Starting phenix.real_space_refine on Wed Aug 5 13:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.map" model { file = "/net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sq5_55107/08_2026/9sq5_55107.cif" } resolution = 3.68 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 60 5.16 5 C 6041 2.51 5 N 1620 2.21 5 O 1808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 9531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6470 Classifications: {'peptide': 824} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 796} Chain breaks: 1 Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2897 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 142 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' ZN': 1, 'Y70': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8553 SG CYS B 323 55.909 56.542 23.447 1.00262.45 S ATOM 8577 SG CYS B 326 57.019 53.613 21.677 1.00275.73 S ATOM 9089 SG CYS B 391 58.476 57.044 20.751 1.00290.73 S ATOM 9112 SG CYS B 394 55.377 56.954 20.220 1.00309.14 S ATOM 9395 SG CYS C 147 46.272 68.849 19.314 1.00369.59 S ATOM 9411 SG CYS C 150 49.752 68.922 20.494 1.00340.50 S Time building chain proxies: 2.25, per 1000 atoms: 0.24 Number of scatterers: 9531 At special positions: 0 Unit cell: (95.485, 98.02, 122.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 60 16.00 O 1808 8.00 N 1620 7.00 C 6041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 386.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 163 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 167 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 147 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 150 " Number of angles added : 8 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 23 sheets defined 17.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.778A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1060 Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1125 through 1137 removed outlier: 3.515A pdb=" N LEU A1129 " --> pdb=" O THR A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.592A pdb=" N THR B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.769A pdb=" N ALA B 196 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.545A pdb=" N PHE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.698A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.586A pdb=" N ILE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'C' and resid 156 through 168 removed outlier: 3.608A pdb=" N LEU C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.778A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A1027 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A1040 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A1029 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A1038 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A1039 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR A 8 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR A1041 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 6 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.608A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR A 45 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.076A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER A 94 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.301A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.582A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.582A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 221 removed outlier: 6.628A pdb=" N ILE A 232 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 219 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 230 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.652A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 313 through 317 removed outlier: 3.517A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 365 removed outlier: 3.904A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.462A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.462A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.278A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.145A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 913 through 917 removed outlier: 6.838A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 954 through 961 removed outlier: 3.984A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AB9, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 66 removed outlier: 13.084A pdb=" N GLU B 132 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N LEU B 168 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 146 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 154 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN B 148 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 78 through 82 removed outlier: 5.618A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN B 148 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 154 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 146 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N LEU B 168 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 13.084A pdb=" N GLU B 132 