Starting phenix.real_space_refine on Fri Aug 7 05:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.map" model { file = "/net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tpl_56108/08_2026/9tpl_56108.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 113 5.16 5 C 12240 2.51 5 N 3261 2.21 5 O 3625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19247 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7322 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 32, 'TRANS': 874} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 7127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7127 Classifications: {'peptide': 878} Link IDs: {'PTRANS': 31, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1256 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "E" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1108 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain breaks: 2 Chain: "F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1120 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19247 At special positions: 0 Unit cell: (94.76, 163.77, 180.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 6 15.00 Mg 2 11.99 O 3625 8.00 N 3261 7.00 C 12240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 832.5 milliseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4478 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 17 sheets defined 59.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 4.034A pdb=" N VAL A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.767A pdb=" N LEU A 93 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.715A pdb=" N SER A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.417A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 198 Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.663A pdb=" N GLN A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.895A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.077A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.581A pdb=" N MET A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 475 through 495 removed outlier: 3.547A pdb=" N VAL A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.596A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.828A pdb=" N PHE A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.588A pdb=" N PHE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.574A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 708 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 768 through 825 removed outlier: 4.373A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 841 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 844 through 911 removed outlier: 3.688A pdb=" N GLU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 850 " --> pdb=" O GLU A 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A 886 " --> pdb=" O GLN A 882 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 removed outlier: 3.734A pdb=" N VAL A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 removed outlier: 4.023A pdb=" N VAL B 8 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Proline residue: B 14 - end of helix No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.605A pdb=" N SER B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 removed outlier: 4.096A pdb=" N TYR B 134 " --> pdb=" O LEU B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 216 through 231 removed outlier: 4.037A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.652A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 283 through 290 removed outlier: 4.138A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.898A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.513A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 4.050A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.705A pdb=" N ILE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.544A pdb=" N MET B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.621A pdb=" N ALA B 550 " --> pdb=" O MET B 546 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.557A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.849A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 723 through 726 Processing helix chain 'B' and resid 738 through 748 Processing helix chain 'B' and resid 768 through 827 removed outlier: 3.663A pdb=" N ASN B 826 " --> pdb=" O MET B 822 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 Processing helix chain 'B' and resid 846 through 919 removed outlier: 3.535A pdb=" N THR B 857 " --> pdb=" O LYS B 853 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.572A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 88 through 94 removed outlier: 4.429A pdb=" N ARG C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.094A pdb=" N LYS C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.902A pdb=" N VAL C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.678A pdb=" N GLU