Starting phenix.real_space_refine on Thu Aug 6 13:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukj_64241/08_2026/9ukj_64241.cif" } resolution = 3.08 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 9484 2.51 5 N 2628 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 15003 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2413 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2357 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2354 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2458 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "G" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 297 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.66, per 1000 atoms: 0.24 Number of scatterers: 15003 At special positions: 0 Unit cell: (95.626, 129.828, 131.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 2819 8.00 N 2628 7.00 C 9484 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: 1.12 Conformation dependent library (CDL) restraints added in 681.9 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 24 sheets defined 48.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.634A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.665A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.558A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.711A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 4.354A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.517A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.633A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 4.332A pdb=" N ILE A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.626A pdb=" N ILE B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.519A pdb=" N TRP B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.669A pdb=" N ILE B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.732A pdb=" N VAL B 226 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 262 removed outlier: 4.516A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.710A pdb=" N ALA B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.142A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 55 through 64 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.743A pdb=" N GLN C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.630A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.601A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 238 through 261 removed outlier: 3.821A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 299 through 314 removed outlier: 4.003A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.512A pdb=" N GLY D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.654A pdb=" N HIS D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.857A pdb=" N PHE D 152 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.657A pdb=" N GLU D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.909A pdb=" N GLN D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 238 through 261 removed outlier: 3.564A pdb=" N ARG D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 299 through 315 removed outlier: 4.297A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.626A pdb=" N ILE E 154 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 234 through 237 removed outlier: 3.746A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 238 through 262 removed outlier: 3.697A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 302 through 315 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 76 through 88 Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.505A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.680A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 160 removed outlier: 3.790A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.535A pdb=" N VAL F 226 " --> pdb=" O HIS F 222 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN F 227 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 261 removed outlier: 3.679A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.679A pdb=" N ALA F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 302 through 315 removed outlier: 3.533A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 391 through 397 removed outlier: 4.031A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.625A pdb=" N VAL A 93 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 136 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE A 182 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 67 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 185 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 69 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.089A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 67 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA B 185 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 69 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 114 Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.015A pdb=" N LEU C 138 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR C 184 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE C 140 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 165 Processing sheet with id=AB3, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 96 removed outlier: 3.640A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 108 through 113 Processing sheet with id=AC1, first strand: chain 'E' and resid 164 through 166 Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.499A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 115 Processing sheet with id=AC5, first strand: chain 'F' and resid 164 through 165 Processing sheet with id=AC6, first strand: chain 'G' and resid 377 through 381 removed outlier: 6.026A pdb=" N TYR G 404 " --> pdb=" O ASP G 380 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1824 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: 2.47 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5047 1.34 - 1.46: 2903 1.46 - 1.58: 7252 1.58 - 1.70: 10 1.70 - 1.81: 108 Bond restraints: 15320 Sorted by residual: bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.685 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 15315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 20772 3.61 - 7.22: 79 7.22 - 10.83: 14 10.83 - 14.44: 1 14.44 - 18.05: 3 Bond angle restraints: 20869 Sorted by residual: angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 108.90 18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 108.99 17.96 3.00e+00 1.11e-01 3.58e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.18 17.77 3.00e+00 1.11e-01 3.51e+01 angle pdb=" CB MET A 29 " pdb=" CG MET A 29 " pdb=" SD MET A 29 " ideal model delta sigma weight residual 112.70 123.96 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA VAL E 95 " pdb=" CB VAL E 95 " pdb=" CG1 VAL E 95 " ideal model delta sigma weight residual 110.40 116.35 -5.95 1.70e+00 3.46e-01 1.23e+01 ... (remaining 20864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7558 17.54 - 35.09: 1083 35.09 - 52.63: 362 52.63 - 70.18: 98 70.18 - 87.72: 49 Dihedral angle restraints: 9150 sinusoidal: 3654 harmonic: 5496 Sorted by residual: dihedral pdb=" CG ARG A 66 " pdb=" CD ARG A 66 " pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sinusoidal sigma weight residual -90.00 -37.57 -52.43 2 1.50e+01 4.44e-03 1.34e+01 dihedral pdb=" CA TYR A 63 " pdb=" C TYR A 63 " pdb=" N ASN A 64 " pdb=" CA ASN A 64 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 168 " pdb=" C ASP E 168 " pdb=" N GLN E 169 " pdb=" CA GLN E 169 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1921 0.054 - 0.108: 408 0.108 - 0.163: 38 0.163 - 0.217: 0 0.217 - 0.271: 3 Chirality restraints: 2370 Sorted by residual: chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2367 not shown) Planarity restraints: 2708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 55 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LEU C 55 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU C 55 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA C 56 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 40 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO B 41 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 176 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO F 177 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 177 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 177 " -0.030 5.00e-02 4.00e+02 ... (remaining 2705 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 87 2.47 - 3.08: 9956 3.08 - 3.68: 22223 3.68 - 4.29: 32762 4.29 - 4.90: 55444 Nonbonded interactions: 120472 Sorted by model distance: nonbonded pdb=" O2G ANP F 401 " pdb="MG MG F 402 " model vdw 1.862 2.170 nonbonded pdb=" O2G ANP E 401 " pdb="MG MG E 402 " model vdw 1.886 2.170 nonbonded pdb=" O2G ANP D 401 " pdb="MG MG D 402 " model vdw 1.890 2.170 nonbonded pdb=" OG SER D 78 " pdb="MG MG D 402 " model vdw 1.912 2.170 nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 2.007 2.170 ... (remaining 120467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 318) selection = (chain 'B' and resid 9 through 318) selection = (chain 'C' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'D' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'E' and (resid 9 through 188 or resid 203 through 318)) selection = (chain 'F' and (resid 9 through 188 or resid 203 through 318)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.270 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.005 0.150 15320 Z= 0.238 Angle : 0.652 18.052 20869 Z= 0.309 Chirality : 0.043 0.271 2370 Planarity : 0.004 0.063 2708 Dihedral : 19.845 87.722 5592 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.50 % Allowed : 34.41 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1863 