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU B 132 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN B 134 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA B 124 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY B 136 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 122 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR B 138 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 120 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 330 through 333 removed outlier: 6.984A pdb=" N LEU B 321 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 350 removed outlier: 7.062A pdb=" N ILE B 398 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL B 388 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG B 373 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLN B 390 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE B 371 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 146 366 hydrogen bonds defined for protein. 987 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: 2.12 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1890 1.32 - 1.45: 2270 1.45 - 1.57: 5470 1.57 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 9719 Sorted by residual: bond pdb=" CA PHE A1007 " pdb=" C PHE A1007 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" C PHE A1007 " pdb=" N CYS A1008 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.26e-02 6.30e+03 5.26e+00 bond pdb=" N CYS A1008 " pdb=" CA CYS A1008 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.18e-02 7.18e+03 5.23e+00 bond pdb=" CB PHE A1007 " pdb=" CG PHE A1007 " ideal model delta sigma weight residual 1.502 1.539 -0.037 2.30e-02 1.89e+03 2.54e+00 bond pdb=" C VAL A 108 " pdb=" O VAL A 108 " ideal model delta sigma weight residual 1.236 1.218 0.019 1.19e-02 7.06e+03 2.42e+00 ... (remaining 9714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 12102 1.32 - 2.64: 870 2.64 - 3.96: 144 3.96 - 5.28: 39 5.28 - 6.60: 10 Bond angle restraints: 13165 Sorted by residual: angle pdb=" N TRP A 207 " pdb=" CA TRP A 207 " pdb=" C TRP A 207 " ideal model delta sigma weight residual 108.19 113.63 -5.44 1.29e+00 6.01e-01 1.78e+01 angle pdb=" C ASN B 351 " pdb=" CA ASN B 351 " pdb=" CB ASN B 351 " ideal model delta sigma weight residual 109.37 115.97 -6.60 1.59e+00 3.96e-01 1.72e+01 angle pdb=" C VAL A 164 " pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta sigma weight residual 122.36 117.80 4.56 1.16e+00 7.43e-01 1.55e+01 angle pdb=" N ILE A 165 " pdb=" CA ILE A 165 " pdb=" C ILE A 165 " ideal model delta sigma weight residual 113.20 116.39 -3.19 9.60e-01 1.09e+00 1.10e+01 angle pdb=" CA VAL A 259 " pdb=" C VAL A 259 " pdb=" N CYS A 260 " ideal model delta sigma weight residual 116.60 121.01 -4.41 1.45e+00 4.76e-01 9.26e+00 ... (remaining 13160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5504 17.78 - 35.56: 278 35.56 - 53.34: 53 53.34 - 71.12: 18 71.12 - 88.90: 7 Dihedral angle restraints: 5860 sinusoidal: 2353 harmonic: 3507 Sorted by residual: dihedral pdb=" CA TRP A 207 " pdb=" C TRP A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta harmonic sigma weight residual 180.00 -149.52 -30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA SER A1021 " pdb=" C SER A1021 " pdb=" N THR A1022 " pdb=" CA THR A1022 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA SER A 781 " pdb=" C SER A 781 " pdb=" N PHE A 782 " pdb=" CA PHE A 782 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 903 0.054 - 0.109: 402 0.109 - 0.163: 144 0.163 - 0.218: 32 0.218 - 0.272: 6 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CA ARG A1102 " pdb=" N ARG A1102 " pdb=" C ARG A1102 " pdb=" CB ARG A1102 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ASN A1111 " pdb=" N ASN A1111 " pdb=" C ASN A1111 " pdb=" CB ASN A1111 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL A 164 " pdb=" N VAL A 164 " pdb=" C VAL A 164 " pdb=" CB VAL A 164 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1484 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 205 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 206 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 223 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1 Y70 B 502 " -0.001 2.00e-02 2.50e+03 8.66e-03 2.44e+00 pdb=" C12 Y70 B 502 " -0.023 2.00e-02 2.50e+03 pdb=" C2 Y70 B 502 " -0.004 2.00e-02 2.50e+03 pdb=" C3 Y70 B 502 " -0.008 2.00e-02 2.50e+03 pdb=" C4 Y70 B 502 " 0.000 2.00e-02 2.50e+03 pdb=" C5 Y70 B 502 " 0.000 2.00e-02 2.50e+03 pdb=" C6 Y70 B 502 " 0.000 2.00e-02 2.50e+03 pdb=" C7 Y70 B 502 " 0.011 2.00e-02 2.50e+03 pdb=" C9 Y70 B 502 " 0.000 2.00e-02 2.50e+03 pdb=" N10 Y70 B 502 " 0.001 2.00e-02 2.50e+03 pdb=" N8 Y70 B 502 " 0.014 2.00e-02 2.50e+03 pdb=" O11 Y70 B 502 " 0.003 2.00e-02 2.50e+03 pdb=" O13 Y70 B 502 " 0.005 2.00e-02 2.50e+03 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2613 2.80 - 3.32: 8974 3.32 - 3.85: 15298 3.85 - 4.37: 18046 4.37 - 4.90: 31309 Nonbonded interactions: 76240 Sorted by model distance: nonbonded pdb=" OG SER A1046 " pdb=" OD2 ASP A1115 " model vdw 2.269 3.040 nonbonded pdb=" O CYS B 326 " pdb=" N GLU B 328 " model vdw 2.342 3.120 nonbonded pdb=" O LEU A1093 " pdb=" OG SER A1096 " model vdw 2.346 3.040 nonbonded pdb=" O ILE B 278 " pdb=" OG SER B 281 " model vdw 2.347 3.040 nonbonded pdb=" O CYS B 323 " pdb=" N GLN B 327 " model vdw 2.363 3.120 ... (remaining 76235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.212 9727 Z= 0.360 Angle : 0.834 22.617 13173 Z= 0.428 Chirality : 0.070 0.272 1487 Planarity : 0.005 0.056 1695 Dihedral : 12.075 88.900 3598 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 0.48 % Allowed : 4.30 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1199 helix: -1.56 (0.32), residues: 165 sheet: -0.60 (0.23), residues: 423 loop : -1.40 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 164 TYR 0.019 0.002 TYR A 193 PHE 0.023 0.002 PHE A1007 TRP 0.018 0.002 TRP A1073 HIS 0.011 0.002 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.35 ( 9719) covalent geometry : angle 0.78240 / 0.42 (13165) hydrogen bonds : bond 0.18423 / 12.05 ( 351) hydrogen bonds : angle 7.75625 / 5.10 ( 987) metal coordination : bond 0.10099 / 5.35 ( 8) metal coordination : angle 11.79247 / 5.92 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.9587 (mt) cc_final: 0.9351 (tp) REVERT: A 276 MET cc_start: 0.9182 (ttp) cc_final: 0.8590 (ptt) REVERT: A 282 MET cc_start: 0.9139 (tpp) cc_final: 0.8839 (tpp) REVERT: A 312 GLU cc_start: 0.8339 (tt0) cc_final: 0.7968 (mt-10) REVERT: A 361 ASP cc_start: 0.8822 (t0) cc_final: 0.8116 (t0) REVERT: A 723 LYS cc_start: 0.9590 (mmtt) cc_final: 0.9368 (mmtm) REVERT: A 812 TYR cc_start: 0.8839 (t80) cc_final: 0.8566 (t80) REVERT: A 871 TYR cc_start: 0.9323 (m-80) cc_final: 0.8851 (m-80) REVERT: A 931 LEU cc_start: 0.9590 (tp) cc_final: 0.9301 (pp) REVERT: A 986 ASP cc_start: 0.9655 (m-30) cc_final: 0.9356 (t0) REVERT: B 88 MET cc_start: 0.9081 (pmm) cc_final: 0.8655 (pmm) REVERT: B 251 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9206 (tm-30) REVERT: B 254 MET cc_start: 0.9467 (mtm) cc_final: 0.9196 (mtt) REVERT: B 255 ASP cc_start: 0.9328 (t70) cc_final: 0.9120 (t0) REVERT: B 308 LEU cc_start: 0.9757 (mt) cc_final: 0.9486 (mt) REVERT: B 311 GLU cc_start: 0.9532 (mt-10) cc_final: 0.9084 (mt-10) REVERT: B 400 TRP cc_start: 0.8660 (m-90) cc_final: 0.8167 (m-90) outliers start: 5 outliers final: 1 residues processed: 200 average time/residue: 0.1092 time to fit residues: 30.1229 Evaluate side-chains 111 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN A1111 ASN B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS B 228 GLN B 297 GLN B 316 ASN B 390 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045960 restraints weight = 44960.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047553 restraints weight = 24866.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048573 restraints weight = 17282.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049266 restraints weight = 13798.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049660 restraints weight = 11899.366| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9727 Z= 0.146 Angle : 0.670 10.820 13173 Z= 0.342 Chirality : 0.046 0.179 1487 Planarity : 0.004 0.049 1695 Dihedral : 5.490 49.557 1316 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.91 % Allowed : 9.84 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.78 (0.23), residues: 1199 helix: 0.39 (0.39), residues: 172 sheet: -0.20 (0.24), residues: 448 loop : -1.00 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 198 TYR 0.015 0.002 TYR A 42 PHE 0.014 0.002 PHE A 949 TRP 0.023 0.002 TRP B 415 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9719) covalent geometry : angle 0.65388 / 0.34 (13165) hydrogen bonds : bond 0.04228 / 2.68 ( 351) hydrogen bonds : angle 5.58502 / 3.69 ( 987) metal coordination : bond 0.01429 / 0.75 ( 8) metal coordination : angle 5.89963 / 3.37 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.8947 (tpp) cc_final: 0.8526 (tpp) REVERT: A 361 ASP cc_start: 0.8853 (t0) cc_final: 0.8327 (t0) REVERT: A 812 TYR cc_start: 0.8811 (t80) cc_final: 0.8529 (t80) REVERT: A 871 TYR cc_start: 0.9162 (m-80) cc_final: 0.8843 (m-80) REVERT: A 910 MET cc_start: 0.8810 (mtp) cc_final: 0.8521 (mmm) REVERT: A 912 LEU cc_start: 0.9423 (mt) cc_final: 0.9148 (mp) REVERT: A 927 MET cc_start: 0.9386 (mmm) cc_final: 0.9164 (mmm) REVERT: A 986 ASP cc_start: 0.9621 (m-30) cc_final: 0.9263 (t0) REVERT: A 997 LEU cc_start: 0.9314 (mp) cc_final: 0.9070 (mp) REVERT: A 1105 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9088 (mpp) REVERT: B 64 MET cc_start: 0.8595 (pmm) cc_final: 0.7913 (mpp) REVERT: B 88 MET cc_start: 0.8919 (pmm) cc_final: 0.8620 (pmm) REVERT: B 127 ASN cc_start: 0.9352 (t0) cc_final: 0.9095 (t0) REVERT: B 137 THR cc_start: 0.9318 (m) cc_final: 0.9091 (t) REVERT: B 242 ARG cc_start: 0.9205 (mtt90) cc_final: 0.8532 (mtm180) REVERT: B 251 GLU cc_start: 0.9464 (mm-30) cc_final: 0.8800 (tm-30) REVERT: B 255 ASP cc_start: 0.9300 (t70) cc_final: 0.9034 (m-30) REVERT: B 315 MET cc_start: 0.9178 (tpp) cc_final: 0.8813 (tmm) REVERT: B 349 TYR cc_start: 0.9071 (m-80) cc_final: 0.8326 (m-10) REVERT: B 400 TRP cc_start: 0.8449 (m-90) cc_final: 0.7910 (m-90) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.1013 time to fit residues: 19.5941 Evaluate side-chains 108 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 89 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044893 restraints weight = 47207.