D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.592A pdb=" N LEU D 80 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 125 Proline residue: D 116 - end of helix removed outlier: 4.115A pdb=" N LYS D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.969A pdb=" N VAL D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 32 through 37 removed outlier: 4.074A pdb=" N MET E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 removed outlier: 4.093A pdb=" N LEU E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 3.995A pdb=" N ILE E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 removed outlier: 3.711A pdb=" N LEU E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.517A pdb=" N ALA E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.885A pdb=" N LEU E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 45 through 56 removed outlier: 3.861A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.706A pdb=" N THR F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.507A pdb=" N ILE F 99 " --> pdb=" O PRO F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.783A pdb=" N VAL F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 137 removed outlier: 3.606A pdb=" N GLN F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 7.448A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.387A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 455 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.840A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.464A pdb=" N LYS B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG B 54 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.474A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER B 173 " --> pdb=" O HIS B 668 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 670 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 175 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS B 672 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY B 245 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 265 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 247 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE B 263 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG B 249 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 261 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS B 251 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 363 through 365 removed outlier: 4.219A pdb=" N LYS B 363 " --> pdb=" O ASP B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.902A pdb=" N SER B 578 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.955A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'D' and resid 148 through 149 1008 hydrogen bonds defined for protein. 2892 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: 3.61 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6256 1.34 - 1.46: 3199 1.46 - 1.58: 9947 1.58 - 1.70: 6 1.70 - 1.82: 202 Bond restraints: 19610 Sorted by residual: bond pdb=" O4 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O3 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O2 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O2 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.97e+00 bond pdb=" O3 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.80e+00 ... (remaining 19605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 25803 1.90 - 3.80: 477 3.80 - 5.70: 84 5.70 - 7.60: 19 7.60 - 9.50: 5 Bond angle restraints: 26388 Sorted by residual: angle pdb=" N ILE A 913 " pdb=" CA ILE A 913 " pdb=" C ILE A 913 " ideal model delta sigma weight residual 113.42 108.28 5.14 1.17e+00 7.31e-01 1.93e+01 angle pdb=" C ILE C 51 " pdb=" N GLU C 52 " pdb=" CA GLU C 52 " ideal model delta sigma weight residual 120.31 114.64 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" N GLU E 121 " pdb=" CA GLU E 121 " pdb=" CB GLU E 121 " ideal model delta sigma weight residual 110.12 114.87 -4.75 1.47e+00 4.63e-01 1.04e+01 angle pdb=" N GLU C 52 " pdb=" CA GLU C 52 " pdb=" CB GLU C 52 " ideal model delta sigma weight residual 110.28 115.28 -5.00 1.55e+00 4.16e-01 1.04e+01 angle pdb=" CA MET B 528 " pdb=" CB MET B 528 " pdb=" CG MET B 528 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.04e+00 ... (remaining 26383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10684 17.73 - 35.46: 993 35.46 - 53.19: 172 53.19 - 70.92: 69 70.92 - 88.65: 45 Dihedral angle restraints: 11963 sinusoidal: 5047 harmonic: 6916 Sorted by residual: dihedral pdb=" CA GLU A 474 " pdb=" C GLU A 474 " pdb=" N GLN A 475 " pdb=" CA GLN A 475 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET D 149 " pdb=" C MET D 149 " pdb=" N GLY D 150 " pdb=" CA GLY D 150 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 11960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1665 0.030 - 0.060: 793 0.060 - 0.091: 249 0.091 - 0.121: 126 0.121 - 0.151: 22 Chirality restraints: 2855 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE A 673 " pdb=" N ILE A 673 " pdb=" C ILE A 673 " pdb=" CB ILE A 673 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2852 not shown) Planarity restraints: 3414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 888 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C GLN B 888 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN B 888 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 889 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 666 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 667 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 667 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 667 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 438 " -0.013 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP B 438 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 438 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 438 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 438 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 438 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 438 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 438 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 438 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 438 " -0.001 2.00e-02 2.50e+03 ... (remaining 3411 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 190 2.56 - 3.15: 16226 3.15 - 3.73: 31507 3.73 - 4.32: 41733 4.32 - 4.90: 69010 Nonbonded interactions: 158666 Sorted by model distance: nonbonded pdb=" O1 PO4 B2002 " pdb="MG MG B2003 " model vdw 1.978 2.170 nonbonded pdb=" OG SER A 242 " pdb="MG MG A2003 " model vdw 2.001 2.170 nonbonded pdb=" O1 PO4 A2002 " pdb="MG MG A2003 " model vdw 2.037 2.170 nonbonded pdb=" OG SER A 271 " pdb=" OE2 GLU A 474 " model vdw 2.039 3.040 nonbonded pdb=" O1B ADP B2001 " pdb="MG MG B2003 " model vdw 2.064 2.170 ... (remaining 158661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 198 or resid 215 through 367 or resid 371 throug \ h 406 or resid 410 through 624 or resid 645 through 2003)) selection = (chain 'B' and (resid 3 through 920 or resid 2001 through 2003)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 39 through 195) } ncs_group { reference = (chain 'E' and (resid 20 through 143 or resid 149 through 162)) selection = (chain 'F' and (resid 20 through 55 or resid 60 through 143 or resid 149 through \ 162)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.180 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19611 Z= 0.174 Angle : 0.649 9.498 26388 Z= 0.333 Chirality : 0.042 0.151 2855 Planarity : 0.004 0.046 3414 Dihedral : 15.554 88.650 7485 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2336 helix: 0.57 (0.15), residues: 1260 sheet: -0.80 (0.40), residues: 168 loop : -0.63 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 870 TYR 0.020 0.001 TYR A 455 PHE 0.027 0.001 PHE A 359 TRP 0.031 0.002 TRP B 438 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (19610) covalent geometry : angle 0.64862 / 0.33 (26388) hydrogen bonds : bond 0.16416 / 10.73 ( 1008) hydrogen bonds : angle 6.29119 / 4.38 ( 2892) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.6837 (t70) cc_final: 0.6496 (t0) REVERT: A 870 ARG cc_start: 0.6274 (ttp80) cc_final: 0.6018 (tmm160) REVERT: B 318 THR cc_start: 0.7183 (p) cc_final: 0.6639 (p) REVERT: B 904 ARG cc_start: 0.4876 (ptt-90) cc_final: 0.3773 (tmm160) REVERT: D 183 ILE cc_start: 0.6486 (pt) cc_final: 0.6243 (pt) REVERT: E 98 THR cc_start: 0.7721 (p) cc_final: 0.7511 (p) REVERT: F 26 ILE cc_start: 0.7529 (tp) cc_final: 0.7283 (mt) REVERT: F 41 ASP cc_start: 0.4408 (p0) cc_final: 0.4158 (p0) REVERT: F 107 ASP cc_start: 0.5462 (p0) cc_final: 0.4775 (p0) REVERT: F 158 ILE cc_start: 0.6818 (pt) cc_final: 0.6335 (tt) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.1441 time to fit residues: 121.9899 Evaluate side-chains 321 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN C 85 GLN C 180 ASN D 120 HIS D 176 GLN E 78 ASN E 126 GLN E 137 GLN E 154 ASN F 25 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.169408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.135705 restraints weight = 38202.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.132075 restraints weight = 49984.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129766 restraints weight = 39891.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130154 restraints weight = 32229.