helix: 0.19 (0.19), residues: 765 sheet: -0.42 (0.32), residues: 269 loop : -0.77 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 66 TYR 0.018 0.001 TYR F 132 PHE 0.010 0.001 PHE A 182 TRP 0.009 0.001 TRP C 90 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (15320) covalent geometry : angle 0.65186 / 0.31 (20869) hydrogen bonds : bond 0.19039 / 12.41 ( 649) hydrogen bonds : angle 7.12253 / 5.02 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 542 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 ASP cc_start: 0.7605 (p0) cc_final: 0.7349 (p0) outliers start: 8 outliers final: 5 residues processed: 544 average time/residue: 0.1502 time to fit residues: 114.8322 Evaluate side-chains 540 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 535 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain F residue 125 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 218 ASN A 227 ASN A 279 ASN B 186 ASN C 227 ASN C 246 ASN F 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107188 restraints weight = 22291.768| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.39 r_work: 0.3218 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15320 Z= 0.118 Angle : 0.510 7.181 20869 Z= 0.266 Chirality : 0.041 0.134 2370 Planarity : 0.004 0.054 2708 Dihedral : 8.216 66.728 2173 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.80 % Allowed : 30.61 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 1863 helix: 0.74 (0.19), residues: 769 sheet: -0.30 (0.32), residues: 277 loop : -0.65 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.017 0.001 TYR F 132 PHE 0.017 0.001 PHE A 259 TRP 0.008 0.001 TRP C 211 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15320) covalent geometry : angle 0.50999 / 0.27 (20869) hydrogen bonds : bond 0.04092 / 2.72 ( 649) hydrogen bonds : angle 5.46195 / 3.81 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 541 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8181 (p0) REVERT: A 250 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.8059 (mmt-90) REVERT: B 63 TYR cc_start: 0.8727 (m-80) cc_final: 0.8454 (m-80) REVERT: B 254 MET cc_start: 0.8423 (mpp) cc_final: 0.7892 (mpp) REVERT: B 296 ASN cc_start: 0.8638 (m-40) cc_final: 0.8234 (m110) REVERT: B 308 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 19 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7852 (mtm-85) REVERT: C 80 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.7710 (m90) REVERT: C 283 PHE cc_start: 0.8286 (m-80) cc_final: 0.8061 (m-80) REVERT: C 302 GLU cc_start: 0.7767 (mp0) cc_final: 0.7523 (mp0) REVERT: C 312 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7830 (ttm110) REVERT: D 25 ASP cc_start: 0.8573 (t0) cc_final: 0.8296 (t0) REVERT: D 44 ASP cc_start: 0.7457 (t0) cc_final: 0.7159 (t0) REVERT: D 133 GLN cc_start: 0.8293 (mt0) cc_final: 0.8084 (mt0) REVERT: D 230 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 237 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: D 243 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7025 (tm-30) REVERT: E 25 ASP cc_start: 0.7743 (t0) cc_final: 0.7452 (t0) REVERT: E 285 ASP cc_start: 0.7690 (t70) cc_final: 0.7401 (t0) REVERT: F 51 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7080 (ttp-110) REVERT: F 125 ASP cc_start: 0.8270 (m-30) cc_final: 0.8020 (m-30) REVERT: F 210 ARG cc_start: 0.8477 (mmp-170) cc_final: 0.8263 (mmp-170) outliers start: 61 outliers final: 28 residues processed: 576 average time/residue: 0.1445 time to fit residues: 117.3364 Evaluate side-chains 565 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 532 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 186 ASN B 227 ASN C 227 ASN C 284 ASN D 80 HIS D 201 GLN F 80 HIS F 89 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104081 restraints weight = 22580.811| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.39 r_work: 0.3166 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 15320 Z= 0.288 Angle : 0.573 7.030 20869 Z= 0.299 Chirality : 0.045 0.158 2370 Planarity : 0.005 0.055 2708 Dihedral : 7.348 68.384 2164 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.30 % Allowed : 29.30 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1863 helix: 0.56 (0.19), residues: 767 sheet: -0.16 (0.33), residues: 253 loop : -0.81 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.014 0.001 TYR F 132 PHE 0.012 0.002 PHE A 182 TRP 0.013 0.002 TRP C 90 HIS 0.011 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (15320) covalent geometry : angle 0.57259 / 0.30 (20869) hydrogen bonds : bond 0.04904 / 3.29 ( 649) hydrogen bonds : angle 5.50368 / 3.85 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 552 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8521 (mtm-85) REVERT: A 135 ASN cc_start: 0.8535 (p0) cc_final: 0.8308 (p0) REVERT: A 