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046421 restraints weight = 26919.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047444 restraints weight = 18660.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048066 restraints weight = 14820.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048544 restraints weight = 12831.001| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9727 Z= 0.189 Angle : 0.646 7.814 13173 Z= 0.327 Chirality : 0.045 0.233 1487 Planarity : 0.004 0.044 1695 Dihedral : 5.192 48.828 1316 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.01 % Allowed : 12.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.50 (0.24), residues: 1199 helix: 0.49 (0.40), residues: 172 sheet: 0.02 (0.24), residues: 454 loop : -0.80 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 111 TYR 0.013 0.001 TYR A 42 PHE 0.011 0.001 PHE A 972 TRP 0.021 0.002 TRP B 264 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 9719) covalent geometry : angle 0.63577 / 0.33 (13165) hydrogen bonds : bond 0.03870 / 2.45 ( 351) hydrogen bonds : angle 5.21185 / 3.45 ( 987) metal coordination : bond 0.01285 / 0.78 ( 8) metal coordination : angle 4.75320 / 2.69 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.9117 (ttp) cc_final: 0.8587 (ptt) REVERT: A 282 MET cc_start: 0.8933 (tpp) cc_final: 0.8515 (tpp) REVERT: A 361 ASP cc_start: 0.8843 (t0) cc_final: 0.8334 (t0) REVERT: A 812 TYR cc_start: 0.8985 (t80) cc_final: 0.8537 (t80) REVERT: A 871 TYR cc_start: 0.9299 (m-80) cc_final: 0.8891 (m-80) REVERT: A 912 LEU cc_start: 0.9465 (mt) cc_final: 0.9220 (mp) REVERT: A 927 MET cc_start: 0.9374 (mmm) cc_final: 0.9119 (mmm) REVERT: A 986 ASP cc_start: 0.9625 (m-30) cc_final: 0.9299 (t0) REVERT: A 997 LEU cc_start: 0.9335 (mp) cc_final: 0.9108 (mp) REVERT: A 1036 MET cc_start: 0.8870 (tmm) cc_final: 0.8528 (tmm) REVERT: A 1105 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9060 (mpp) REVERT: B 64 MET cc_start: 0.8657 (pmm) cc_final: 0.7949 (mpp) REVERT: B 88 MET cc_start: 0.9027 (pmm) cc_final: 0.8659 (pmm) REVERT: B 137 THR cc_start: 0.9276 (m) cc_final: 0.9046 (t) REVERT: B 242 ARG cc_start: 0.9271 (mtt90) cc_final: 0.8570 (mtm180) REVERT: B 251 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9130 (tm-30) REVERT: B 255 ASP cc_start: 0.9300 (t70) cc_final: 0.9031 (t0) REVERT: B 267 ASN cc_start: 0.8827 (t0) cc_final: 0.8473 (m-40) REVERT: B 311 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8950 (mt-10) REVERT: B 349 TYR cc_start: 0.9177 (m-80) cc_final: 0.8486 (m-10) REVERT: B 400 TRP cc_start: 0.8311 (m-90) cc_final: 0.7789 (m-90) outliers start: 21 outliers final: 12 residues processed: 117 average time/residue: 0.0893 time to fit residues: 15.5823 Evaluate side-chains 107 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 415 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045858 restraints weight = 46131.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.047450 restraints weight = 25697.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.048444 restraints weight = 17591.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049153 restraints weight = 13951.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049599 restraints weight = 11985.305| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9727 Z= 0.117 Angle : 0.595 11.692 13173 Z= 0.299 Chirality : 0.044 0.161 1487 Planarity : 0.004 0.046 1695 Dihedral : 4.884 46.018 1316 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.39 % Allowed : 12.70 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.37 (0.24), residues: 1199 helix: 0.49 (0.40), residues: 171 sheet: 0.14 (0.24), residues: 450 loop : -0.72 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.020 0.001 TYR A 871 PHE 0.011 0.001 PHE A 972 TRP 0.019 0.002 TRP B 264 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9719) covalent geometry : angle 0.58878 / 0.30 (13165) hydrogen bonds : bond 0.03352 / 2.11 ( 351) hydrogen bonds : angle 4.85800 / 3.23 ( 987) metal coordination : bond 0.00610 / 0.40 ( 8) metal coordination : angle 3.51307 / 2.