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130338 restraints weight = 26006.540| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 19611 Z= 0.223 Angle : 0.790 12.410 26388 Z= 0.403 Chirality : 0.047 0.207 2855 Planarity : 0.005 0.055 3414 Dihedral : 5.680 59.580 2588 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 10.87 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2336 helix: 0.33 (0.14), residues: 1298 sheet: -1.12 (0.38), residues: 175 loop : -0.84 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 40 TYR 0.018 0.002 TYR A 410 PHE 0.023 0.002 PHE B 553 TRP 0.022 0.002 TRP B 438 HIS 0.009 0.002 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (19610) covalent geometry : angle 0.79034 / 0.40 (26388) hydrogen bonds : bond 0.04687 / 3.14 ( 1008) hydrogen bonds : angle 4.99591 / 3.45 ( 2892) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 327 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7837 (mtm) REVERT: A 887 LEU cc_start: 0.8539 (mp) cc_final: 0.8110 (tp) REVERT: B 524 ILE cc_start: 0.7533 (mm) cc_final: 0.7327 (mm) REVERT: D 138 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6555 (ttm110) REVERT: F 26 ILE cc_start: 0.7882 (tp) cc_final: 0.7457 (mt) REVERT: F 43 PHE cc_start: 0.4703 (t80) cc_final: 0.4311 (t80) outliers start: 47 outliers final: 23 residues processed: 355 average time/residue: 0.1434 time to fit residues: 79.0452 Evaluate side-chains 292 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 867 GLU Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 95 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS C 180 ASN D 176 GLN E 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.167546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.135754 restraints weight = 39364.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132028 restraints weight = 54636.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.129756 restraints weight = 44419.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130087 restraints weight = 37889.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130329 restraints weight = 29422.762| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19611 Z= 0.235 Angle : 0.748 10.818 26388 Z= 0.382 Chirality : 0.047 0.228 2855 Planarity : 0.005 0.060 3414 Dihedral : 5.793 59.965 2588 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 3.29 % Allowed : 14.50 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2336 helix: 0.35 (0.14), residues: 1296 sheet: -1.44 (0.39), residues: 165 loop : -0.90 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 777 TYR 0.023 0.002 TYR F 118 PHE 0.038 0.002 PHE B 46 TRP 0.031 0.002 TRP A 508 HIS 0.044 0.002 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (19610) covalent geometry : angle 0.74848 / 0.38 (26388) hydrogen bonds : bond 0.04799 / 3.22 ( 1008) hydrogen bonds : angle 4.98608 / 3.45 ( 2892) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 0.803 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: A 258 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 352 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8906 (tt) REVERT: A 515 MET cc_start: 0.8102 (mmm) cc_final: 0.7388 (mmm) REVERT: A 690 MET cc_start: 0.8332 (tpp) cc_final: 0.8060 (tpp) REVERT: A 830 MET cc_start: 0.5290 (pmm) cc_final: 0.5013 (ptp) REVERT: A 887 LEU cc_start: 0.8517 (mp) cc_final: 0.8178 (tp) REVERT: B 220 ILE cc_start: 0.7737 (tp) cc_final: 0.7425 (tt) REVERT: C 54 PHE cc_start: 0.6473 (m-80) cc_final: 0.6109 (m-80) REVERT: E 90 LEU cc_start: 0.6140 (pp) cc_final: 0.5879 (mp) REVERT: F 37 ASP cc_start: 0.5963 (t0) cc_final: 0.5668 (t0) REVERT: F 41 ASP cc_start: 0.4849 (p0) cc_final: 0.4550 (p0) REVERT: F 43 PHE cc_start: 0.4592 (t80) cc_final: 0.3946 (t80) REVERT: F 104 LYS cc_start: 0.8468 (pttp) cc_final: 0.8035 (pttm) REVERT: F 107 ASP cc_start: 0.5573 (p0) cc_final: 0.5292 (p0) REVERT: F 158 ILE cc_start: 0.7271 (pt) cc_final: 0.6741 (tt) outliers start: 68 outliers final: 32 residues processed: 332 average time/residue: 0.1390 time to fit residues: 72.4772 Evaluate side-chains 274 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 GLN A 895 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 GLN C 75 GLN D 176 GLN E 137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.168962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132857 restraints weight = 38347.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.133275 restraints weight = 48205.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.132889 restraints weight = 32128.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131893 restraints weight = 30305.