0.2124 time to fit residues: 169.4323 Evaluate side-chains 464 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 402 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1297 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1540 TRP Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [295, 462, 336, 80, 275, 453, 448, 299, 430, 370, 121] chunk 295 optimal weight: 2.9990 chunk 462 optimal weight: 3.9990 chunk 336 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 453 optimal weight: 3.9990 chunk 448 optimal weight: 0.9990 chunk 299 optimal weight: 0.0570 chunk 430 optimal weight: 0.5980 chunk 370 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1694 ASN E 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.074695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057125 restraints weight = 236954.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058495 restraints weight = 129110.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059359 restraints weight = 87962.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.059929 restraints weight = 69076.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.060224 restraints weight = 58998.164| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43592 Z= 0.102 Angle : 0.606 19.526 58994 Z= 0.287 Chirality : 0.038 0.335 6662 Planarity : 0.003 0.050 7438 Dihedral : 4.077 55.300 5788 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 1.42 % Allowed : 15.79 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.12), residues: 5188 helix: 2.37 (0.09), residues: 3448 sheet: 1.51 (0.45), residues: 112 loop : -1.39 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 40 TYR 0.038 0.001 TYR F 176 PHE 0.053 0.001 PHE A 402 TRP 0.020 0.001 TRP F 279 HIS 0.003 0.000 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (43590) covalent geometry : angle 0.60585 / 0.29 (58990) SS BOND : bond 0.00146 / 0.07 ( 2) SS BOND : angle 1.47343 / 0.71 ( 4) hydrogen bonds : bond 0.03056 / 2.00 ( 2552) hydrogen bonds : angle 3.43068 / 2.45 ( 7632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8804 (tp) cc_final: 0.8564 (pp) REVERT: A 76 ASP cc_start: 0.7763 (m-30) cc_final: 0.7310 (t0) REVERT: A 200 MET cc_start: 0.7886 (mmm) cc_final: 0.7678 (mmm) REVERT: A 374 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7893 (t80) REVERT: A 508 ARG cc_start: 0.9051 (ptp-170) cc_final: 0.8843 (ptp-170) REVERT: A 659 GLN cc_start: 0.9685 (mm-40) cc_final: 0.9458 (mm-40) REVERT: A 719 ASN cc_start: 0.8556 (m-40) cc_final: 0.8224 (p0) REVERT: A 777 LEU cc_start: 0.8989 (mt) cc_final: 0.8654 (mt) REVERT: A 902 MET cc_start: 0.8997 (mmm) cc_final: 0.8622 (mmm) REVERT: A 950 MET cc_start: 0.8759 (tmm) cc_final: 0.8483 (tmm) REVERT: A 1199 MET cc_start: 0.8967 (tmm) cc_final: 0.8405 (tmm) REVERT: A 1227 MET cc_start: 0.7614 (tpp) cc_final: 0.7266 (tpt) REVERT: A 1284 GLN cc_start: 0.8643 (mp10) cc_final: 0.8392 (mp10) REVERT: A 1381 THR cc_start: 0.9060 (t) cc_final: 0.8841 (t) REVERT: A 1486 MET cc_start: 0.8320 (mmm) cc_final: 0.8057 (mmm) REVERT: A 1943 MET cc_start: 0.9125 (tpt) cc_final: 0.8875 (tpp) REVERT: A 1964 MET cc_start: 0.7807 (tpt) cc_final: 0.7528 (tpt) REVERT: A 2002 MET cc_start: 0.8693 (ppp) cc_final: 0.8196 (ppp) REVERT: A 2065 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7886 (ttt) REVERT: B 188 ILE cc_start: 0.8144 (mt) cc_final: 0.7918 (pt) REVERT: B 374 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 456 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (pp20) REVERT: B 492 LEU cc_start: 0.8195 (tp) cc_final: 0.7831 (pp) REVERT: B 902 MET cc_start: 0.9024 (mmm) cc_final: 0.8762 (mmm) REVERT: B 1063 MET cc_start: 0.8464 (tmm) cc_final: 0.7975 (tmm) REVERT: B 1199 MET cc_start: 0.8833 (tmm) cc_final: 0.8163 (tmm) REVERT: B 1258 MET cc_start: 0.8770 (tmm) cc_final: 0.8522 (tmm) REVERT: C 1 MET cc_start: 0.7534 (tmm) cc_final: 0.6933 (tpt) REVERT: C 22 LEU cc_start: 0.8444 (tt) cc_final: 0.8202 (tt) REVERT: C 38 TRP cc_start: 