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.9104 (ttp) cc_final: 0.8587 (ptt) REVERT: A 282 MET cc_start: 0.8946 (tpp) cc_final: 0.8491 (tpp) REVERT: A 361 ASP cc_start: 0.8861 (t0) cc_final: 0.8438 (t0) REVERT: A 812 TYR cc_start: 0.8990 (t80) cc_final: 0.8629 (t80) REVERT: A 871 TYR cc_start: 0.9076 (m-80) cc_final: 0.8820 (m-80) REVERT: A 910 MET cc_start: 0.9001 (mtp) cc_final: 0.8715 (mmm) REVERT: A 927 MET cc_start: 0.9266 (mmm) cc_final: 0.8952 (mmm) REVERT: A 986 ASP cc_start: 0.9617 (m-30) cc_final: 0.9299 (t70) REVERT: A 997 LEU cc_start: 0.9320 (mp) cc_final: 0.9106 (mp) REVERT: A 1036 MET cc_start: 0.8900 (tmm) cc_final: 0.8660 (tmm) REVERT: A 1105 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9040 (mpp) REVERT: B 64 MET cc_start: 0.8667 (pmm) cc_final: 0.7880 (mpp) REVERT: B 88 MET cc_start: 0.9031 (pmm) cc_final: 0.8687 (pmm) REVERT: B 137 THR cc_start: 0.9165 (m) cc_final: 0.8909 (t) REVERT: B 242 ARG cc_start: 0.9238 (mtt90) cc_final: 0.8566 (mtt180) REVERT: B 251 GLU cc_start: 0.9489 (mm-30) cc_final: 0.8803 (tm-30) REVERT: B 255 ASP cc_start: 0.9234 (t70) cc_final: 0.8988 (m-30) REVERT: B 315 MET cc_start: 0.9459 (tpp) cc_final: 0.8929 (tmm) REVERT: B 349 TYR cc_start: 0.9072 (m-80) cc_final: 0.8390 (m-10) REVERT: B 400 TRP cc_start: 0.8194 (m-90) cc_final: 0.7723 (m-90) outliers start: 25 outliers final: 10 residues processed: 117 average time/residue: 0.0839 time to fit residues: 14.3495 Evaluate side-chains 107 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 970 ASN B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044773 restraints weight = 48214.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.046371 restraints weight = 27294.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047399 restraints weight = 18871.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047868 restraints weight = 15087.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048401 restraints weight = 13429.392| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9727 Z= 0.170 Angle : 0.604 9.392 13173 Z= 0.301 Chirality : 0.043 0.153 1487 Planarity : 0.004 0.044 1695 Dihedral : 4.824 43.481 1316 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.67 % Allowed : 13.18 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.32 (0.25), residues: 1199 helix: 0.58 (0.40), residues: 172 sheet: 0.01 (0.24), residues: 475 loop : -0.55 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.015 0.001 TYR A 871 PHE 0.010 0.001 PHE A 972 TRP 0.028 0.002 TRP B 264 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 9719) covalent geometry : angle 0.59474 / 0.30 (13165) hydrogen bonds : bond 0.03311 / 2.11 ( 351) hydrogen bonds : angle 4.78867 / 3.18 ( 987) metal coordination : bond 0.01136 / 0.60 ( 8) metal coordination : angle 4.39240 / 2.49 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.375 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 276 MET cc_start: 0.9078 (ttp) cc_final: 0.8593 (ptt) REVERT: A 282 MET cc_start: 0.8976 (tpp) cc_final: 0.8550 (tpp) REVERT: A 361 ASP cc_start: 0.8893 (t0) cc_final: 0.8476 (t0) REVERT: A 812 TYR cc_start: 0.8901 (t80) cc_final: 0.8538 (t80) REVERT: A 927 MET cc_start: 0.9272 (mmm) cc_final: 0.9042 (mmm) REVERT: A 970 ASN cc_start: 0.7663 (t0) cc_final: 0.7391 (t0) REVERT: A 986 ASP cc_start: 0.9596 (m-30) cc_final: 0.9261 (t0) REVERT: A 997 LEU cc_start: 0.9339 (mp) cc_final: 0.9128 (mp) REVERT: A 1036 MET cc_start: 0.8963 (tmm) cc_final: 0.8699 (tmm) REVERT: A 1105 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9035 (mpp) REVERT: B 73 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (t-170) REVERT: B 88 MET cc_start: 0.9034 (pmm) cc_final: 0.8656 (pmm) REVERT: B 129 GLN cc_start: 0.8507 (mp10) cc_final: 0.8290 (pm20) REVERT: B 137 THR cc_start: 0.9200 (m) cc_final: 0.8997 (t) REVERT: B 242 ARG cc_start: 0.9211 (mtt90) cc_final: 0.8590 (mtt180) REVERT: B 251 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9169 (tm-30) REVERT: B 255 ASP cc_start: 0.9200 (t70) cc_final: 0.8919 (t0) REVERT: B 261 LEU cc_start: 0.9614 (mm) cc_final: 0.9296 (mm) REVERT: B 306 GLN cc_start: 0.9160 (mt0) cc_final: 0.8841 (pt0) REVERT: B 346 MET cc_start: 0.9542 (tpp) cc_final: 0.9259 (tpp) REVERT: B 349 TYR cc_start: 0.9116 (m-80) cc_final: 0.8419 (m-10) REVERT: B 400 TRP cc_start: 0.8235 (m-90) cc_final: 0.7747 (m-90) REVERT: B 409 MET cc_start: 0.3440 (ptt) cc_final: 0.2264 (ptt) outliers start: 28 outliers final: 18 residues processed: 114 average time/residue: 0.0838 time to fit residues: 14.1427 Evaluate side-chains 112 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 110 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** 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 = 0.3521 r_free = 0.3521 target = 0.064546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045105 restraints weight = 45895.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046643 restraints weight = 26128.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047492 restraints weight = 18030.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048257 restraints weight = 14686.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048789 restraints weight = 12469.997| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9727 Z= 0.123 Angle : 0.580 9.135 13173 Z= 0.287 Chirality : 0.043 0.166 1487 Planarity : 0.003 0.048 1695 Dihedral : 4.678 40.612 1316 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.10 % Allowed : 14.90 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.30 (0.25), residues: 1199 helix: 0.59 (0.40), residues: 174 sheet: -0.08 (0.24), residues: 489 loop : -0.44 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.020 0.001 TYR A 871 PHE 0.008 0.001 PHE A 972 TRP 0.032 0.002 TRP B 264 HIS 0.014 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9719) covalent geometry : angle 0.57387 / 0.29 (13165) hydrogen bonds : bond 0.03110 / 1.98 ( 351) hydrogen bonds : angle 4.65125 / 3.09 ( 987) metal coordination : bond 0.00556 / 0.33 ( 8) metal coordination : angle 3.48840 / 2.