250 ARG cc_start: 0.8293 (mmt-90) cc_final: 0.8033 (mmt-90) REVERT: A 271 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7424 (ttm-80) REVERT: B 50 ASP cc_start: 0.8059 (t0) cc_final: 0.7832 (t0) REVERT: B 63 TYR cc_start: 0.8835 (m-80) cc_final: 0.8480 (m-80) REVERT: B 163 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7640 (mtt-85) REVERT: B 254 MET cc_start: 0.8499 (mpp) cc_final: 0.8045 (mpp) REVERT: B 308 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7663 (mm-30) REVERT: C 20 GLU cc_start: 0.8107 (mp0) cc_final: 0.7731 (mp0) REVERT: C 66 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8232 (mtt-85) REVERT: C 80 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8112 (m90) REVERT: C 100 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7513 (m90) REVERT: C 302 GLU cc_start: 0.7764 (mp0) cc_final: 0.7533 (mp0) REVERT: D 25 ASP cc_start: 0.8600 (t0) cc_final: 0.8377 (t0) REVERT: D 44 ASP cc_start: 0.7657 (t0) cc_final: 0.7235 (t0) REVERT: D 231 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8886 (p) REVERT: D 237 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: D 243 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7169 (tm-30) REVERT: E 25 ASP cc_start: 0.7785 (t0) cc_final: 0.7511 (t0) REVERT: E 44 ASP cc_start: 0.7777 (t0) cc_final: 0.7553 (t0) REVERT: F 51 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7133 (ttp-110) REVERT: F 125 ASP cc_start: 0.8277 (m-30) cc_final: 0.8058 (m-30) outliers start: 85 outliers final: 51 residues processed: 599 average time/residue: 0.1483 time to fit residues: 124.7422 Evaluate side-chains 604 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 546 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 296 ASN B 227 ASN C 227 ASN D 133 GLN D 201 GLN E 96 ASN E 133 GLN F 80 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107245 restraints weight = 22131.773| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.38 r_work: 0.3218 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15320 Z= 0.115 Angle : 0.491 6.414 20869 Z= 0.259 Chirality : 0.041 0.124 2370 Planarity : 0.004 0.053 2708 Dihedral : 6.104 58.754 2164 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.18 % Allowed : 31.36 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1863 helix: 0.83 (0.19), residues: 766 sheet: -0.14 (0.33), residues: 257 loop : -0.72 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.008 0.001 TYR B 310 PHE 0.007 0.001 PHE E 288 TRP 0.008 0.001 TRP C 211 HIS 0.014 0.001 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (15320) covalent geometry : angle 0.49118 / 0.26 (20869) hydrogen bonds : bond 0.03438 / 2.28 ( 649) hydrogen bonds : angle 5.18651 / 3.62 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 534 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7864 (mmt-90) REVERT: A 271 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7104 (ttm-80) REVERT: B 27 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: B 63 TYR cc_start: 0.8673 (m-80) cc_final: 0.8247 (m-80) REVERT: B 163 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7334 (mtt-85) REVERT: B 254 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: B 296 ASN cc_start: 0.8567 (m-40) cc_final: 0.8078 (m110) REVERT: B 308 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7367 (mm-30) REVERT: C 19 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: C 20 GLU cc_start: 0.7966 (mp0) cc_final: 0.7687 (mp0) REVERT: C 66 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: C 80 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7749 (m90) REVERT: C 100 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7135 (m90) REVERT: C 302 GLU cc_start: 0.7485 (mp0) cc_final: 0.7246 (mp0) REVERT: C 308 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6560 (tm-30) REVERT: D 25 ASP cc_start: 0.8497 (t0) cc_final: 0.8244 (t0) REVERT: D 44 ASP cc_start: 0.7420 (t0) cc_final: 0.6945 (t0) REVERT: D 133 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: D 231 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8757 (p) REVERT: D 237 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: D 243 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6668 (tm-30) REVERT: E 25 ASP cc_start: 0.7532 (t0) cc_final: 0.7243 (t0) REVERT: E 44 ASP cc_start: 0.7548 (t0) cc_final: 0.7340 (t0) REVERT: F 51 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7025 (ttp-110) REVERT: F 132 TYR cc_start: 0.8734 (t80) cc_final: 0.8503 (t80) REVERT: F 164 LEU cc_start: 0.7724 (tp) cc_final: 0.7395 (tt) outliers start: 67 outliers final: 40 residues processed: 565 average time/residue: 0.1508 time to fit residues: 119.2877 Evaluate side-chains 574 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 523 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 260 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 