0.6637 (m-90) cc_final: 0.5706 (t-100) REVERT: C 40 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7338 (ttt90) REVERT: C 41 GLN cc_start: 0.7494 (tt0) cc_final: 0.6337 (tp-100) REVERT: C 84 MET cc_start: 0.3328 (OUTLIER) cc_final: 0.2531 (tmm) REVERT: D 267 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 338 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8879 (tmm) REVERT: D 486 ASP cc_start: 0.8194 (m-30) cc_final: 0.7849 (t0) REVERT: D 588 SER cc_start: 0.8739 (m) cc_final: 0.8400 (t) REVERT: D 614 LYS cc_start: 0.9506 (tttp) cc_final: 0.9212 (ptmm) REVERT: D 746 MET cc_start: 0.8447 (mmm) cc_final: 0.8223 (mmp) REVERT: E 27 TYR cc_start: 0.6938 (m-10) cc_final: 0.6707 (m-10) REVERT: F 153 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8644 (pp20) REVERT: F 192 ARG cc_start: 0.8058 (tpt90) cc_final: 0.7278 (ptm160) REVERT: F 267 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7732 (mp0) REVERT: F 387 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: G 63 PHE cc_start: 0.8906 (m-10) cc_final: 0.8620 (m-10) REVERT: G 157 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7724 (mm) REVERT: G 262 ASP cc_start: 0.8748 (m-30) cc_final: 0.8375 (m-30) REVERT: H 38 TRP cc_start: 0.6172 (m-90) cc_final: 0.5681 (m100) REVERT: H 40 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8640 (ttm-80) REVERT: H 95 TYR cc_start: 0.8270 (m-10) cc_final: 0.7772 (m-10) outliers start: 66 outliers final: 52 residues processed: 454 average time/residue: 0.2148 time to fit residues: 168.2947 Evaluate side-chains 458 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1540 TRP Chi-restraints excluded: chain A residue 1565 THR Chi-restraints excluded: chain A residue 1578 LEU Chi-restraints excluded: chain A residue 1800 LYS Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 374 TYR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1297 ILE Chi-restraints excluded: chain B residue 1532 TYR Chi-restraints excluded: chain B residue 1578 LEU Chi-restraints excluded: chain B residue 1689 TRP Chi-restraints excluded: chain B residue 1694 ASN Chi-restraints excluded: chain B residue 1800 LYS Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 690 HIS Chi-restraints excluded: chain D residue 706 TYR Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: [306, 264, 489, 152, 48, 99, 6, 107, 87, 162, 341] chunk 306 optimal weight: 4.9990 chunk 264 optimal weight: 0.1980 chunk 489 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1694 ASN E 166 HIS F 763 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.073928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056372 restraints weight = 238416.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057694 restraints weight = 130264.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.058497 restraints weight = 88580.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059099 restraints weight = 70186.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059424 restraints weight = 59818.830| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43592 Z= 0.111 Angle : 0.614 17.696 58994 Z= 0.291 Chirality : 0.038 0.327 6662 Planarity : 0.003 0.052 7438 Dihedral : 4.093 56.698 5788 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 1.35 % Allowed : 15.79 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.12), residues: 5188 helix: 2.36 (0.09), residues: 3448 sheet: 1.52 (0.45), residues: 112 loop : -1.39 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 40 TYR 0.039 0.001 TYR F 176 PHE 0.059 0.001 PHE A 402 TRP 0.019 0.001 TRP F 279 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (43590) covalent geometry : angle 0.61342 / 0.29 (58990) SS BOND : bond 0.00105 / 0.05 ( 2) SS BOND : angle 1.55513 / 0.77 ( 4) hydrogen bonds : bond 0.03288 / 2.16 ( 2552) hydrogen bonds : angle 3.47513 / 2.49 ( 7632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9756.90 seconds wall clock time: 167 minutes 49.78 seconds (10069.78 seconds total)