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132373 restraints weight = 26280.656| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19611 Z= 0.145 Angle : 0.652 9.473 26388 Z= 0.327 Chirality : 0.042 0.185 2855 Planarity : 0.004 0.046 3414 Dihedral : 5.508 59.368 2588 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 2.51 % Allowed : 17.79 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2336 helix: 0.55 (0.15), residues: 1298 sheet: -1.20 (0.40), residues: 162 loop : -0.91 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 904 TYR 0.014 0.002 TYR D 185 PHE 0.026 0.001 PHE E 82 TRP 0.017 0.002 TRP B 438 HIS 0.005 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (19610) covalent geometry : angle 0.65161 / 0.33 (26388) hydrogen bonds : bond 0.03902 / 2.61 ( 1008) hydrogen bonds : angle 4.68498 / 3.25 ( 2892) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.718 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: A 496 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 531 MET cc_start: 0.7715 (mtp) cc_final: 0.7487 (mtp) REVERT: A 830 MET cc_start: 0.5269 (pmm) cc_final: 0.4992 (pmm) REVERT: B 220 ILE cc_start: 0.7697 (tp) cc_final: 0.7482 (tt) REVERT: B 230 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 341 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.5332 (t80) REVERT: B 388 MET cc_start: 0.6660 (ppp) cc_final: 0.6450 (ppp) REVERT: B 690 MET cc_start: 0.7416 (tpp) cc_final: 0.6881 (tpp) REVERT: C 54 PHE cc_start: 0.6304 (m-80) cc_final: 0.6049 (m-80) REVERT: E 90 LEU cc_start: 0.6105 (pp) cc_final: 0.5802 (mp) REVERT: F 43 PHE cc_start: 0.4398 (t80) cc_final: 0.4033 (t80) REVERT: F 158 ILE cc_start: 0.7077 (pt) cc_final: 0.6500 (tt) outliers start: 52 outliers final: 32 residues processed: 304 average time/residue: 0.1453 time to fit residues: 68.8954 Evaluate side-chains 274 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 230 optimal weight: 0.9980 chunk 14 optimal weight: 0.0470 chunk 154 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 726 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 334 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN D 176 GLN E 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.169086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.139638 restraints weight = 37516.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.131407 restraints weight = 41232.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130710 restraints weight = 42091.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130851 restraints weight = 31015.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.131262 restraints weight = 26788.065| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19611 Z= 0.130 Angle : 0.631 12.654 26388 Z= 0.316 Chirality : 0.042 0.190 2855 Planarity : 0.004 0.048 3414 Dihedral : 5.283 58.083 2588 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.71 % Allowed : 18.56 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2336 helix: 0.72 (0.15), residues: 1300 sheet: -1.09 (0.41), residues: 160 loop : -0.87 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 858 TYR 0.028 0.001 TYR B 501 PHE 0.024 0.001 PHE E 82 TRP 0.015 0.001 TRP A 829 HIS 0.005 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19610) covalent geometry : angle 0.63127 / 0.32 (26388) hydrogen bonds : bond 0.03711 / 2.49 ( 1008) hydrogen bonds : angle 4.55275 / 3.17 ( 2892) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7729 (tmm) cc_final: 0.7417 (ttp) REVERT: A 474 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 496 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 531 MET cc_start: 0.7678 (mtp) cc_final: 0.7369 (mtp) REVERT: A 830 MET cc_start: 0.5292 (pmm) cc_final: 0.5012 (ptp) REVERT: B 341 PHE cc_start: 0.5632 (OUTLIER) cc_final: 0.5263 (t80) REVERT: B 690 MET cc_start: 0.7566 (tpp) cc_final: 0.7063 (tpp) REVERT: C 54 PHE cc_start: 0.6642 (m-80) cc_final: 0.6233 (m-80) REVERT: D 66 LYS cc_start: 0.4427 (pttm) cc_final: 0.3730 (ptpp) REVERT: E 90 LEU cc_start: 0.6262 (pp) cc_final: 0.5817 (mp) REVERT: F 43 PHE cc_start: 0.4570 (t80) cc_final: 0.4207 (t80) REVERT: F 123 LEU cc_start: 0.5528 (pp) cc_final: 0.5206 (tt) REVERT: F 158 ILE cc_start: 0.7438 (pt) cc_final: 0.6888 (tt) outliers start: 56 outliers final: 38 residues processed: 296 average time/residue: 0.1417 time to fit residues: 65.2614 Evaluate side-chains 281 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN D 176 GLN E 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.164769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.135920 restraints weight = 37428.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130427 restraints weight = 49266.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127219 restraints weight = 41207.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127533 restraints weight = 38472.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.127755 restraints weight = 31903.123| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19611 Z= 0.237 Angle : 0.743 13.744 26388 Z= 0.372 Chirality : 0.046 0.308 2855 Planarity : 0.004 0.050 3414 Dihedral : 5.552 59.686 2588 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 3.38 % Allowed : 19.09 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2336 helix: 0.42 (0.14), residues: 1308 sheet: -1.32 (0.38), residues: 170 loop : -1.05 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 694 TYR 0.020 0.002 TYR A 386 PHE 0.039 0.002 PHE D 61 TRP 0.017 0.002 TRP A 829 HIS 0.006 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (19610) covalent geometry : angle 