106 optimal weight: 0.0170 chunk 33 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 296 ASN B 186 ASN B 227 ASN C 227 ASN D 80 HIS D 133 GLN E 155 GLN E 186 ASN F 80 HIS F 83 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106368 restraints weight = 22442.949| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.39 r_work: 0.3203 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15320 Z= 0.159 Angle : 0.505 7.133 20869 Z= 0.265 Chirality : 0.042 0.121 2370 Planarity : 0.004 0.051 2708 Dihedral : 6.071 58.878 2164 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.36 % Allowed : 31.17 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1863 helix: 0.83 (0.19), residues: 769 sheet: -0.14 (0.33), residues: 257 loop : -0.75 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 66 TYR 0.007 0.001 TYR A 143 PHE 0.009 0.001 PHE E 288 TRP 0.009 0.001 TRP C 90 HIS 0.015 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15320) covalent geometry : angle 0.50490 / 0.26 (20869) hydrogen bonds : bond 0.03705 / 2.47 ( 649) hydrogen bonds : angle 5.16286 / 3.60 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 531 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: A 168 ASP cc_start: 0.7716 (t0) cc_final: 0.7514 (t0) REVERT: A 271 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7137 (ttm-80) REVERT: A 285 ASP cc_start: 0.7754 (t70) cc_final: 0.7455 (t0) REVERT: B 27 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: B 63 TYR cc_start: 0.8727 (m-80) cc_final: 0.8286 (m-80) REVERT: B 163 ARG cc_start: 0.7591 (mtt-85) cc_final: 0.7347 (mtt-85) REVERT: B 254 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7901 (mpp) REVERT: C 20 GLU cc_start: 0.7968 (mp0) cc_final: 0.7709 (mp0) REVERT: C 66 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8060 (mtt-85) REVERT: C 80 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7855 (m90) REVERT: C 100 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7179 (m90) REVERT: C 302 GLU cc_start: 0.7492 (mp0) cc_final: 0.7257 (mp0) REVERT: C 308 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: D 25 ASP cc_start: 0.8511 (t0) cc_final: 0.8286 (t0) REVERT: D 44 ASP cc_start: 0.7434 (t0) cc_final: 0.6925 (t0) REVERT: D 133 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: D 231 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8774 (p) REVERT: D 237 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: D 243 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6707 (tm-30) REVERT: E 25 ASP cc_start: 0.7557 (t0) cc_final: 0.7268 (t0) REVERT: E 285 ASP cc_start: 0.7419 (t0) cc_final: 0.6913 (t0) REVERT: F 51 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7035 (ttp-110) REVERT: F 132 TYR cc_start: 0.8756 (t80) cc_final: 0.8528 (t80) REVERT: F 302 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7492 (mt-10) outliers start: 70 outliers final: 42 residues processed: 566 average time/residue: 0.1465 time to fit residues: 116.4107 Evaluate side-chains 578 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 525 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 GLN Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 296 ASN B 186 ASN B 227 ASN C 227 ASN D 201 GLN E 64 ASN E 96 ASN E 186 ASN E 207 GLN F 80 HIS F 83 GLN F 238 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105284 restraints weight = 22344.135| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.37 r_work: 0.3186 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15320 Z= 0.221 Angle : 0.536 7.745 20869 Z= 0.281 Chirality : 0.043 0.138 2370 Planarity : 0.004 0.051 2708 Dihedral : 6.112 59.007 2164 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.86 % Allowed : 30.92 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1863 helix: 0.75 (0.19), residues: 763 sheet: -0.32 (0.32), residues: 277 loop : -0.79 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.009 0.001 TYR B 143 PHE 0.010 0.001 PHE E 288 TRP 0.012 0.001 TRP C 90 HIS 0.012 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (15320) covalent geometry : angle 0.53629 / 0.28 (20869) hydrogen bonds : bond 0.04145 / 2.76 ( 649) hydrogen bonds : angle 5.23720 / 3.65 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 527 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8512 (mtm-85) REVERT: A 135 ASN cc_start: 0.8559 (p0) cc_final: 0.8326 (p0) REVERT: A 168 ASP cc_start: 0.7879 (t0) cc_final: 0.7650 (t0) REVERT: A 271 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7460 (ttm-80) REVERT: B 63 TYR cc_start: 0.8864 (m-80) cc_final: 0.8413 (m-80) REVERT: B 163 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7690 (mtt-85) REVERT: B 254 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (mpp) REVERT: C 20 GLU cc_start: 0.8130 (mp0) cc_final: 0.7814 (mp0) REVERT: C 66 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (mtt-85) REVERT: C 80 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8118 (m90) REVERT: C 100 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7420 (m90) REVERT: C 302 GLU cc_start: 0.7766 (mp0) cc_final: 0.7502 (mp0) REVERT: C 308 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: D 25 ASP cc_start: 0.8613 (t0) cc_final: 0.8302 (t0) REVERT: D 44 ASP cc_start: 0.7681 (t0) cc_final: 0.7161 (t0) REVERT: D 133 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: D 231 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8849 (p) REVERT: D 237 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: D 243 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7046 (tm-30) REVERT: E 25 ASP cc_start: 0.7755 (t0) cc_final: 0.7471 (t0) REVERT: E 44 ASP cc_start: 0.7842 (t0) cc_final: 0.7531 (t0) REVERT: E 163 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7305 (mtt-85) REVERT: E 285 ASP cc_start: 0.7694 (t0) cc_final: 0.7156 (t0) REVERT: F 29 MET cc_start: 0.8389 (mmm) cc_final: 0.8115 (mpp) REVERT: F 51 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7117 (ttp-110) REVERT: F 132 TYR cc_start: 0.8826 (t80) cc_final: 0.8616 (t80) REVERT: F 302 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7776 (mt-10) outliers start: 78 outliers final: 51 residues processed: 570 average time/residue: 0.1444 time to fit residues: 115.0081 Evaluate side-chains 588 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 527 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 296 ASN B 227 ASN C 227 ASN D 133 GLN D 201 GLN E 96 ASN F 80 HIS F 83 GLN F 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106289 restraints weight = 22178.341| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.37 r_work: 0.3201 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15320 Z= 0.162 Angle : 0.521 8.607 20869 Z= 0.273 Chirality : 0.042 0.134 2370 Planarity : 0.004 0.050 2708 Dihedral : 5.865 63.664 2164 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.49 % Allowed : 31.42 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1863 helix: 0.81 (0.19), residues: 762 sheet: -0.31 (0.32), residues: 277 loop : -0.72 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.007 0.001 TYR F 143 PHE 0.010 0.001 PHE A 259 TRP 0.010 0.001 TRP C 90 HIS 0.010 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (15320) covalent geometry : angle 0.52058 / 0.27 (20869) hydrogen bonds : bond 0.03774 / 2.51 ( 649) hydrogen bonds : angle 5.16214 / 3.60 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 527 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8455 (mtm-85) REVERT: A 135 ASN cc_start: 0.8549 (p0) cc_final: 0.8321 (p0) REVERT: A 168 ASP cc_start: 0.7884 (t0) cc_final: 0.7659 (t0) REVERT: A 271 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (ttm-80) REVERT: B 27 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: B 63 TYR cc_start: 0.8850 (m-80) cc_final: 0.8347 (m-80) REVERT: B 163 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7637 (mtt-85) REVERT: B 254 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8190 (mpp) REVERT: C 19 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7768 (mtm-85) REVERT: C 20 GLU cc_start: 0.8128 (mp0) cc_final: 0.7810 (mp0) REVERT: C 66 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (mtt-85) REVERT: C 80 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8036 (m90) REVERT: C 100 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7364 (m90) REVERT: C 302 GLU cc_start: 0.7750 (mp0) cc_final: 0.7488 (mp0) REVERT: C 308 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: D 25 ASP cc_start: 0.8523 (t0) cc_final: 0.8284 (t0) REVERT: D 44 ASP cc_start: 0.7665 (t0) cc_final: 0.7135 (t0) REVERT: D 133 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: D 231 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8832 (p) REVERT: D 237 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: D 243 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7018 (tm-30) REVERT: E 25 ASP cc_start: 0.7742 (t0) cc_final: 0.7452 (t0) REVERT: E 44 ASP cc_start: 0.7841 (t0) cc_final: 0.7545 (t0) REVERT: E 285 ASP cc_start: 0.7695 (t0) cc_final: 0.7152 (t0) REVERT: F 29 MET cc_start: 0.8380 (mmm) cc_final: 0.8101 (mpp) REVERT: F 51 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7098 (ttp-110) REVERT: F 132 TYR cc_start: 0.8801 (t80) cc_final: 0.8510 (t80) REVERT: F 250 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7423 (mtm-85) REVERT: F 302 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 72 outliers final: 55 residues processed: 563 average time/residue: 0.1431 time to fit residues: 112.9847 Evaluate side-chains 591 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 525 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 129 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 296 ASN B 186 