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.302 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 276 MET cc_start: 0.9093 (ttp) cc_final: 0.8605 (ptt) REVERT: A 282 MET cc_start: 0.8973 (tpp) cc_final: 0.8507 (tpp) REVERT: A 361 ASP cc_start: 0.8927 (t0) cc_final: 0.8520 (t0) REVERT: A 812 TYR cc_start: 0.8949 (t80) cc_final: 0.8577 (t80) REVERT: A 910 MET cc_start: 0.9165 (mmm) cc_final: 0.8917 (mmm) REVERT: A 970 ASN cc_start: 0.7704 (t0) cc_final: 0.7372 (t0) REVERT: A 986 ASP cc_start: 0.9599 (m-30) cc_final: 0.9257 (t0) REVERT: A 1036 MET cc_start: 0.8949 (tmm) cc_final: 0.8688 (tmm) REVERT: A 1105 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9036 (mpp) REVERT: B 88 MET cc_start: 0.9028 (pmm) cc_final: 0.8640 (pmm) REVERT: B 129 GLN cc_start: 0.8512 (mp10) cc_final: 0.8297 (pm20) REVERT: B 137 THR cc_start: 0.9188 (m) cc_final: 0.8959 (t) REVERT: B 242 ARG cc_start: 0.9211 (mtt90) cc_final: 0.8553 (mtt180) REVERT: B 251 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9116 (tm-30) REVERT: B 254 MET cc_start: 0.9722 (mmt) cc_final: 0.9461 (mmt) REVERT: B 255 ASP cc_start: 0.9134 (t70) cc_final: 0.8841 (t0) REVERT: B 308 LEU cc_start: 0.9821 (mt) cc_final: 0.9606 (mt) REVERT: B 346 MET cc_start: 0.9542 (tpp) cc_final: 0.9270 (tpp) REVERT: B 349 TYR cc_start: 0.9042 (m-80) cc_final: 0.8323 (m-10) REVERT: B 400 TRP cc_start: 0.8173 (m-90) cc_final: 0.7717 (m-90) REVERT: B 409 MET cc_start: 0.3317 (ptt) cc_final: 0.2363 (ptt) REVERT: B 422 LEU cc_start: 0.8533 (mm) cc_final: 0.8115 (mm) outliers start: 22 outliers final: 15 residues processed: 113 average time/residue: 0.0911 time to fit residues: 15.2168 Evaluate side-chains 104 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 0.0370 chunk 94 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.065726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046474 restraints weight = 45351.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048037 restraints weight = 25532.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049113 restraints weight = 17525.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049807 restraints weight = 13679.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050258 restraints weight = 11658.174| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9727 Z= 0.102 Angle : 0.590 12.584 13173 Z= 0.287 Chirality : 0.044 0.357 1487 Planarity : 0.003 0.046 1695 Dihedral : 4.415 28.304 1313 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.20 % Allowed : 15.28 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.28 (0.25), residues: 1199 helix: 0.49 (0.40), residues: 174 sheet: 0.08 (0.24), residues: 469 loop : -0.53 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.013 0.001 TYR A 871 PHE 0.010 0.001 PHE A1030 TRP 0.022 0.002 TRP B 264 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9719) covalent geometry : angle 0.58559 / 0.29 (13165) hydrogen bonds : bond 0.03063 / 1.95 ( 351) hydrogen bonds : angle 4.51279 / 3.00 ( 987) metal coordination : bond 0.00424 / 0.24 ( 8) metal coordination : angle 2.91580 / 1.72 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.402 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 276 MET cc_start: 0.9111 (ttp) cc_final: 0.8583 (ptt) REVERT: A 282 MET cc_start: 0.8983 (tpp) cc_final: 0.8490 (tpp) REVERT: A 361 ASP cc_start: 0.8972 (t0) cc_final: 0.8561 (t0) REVERT: A 812 TYR cc_start: 0.8984 (t80) cc_final: 0.8631 (t80) REVERT: A 970 ASN cc_start: 0.7628 (t0) cc_final: 0.7294 (t0) REVERT: A 986 ASP cc_start: 0.9624 (m-30) cc_final: 0.9281 (t0) REVERT: A 1036 MET cc_start: 0.8930 (tmm) cc_final: 0.8682 (tmm) REVERT: A 1105 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.9047 (mpp) REVERT: B 64 MET cc_start: 0.8619 (pmm) cc_final: 0.7912 (mpp) REVERT: B 88 MET cc_start: 0.8995 (pmm) cc_final: 0.8579 (pmm) REVERT: B 137 THR cc_start: 0.9136 (m) cc_final: 0.8907 (t) REVERT: B 185 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8846 (mt) REVERT: B 242 ARG cc_start: 0.9240 (mtt90) cc_final: 0.8440 (mtm180) REVERT: B 251 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9083 (tm-30) REVERT: B 254 MET cc_start: 0.9738 (mmt) cc_final: 0.9528 (mmt) REVERT: B 255 ASP cc_start: 0.9102 (t70) cc_final: 0.8871 (t0) REVERT: B 308 LEU cc_start: 0.9816 (mt) cc_final: 0.9614 (mt) REVERT: B 315 MET cc_start: 0.9176 (tmm) cc_final: 0.8877 (tmm) REVERT: B 346 MET cc_start: 0.9550 (tpp) cc_final: 0.9315 (tpp) REVERT: B 349 TYR cc_start: 0.8999 (m-80) cc_final: 0.8236 (m-10) REVERT: B 400 TRP cc_start: 0.8153 (m-90) cc_final: 0.7706 (m-90) REVERT: B 409 MET cc_start: 0.3237 (ptt) cc_final: 0.2376 (ptt) REVERT: B 422 LEU cc_start: 0.8539 (mm) cc_final: 0.8086 (mm) outliers start: 23 outliers final: 15 residues processed: 115 average time/residue: 0.0917 time to fit residues: 15.6365 Evaluate side-chains 108 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046263 restraints weight = 45893.