0.74301 / 0.37 (26388) hydrogen bonds : bond 0.04354 / 2.91 ( 1008) hydrogen bonds : angle 4.78627 / 3.32 ( 2892) Misc. bond : bond 0.00166 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 0.758 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: A 483 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 531 MET cc_start: 0.7990 (mtp) cc_final: 0.7783 (mtp) REVERT: A 684 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7010 (ttt) REVERT: A 686 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: B 341 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5295 (t80) REVERT: B 500 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7060 (tt0) REVERT: B 690 MET cc_start: 0.7804 (tpp) cc_final: 0.7508 (tpt) REVERT: B 834 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 54 PHE cc_start: 0.6424 (m-80) cc_final: 0.6052 (m-80) REVERT: D 66 LYS cc_start: 0.4319 (pttm) cc_final: 0.3663 (ptpp) REVERT: E 90 LEU cc_start: 0.6291 (pp) cc_final: 0.5791 (mp) REVERT: F 23 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6210 (mm-40) REVERT: F 26 ILE cc_start: 0.7749 (tp) cc_final: 0.7366 (mt) REVERT: F 37 ASP cc_start: 0.5838 (t0) cc_final: 0.5539 (t0) REVERT: F 41 ASP cc_start: 0.5095 (p0) cc_final: 0.4794 (p0) REVERT: F 43 PHE cc_start: 0.4683 (t80) cc_final: 0.4337 (t80) REVERT: F 104 LYS cc_start: 0.8455 (pttm) cc_final: 0.8040 (tptp) REVERT: F 107 ASP cc_start: 0.5723 (p0) cc_final: 0.5136 (p0) REVERT: F 123 LEU cc_start: 0.5416 (pp) cc_final: 0.5110 (tt) REVERT: F 134 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5975 (pp20) REVERT: F 152 TYR cc_start: 0.6058 (p90) cc_final: 0.5476 (p90) REVERT: F 158 ILE cc_start: 0.7404 (pt) cc_final: 0.6660 (tt) outliers start: 70 outliers final: 42 residues processed: 310 average time/residue: 0.1428 time to fit residues: 68.5051 Evaluate side-chains 291 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 134 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 135 optimal weight: 0.5980 chunk 169 optimal weight: 0.0470 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.0170 chunk 15 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 222 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 490 ASN B 562 ASN B 564 GLN D 176 GLN D 191 HIS E 137 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125965 restraints weight = 35740.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122660 restraints weight = 49266.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116758 restraints weight = 33147.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117174 restraints weight = 39457.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117882 restraints weight = 34618.173| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19611 Z= 0.125 Angle : 0.664 11.357 26388 Z= 0.331 Chirality : 0.042 0.337 2855 Planarity : 0.004 0.051 3414 Dihedral : 5.284 57.189 2588 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 2.51 % Allowed : 20.44 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2336 helix: 0.64 (0.15), residues: 1309 sheet: -1.16 (0.38), residues: 170 loop : -0.95 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 870 TYR 0.017 0.001 TYR B 501 PHE 0.019 0.001 PHE B 856 TRP 0.014 0.001 TRP B 438 HIS 0.010 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19610) covalent geometry : angle 0.66446 / 0.33 (26388) hydrogen bonds : bond 0.03730 / 2.52 ( 1008) hydrogen bonds : angle 4.52832 / 3.16 ( 2892) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: A 496 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 531 MET cc_start: 0.8009 (mtp) cc_final: 0.7741 (mtp) REVERT: A 686 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: B 341 PHE cc_start: 0.5850 (OUTLIER) cc_final: 0.5401 (t80) REVERT: B 500 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6836 (tt0) REVERT: B 690 MET cc_start: 0.7854 (tpp) cc_final: 0.7496 (tpp) REVERT: B 834 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7903 (t80) REVERT: C 54 PHE cc_start: 0.6942 (m-80) cc_final: 0.6466 (m-80) REVERT: C 59 MET cc_start: 0.6543 (mpp) cc_final: 0.5354 (mmt) REVERT: D 66 LYS cc_start: 0.4692 (pttm) cc_final: 0.3966 (ptpp) REVERT: E 90 LEU cc_start: 0.6500 (pp) cc_final: 0.5951 (mp) REVERT: F 26 ILE cc_start: 0.7928 (tp) cc_final: 0.7543 (mt) REVERT: F 37 ASP cc_start: 0.5889 (t0) cc_final: 0.5580 (t0) REVERT: F 41 ASP cc_start: 0.5372 (p0) cc_final: 0.5085 (p0) REVERT: F 43 PHE cc_start: 0.4851 (t80) cc_final: 0.4151 (t80) REVERT: F 104 LYS cc_start: 0.8730 (pttm) cc_final: 0.8219 (tptp) REVERT: F 107 ASP cc_start: 0.6182 (p0) cc_final: 0.5920 (p0) REVERT: F 123 LEU cc_start: 0.5932 (pp) cc_final: 0.5639 (tt) REVERT: F 134 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6122 (pp20) REVERT: F 158 ILE cc_start: 0.7903 (pt) cc_final: 0.7292 (tt) outliers start: 52 outliers final: 33 residues processed: 295 average time/residue: 0.1406 time to fit residues: 64.1021 Evaluate side-chains 278 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 134 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.0050 chunk 231 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125973 restraints weight = 35646.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121683 restraints weight = 48533.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115692 restraints weight = 30702.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115788 restraints weight = 34571.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116397 restraints weight = 28634.578| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19611 Z= 0.134 Angle : 0.674 11.667 26388 Z= 0.334 Chirality : 0.043 0.407 2855 Planarity : 0.004 0.053 3414 Dihedral : 5.232 58.481 2588 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 2.61 % Allowed : 20.59 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2336 helix: 0.66 (0.15), residues: 1312 sheet: -1.05 (0.40), residues: 160 loop : -0.91 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 870 TYR 0.026 0.001 TYR A 386 PHE 0.028 0.001 PHE E 53 TRP 0.027 0.002 TRP A 827 HIS 0.011 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (19610) covalent geometry : angle 0.67382 / 0.33 (26388) hydrogen bonds : bond 0.03656 / 2.46 ( 1008) hydrogen bonds : angle 4.52764 / 3.15 ( 2892) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 0.774 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: A 474 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 483 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 531 MET cc_start: 0.8091 (mtp) cc_final: 0.7763 (mtp) REVERT: A 686 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: B 341 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5302 (t80) REVERT: B 500 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7098 (tt0) REVERT: B 690 MET cc_start: 0.8174 (tpp) cc_final: 0.7491 (tpp) REVERT: B 822 MET cc_start: 0.5948 (mmp) cc_final: 0.5206 (mmp) REVERT: B 834 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 54 PHE cc_start: 0.6951 (m-80) cc_final: 0.6474 (m-80) REVERT: D 66 LYS cc_start: 0.4687 (pttm) cc_final: 0.3986 (ptpp) REVERT: D 80 LEU cc_start: 0.9276 (tp) cc_final: 0.8912 (mm) REVERT: D 108 MET cc_start: 0.5550 (tpt) cc_final: 0.5315 (tpt) REVERT: E 90 LEU cc_start: 0.6467 (pp) cc_final: 0.5893 (mp) REVERT: F 26 ILE cc_start: 0.7903 (tp) cc_final: 0.7641 (mt) REVERT: F 43 PHE cc_start: 0.4875 (t80) cc_final: 0.4494 (t80) REVERT: F 104 LYS cc_start: 0.8631 (pttm) cc_final: 0.8055 (tptp) REVERT: F 123 LEU cc_start: 0.5908 (pp) cc_final: 0.5585 (tt) REVERT: F 158 ILE cc_start: 0.7888 (pt) cc_final: 0.7225 (tt) outliers start: 54 outliers final: 39 residues processed: 291 average time/residue: 0.1484 time to fit residues: 66.9202 Evaluate side-chains 284 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 884 LYS Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.159749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127516 restraints weight = 35264.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120159 restraints weight = 46093.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117678 restraints weight = 42064.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118402 restraints weight = 35733.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118262 restraints weight = 30452.875| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19611 Z= 0.158 Angle : 0.691 10.913 26388 Z= 0.344 Chirality : 0.044 0.274 2855 Planarity : 0.004 0.054 3414 Dihedral : 5.282 59.567 2588 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 2.27 % Allowed : 21.41 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2336 helix: 0.66 (0.15), residues: 1311 sheet: -0.85 (0.41), residues: 148 loop : -1.00 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 870 TYR 0.028 0.002 TYR D 130 PHE 0.019 0.001 PHE E 53 TRP 0.025 0.002 TRP A 829 HIS 0.011 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (19610) covalent geometry : angle 0.69070 / 0.34 (26388) hydrogen bonds : bond 0.03759 / 2.51 ( 1008) hydrogen bonds : angle 4.57142 / 3.18 ( 2892) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: A 531 MET cc_start: 0.8070 (mtp) cc_final: 0.7744 (mtp) REVERT: B 341 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5333 (t80) REVERT: B 500 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7168 (tt0) REVERT: B 690 MET cc_start: 0.8138 (tpp) cc_final: 0.7433 (tpp) REVERT: B 834 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 54 PHE cc_start: 0.6757 (m-80) cc_final: 0.6329 (m-80) REVERT: C 59 MET cc_start: 0.6289 (mpp) cc_final: 0.4891 (mmt) REVERT: D 66 LYS cc_start: 0.4430 (pttm) cc_final: 0.3814 (ptpp) REVERT: D 80 LEU cc_start: 0.9094 (tp) cc_final: 0.8788 (mm) REVERT: D 109 MET cc_start: 0.2337 (ppp) cc_final: 0.1945 (ppp) REVERT: E 90 LEU cc_start: 0.6360 (pp) cc_final: 