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047870 restraints weight = 25588.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048927 restraints weight = 17680.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049605 restraints weight = 13980.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.049916 restraints weight = 12013.711| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9727 Z= 0.137 Angle : 0.626 16.024 13173 Z= 0.302 Chirality : 0.044 0.414 1487 Planarity : 0.003 0.045 1695 Dihedral : 4.408 28.439 1313 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 16.05 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.25), residues: 1199 helix: 0.61 (0.40), residues: 174 sheet: -0.01 (0.24), residues: 478 loop : -0.42 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 70 TYR 0.016 0.001 TYR A 871 PHE 0.012 0.001 PHE A1076 TRP 0.017 0.002 TRP B 264 HIS 0.011 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9719) covalent geometry : angle 0.62295 / 0.30 (13165) hydrogen bonds : bond 0.03094 / 2.00 ( 351) hydrogen bonds : angle 4.54249 / 3.02 ( 987) metal coordination : bond 0.00399 / 0.24 ( 8) metal coordination : angle 2.72746 / 1.60 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.478 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 276 MET cc_start: 0.9120 (ttp) cc_final: 0.8581 (ptt) REVERT: A 282 MET cc_start: 0.8991 (tpp) cc_final: 0.8514 (tpp) REVERT: A 361 ASP cc_start: 0.9027 (t0) cc_final: 0.8568 (t0) REVERT: A 812 TYR cc_start: 0.8996 (t80) cc_final: 0.8622 (t80) REVERT: A 970 ASN cc_start: 0.7708 (t0) cc_final: 0.7378 (t0) REVERT: A 986 ASP cc_start: 0.9634 (m-30) cc_final: 0.9291 (t0) REVERT: A 1036 MET cc_start: 0.8959 (tmm) cc_final: 0.8685 (tmm) REVERT: A 1105 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9028 (mpp) REVERT: B 88 MET cc_start: 0.9002 (pmm) cc_final: 0.8588 (pmm) REVERT: B 137 THR cc_start: 0.9207 (m) cc_final: 0.8982 (t) REVERT: B 185 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8802 (mt) REVERT: B 242 ARG cc_start: 0.9240 (mtt90) cc_final: 0.8448 (mtm180) REVERT: B 251 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9056 (tm-30) REVERT: B 255 ASP cc_start: 0.9134 (t70) cc_final: 0.8867 (t0) REVERT: B 315 MET cc_start: 0.9206 (tmm) cc_final: 0.8907 (tmm) REVERT: B 349 TYR cc_start: 0.9038 (m-80) cc_final: 0.8247 (m-10) REVERT: B 400 TRP cc_start: 0.8257 (m-90) cc_final: 0.7724 (m-90) REVERT: B 422 LEU cc_start: 0.8469 (mm) cc_final: 0.8033 (mm) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 0.0879 time to fit residues: 14.1790 Evaluate side-chains 111 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 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 = 0.3551 r_free = 0.3551 target = 0.065846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045863 restraints weight = 46149.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047502 restraints weight = 26054.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048567 restraints weight = 17809.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049269 restraints weight = 14003.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.049668 restraints weight = 12034.537| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9727 Z= 0.113 Angle : 0.651 15.758 13173 Z= 0.310 Chirality : 0.045 0.374 1487 Planarity : 0.003 0.045 1695 Dihedral : 4.363 27.798 1313 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.91 % Allowed : 15.95 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.23 (0.25), residues: 1199 helix: 0.50 (0.39), residues: 175 sheet: 0.02 (0.24), residues: 477 loop : -0.39 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 70 TYR 0.014 0.001 TYR A 871 PHE 0.012 0.001 PHE A1076 TRP 0.015 0.002 TRP B 264 HIS 0.004 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9719) covalent geometry : angle 0.64834 / 0.31 (13165) hydrogen bonds : bond 0.03060 / 1.98 ( 351) hydrogen bonds : angle 4.52731 / 3.03 ( 987) metal coordination : bond 0.00348 / 0.20 ( 8) metal coordination : angle 2.45162 / 1.45 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.452 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 276 MET cc_start: 0.9176 (ttp) cc_final: 0.8564 (ptt) REVERT: A 282 MET cc_start: 0.9012 (tpp) cc_final: 0.8530 (tpp) REVERT: A 361 ASP cc_start: 0.9039 (t0) cc_final: 0.8595 (t0) REVERT: A 812 TYR cc_start: 0.8996 (t80) cc_final: 0.8638 (t80) REVERT: A 871 TYR cc_start: 0.9220 (m-80) cc_final: 0.8958 (m-80) REVERT: A 908 ASN cc_start: 0.9134 (p0) cc_final: 0.8889 (p0) REVERT: A 970 ASN cc_start: 0.7674 (t0) cc_final: 0.7346 (t0) REVERT: A 986 ASP cc_start: 0.9639 (m-30) cc_final: 0.9293 (t0) REVERT: A 1036 MET cc_start: 0.8939 (tmm) cc_final: 0.8666 (tmm) REVERT: A 1105 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9036 (mpp) REVERT: B 64 MET cc_start: 0.8693 (pmm) cc_final: 0.8168 (mpp) REVERT: B 88 MET cc_start: 0.9026 (pmm) cc_final: 0.8783 (pmm) REVERT: B 137 THR cc_start: 0.9209 (m) cc_final: 0.8985 (t) REVERT: B 185 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8799 (mt) REVERT: B 242 ARG cc_start: 0.9243 (mtt90) cc_final: 0.8459 (mtm180) REVERT: B 251 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9054 (tm-30) REVERT: B 255 ASP cc_start: 0.9093 (t70) cc_final: 0.8830 (t0) REVERT: B 315 MET cc_start: 0.9223 (tmm) cc_final: 0.8915 (tmm) REVERT: B 349 TYR cc_start: 0.9016 (m-80) cc_final: 0.8148 (m-10) REVERT: B 400 TRP cc_start: 0.8261 (m-90) cc_final: 0.7727 (m-90) REVERT: B 422 LEU cc_start: 0.8477 (mm) cc_final: 0.8040 (mm) outliers start: 20 outliers final: 18 residues processed: 108 average time/residue: 0.0788 time to fit residues: 13.0120 Evaluate side-chains 110 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 90 optimal weight: 0.0030 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045669 restraints weight = 45838.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047262 restraints weight = 26249.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048351 restraints weight = 18160.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048987 restraints weight = 14252.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049481 restraints weight = 12344.303| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9727 Z= 0.122 Angle : 0.662 14.212 13173 Z= 0.314 Chirality : 0.045 0.344 1487 Planarity : 0.003 0.047 1695 Dihedral : 4.324 27.558 1313 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.10 % Allowed : 16.14 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.27 (0.25), residues: 1199 helix: 0.46 (0.40), residues: 174 sheet: 0.00 (0.24), residues: 475 loop : -0.42 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 309 TYR 0.014 0.001 TYR A 871 PHE 0.011 0.001 PHE A1076 TRP 0.013 0.001 TRP B 415 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9719) covalent geometry : angle 0.66016 / 0.31 (13165) hydrogen bonds : bond 0.03058 / 2.00 ( 351) hydrogen bonds : angle 4.59401 / 3.06 ( 987) metal coordination : bond 0.00327 / 0.19 ( 8) metal coordination : angle 2.28238 / 1.35 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.400 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 276 MET cc_start: 0.9122 (ttp) cc_final: 0.8529 (ptm) REVERT: A 282 MET cc_start: 0.9029 (tpp) cc_final: 0.8556 (tpp) REVERT: A 361 ASP cc_start: 0.9046 (t0) cc_final: 0.8616 (t0) REVERT: A 812 TYR cc_start: 0.8971 (t80) cc_final: 0.8624 (t80) REVERT: A 871 TYR cc_start: 0.9190 (m-80) cc_final: 0.8926 (m-80) REVERT: A 970 ASN cc_start: 0.7633 (t0) cc_final: 0.7323 (t0) REVERT: A 986 ASP cc_start: 0.9613 (m-30) cc_final: 0.9277 (t0) REVERT: A 1036 MET cc_start: 0.8950 (tmm) cc_final: 0.8680 (tmm) REVERT: A 1105 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8982 (mpp) REVERT: B 88 MET cc_start: 0.9060 (pmm) cc_final: 0.8635 (pmm) REVERT: B 137 THR cc_start: 0.9214 (m) cc_final: 0.8997 (t) REVERT: B 185 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 251 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9026 (tm-30) REVERT: B 255 ASP cc_start: 0.9076 (t70) cc_final: 0.8854 (t0) REVERT: B 315 MET cc_start: 0.9241 (tmm) cc_final: 0.8914 (tmm) REVERT: B 349 TYR cc_start: 0.8967 (m-80) cc_final: 0.8071 (m-10) REVERT: B 400 TRP cc_start: 0.8261 (m-90) cc_final: 0.7745 (m-90) REVERT: B 422 LEU cc_start: 0.8480 (mm) cc_final: 0.8044 (mm) outliers start: 22 outliers final: 16 residues processed: 104 average time/residue: 0.0886 time to fit residues: 13.8906 Evaluate side-chains 104 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 58 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 24 optimal weight: 0.0050 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045785 restraints weight = 44743.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.047350 restraints weight = 25370.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048244 restraints weight = 17459.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049027 restraints weight = 14069.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049461 restraints weight = 11872.274| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 9727 Z= 0.211 Angle : 0.970 59.199 13173 Z= 0.529 Chirality : 0.048 0.691 1487 Planarity : 0.003 0.048 1695 Dihedral : 4.318 27.556 1313 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.91 % Allowed : 16.62 % Favored : 81.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.17 % 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: -0.28 (0.25), residues: 1199 helix: 0.43 (0.40), residues: 174 sheet: -0.00 (0.24), residues: 475 loop : -0.42 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 158 TYR 0.012 0.001 TYR A 871 PHE 0.010 0.001 PHE A1076 TRP 0.013 0.001 TRP B 415 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 ( 9719) covalent geometry : angle 0.96912 / 0.53 (13165) hydrogen bonds : bond 0.03151 / 2.04 ( 351) hydrogen bonds : angle 4.59770 / 3.07 ( 987) metal coordination : bond 0.00320 / 0.19 ( 8) metal coordination : angle 2.27973 / 1.35 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.13 seconds wall clock time: 29 minutes 52.54 seconds (1792.54 seconds total)