0.5788 (mp) REVERT: F 26 ILE cc_start: 0.7837 (tp) cc_final: 0.7537 (mt) REVERT: F 37 ASP cc_start: 0.5799 (t0) cc_final: 0.5395 (t0) REVERT: F 41 ASP cc_start: 0.5138 (p0) cc_final: 0.4883 (p0) REVERT: F 43 PHE cc_start: 0.4622 (t80) cc_final: 0.3916 (t80) REVERT: F 104 LYS cc_start: 0.8337 (pttm) cc_final: 0.7770 (tptp) REVERT: F 123 LEU cc_start: 0.5544 (pp) cc_final: 0.5248 (tt) REVERT: F 158 ILE cc_start: 0.7606 (pt) cc_final: 0.6925 (tt) outliers start: 47 outliers final: 33 residues processed: 290 average time/residue: 0.1515 time to fit residues: 67.8622 Evaluate side-chains 275 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 229 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 223 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 720 GLN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126067 restraints weight = 35558.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120519 restraints weight = 46123.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114525 restraints weight = 33488.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114762 restraints weight = 35853.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115223 restraints weight = 28779.044| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19611 Z= 0.136 Angle : 0.709 14.259 26388 Z= 0.349 Chirality : 0.044 0.298 2855 Planarity : 0.004 0.055 3414 Dihedral : 5.239 58.558 2588 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 2.08 % Allowed : 22.09 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2336 helix: 0.60 (0.15), residues: 1323 sheet: -1.06 (0.39), residues: 160 loop : -1.03 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 870 TYR 0.023 0.001 TYR D 130 PHE 0.030 0.001 PHE E 53 TRP 0.026 0.002 TRP A 829 HIS 0.010 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19610) covalent geometry : angle 0.70925 / 0.35 (26388) hydrogen bonds : bond 0.03667 / 2.44 ( 1008) hydrogen bonds : angle 4.58603 / 3.19 ( 2892) Misc. bond : bond 0.00053 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.798 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: A 352 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 474 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 496 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 531 MET cc_start: 0.8103 (mtp) cc_final: 0.7759 (mtp) REVERT: B 341 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5597 (t80) REVERT: B 500 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 690 MET cc_start: 0.8081 (tpp) cc_final: 0.7424 (tpp) REVERT: B 798 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7592 (mpt180) REVERT: B 822 MET cc_start: 0.6021 (mmp) cc_final: 0.5684 (tpt) REVERT: B 834 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 54 PHE cc_start: 0.6954 (m-80) cc_final: 0.6473 (m-80) REVERT: C 59 MET cc_start: 0.6499 (mpp) cc_final: 0.5011 (mmt) REVERT: D 66 LYS cc_start: 0.4602 (pttm) cc_final: 0.3960 (ptpp) REVERT: D 80 LEU cc_start: 0.9269 (tp) cc_final: 0.8852 (mm) REVERT: D 109 MET cc_start: 0.2576 (ppp) cc_final: 0.2239 (ppp) REVERT: D 140 PHE cc_start: 0.7624 (m-80) cc_final: 0.7398 (m-80) REVERT: E 90 LEU cc_start: 0.6426 (pp) cc_final: 0.5827 (mp) REVERT: F 43 PHE cc_start: 0.4833 (t80) cc_final: 0.4461 (t80) REVERT: F 104 LYS cc_start: 0.8643 (pttm) cc_final: 0.7989 (tptp) outliers start: 43 outliers final: 34 residues processed: 281 average time/residue: 0.1480 time to fit residues: 64.4124 Evaluate side-chains 276 residues out of total 2069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.161393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126026 restraints weight = 35582.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122513 restraints weight = 48076.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117119 restraints weight = 31112.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116529 restraints weight = 40557.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116922 restraints weight = 37411.001| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19611 Z= 0.127 Angle : 0.709 16.072 26388 Z= 0.348 Chirality : 0.044 0.295 2855 Planarity : 0.004 0.055 3414 Dihedral : 5.208 59.134 2588 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.03 % Allowed : 22.18 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2336 helix: 0.64 (0.15), residues: 1322 sheet: -0.93 (0.40), residues: 158 loop : -1.05 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 870 TYR 0.024 0.001 TYR A 386 PHE 0.026 0.001 PHE A 856 TRP 0.030 0.002 TRP A 827 HIS 0.006 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19610) covalent geometry : angle 0.70863 / 0.35 (26388) hydrogen bonds : bond 0.03602 / 2.39 ( 1008) hydrogen bonds : angle 4.58905 / 3.19 ( 2892) Misc. bond : bond 0.00044 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.30 seconds wall clock time: 61 minutes 50.75 seconds (3710.75 seconds total)