ASN C 227 ASN D 80 HIS D 133 GLN D 201 GLN E 96 ASN E 186 ASN F 80 HIS F 83 GLN F 238 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105538 restraints weight = 22393.403| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.38 r_work: 0.3187 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15320 Z= 0.212 Angle : 0.550 10.768 20869 Z= 0.287 Chirality : 0.043 0.142 2370 Planarity : 0.004 0.050 2708 Dihedral : 5.908 66.652 2164 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.86 % Allowed : 30.99 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1863 helix: 0.72 (0.19), residues: 763 sheet: -0.15 (0.34), residues: 247 loop : -0.78 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.009 0.001 TYR D 143 PHE 0.010 0.001 PHE E 288 TRP 0.011 0.001 TRP C 90 HIS 0.009 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (15320) covalent geometry : angle 0.55018 / 0.29 (20869) hydrogen bonds : bond 0.04063 / 2.72 ( 649) hydrogen bonds : angle 5.20972 / 3.63 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 527 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7874 (t0) cc_final: 0.7648 (t0) REVERT: A 271 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7492 (ttm-80) REVERT: B 27 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 163 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: B 254 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8190 (mpp) REVERT: C 19 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7944 (mtm-85) REVERT: C 20 GLU cc_start: 0.8126 (mp0) cc_final: 0.7808 (mp0) REVERT: C 66 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8251 (mtt-85) REVERT: C 80 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8107 (m90) REVERT: C 100 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7415 (m90) REVERT: C 302 GLU cc_start: 0.7760 (mp0) cc_final: 0.7520 (mp0) REVERT: C 308 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: D 25 ASP cc_start: 0.8517 (t0) cc_final: 0.8298 (t0) REVERT: D 44 ASP cc_start: 0.7713 (t0) cc_final: 0.7175 (t0) REVERT: D 133 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: D 231 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8829 (p) REVERT: D 237 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: D 243 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7028 (tm-30) REVERT: E 25 ASP cc_start: 0.7751 (t0) cc_final: 0.7461 (t0) REVERT: E 44 ASP cc_start: 0.7867 (t0) cc_final: 0.7564 (t0) REVERT: E 285 ASP cc_start: 0.7711 (t0) cc_final: 0.7169 (t70) REVERT: F 29 MET cc_start: 0.8389 (mmm) cc_final: 0.8105 (mpp) REVERT: F 51 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7104 (ttp-110) REVERT: F 132 TYR cc_start: 0.8797 (t80) cc_final: 0.8518 (t80) REVERT: F 250 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7468 (mtm-85) REVERT: F 302 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7759 (mt-10) outliers start: 78 outliers final: 60 residues processed: 569 average time/residue: 0.1455 time to fit residues: 116.3525 Evaluate side-chains 595 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 524 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 167 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 0.0370 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 261 ASN A 296 ASN B 227 ASN C 227 ASN E 186 ASN F 80 HIS F 83 GLN F 155 GLN F 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107079 restraints weight = 22396.142| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.40 r_work: 0.3214 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15320 Z= 0.124 Angle : 0.524 12.621 20869 Z= 0.274 Chirality : 0.041 0.126 2370 Planarity : 0.004 0.049 2708 Dihedral : 5.673 71.638 2164 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.87 % Allowed : 32.23 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1863 helix: 0.87 (0.19), residues: 766 sheet: -0.16 (0.33), residues: 257 loop : -0.67 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.009 0.001 TYR B 63 PHE 0.010 0.001 PHE A 259 TRP 0.008 0.001 TRP C 90 HIS 0.008 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (15320) covalent geometry : angle 0.52396 / 0.27 (20869) hydrogen bonds : bond 0.03432 / 2.28 ( 649) hydrogen bonds : angle 5.08904 / 3.54 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 526 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8534 (mtm-85) REVERT: A 135 ASN cc_start: 0.8340 (p0) cc_final: 0.8122 (p0) REVERT: A 168 ASP cc_start: 0.7729 (t0) cc_final: 0.7514 (t0) REVERT: A 271 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7185 (ttm-80) REVERT: B 27 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: B 163 ARG cc_start: 0.7588 (mtt-85) cc_final: 0.7355 (mtt-85) REVERT: B 254 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7906 (mpp) REVERT: C 19 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7722 (mtm-85) REVERT: C 20 GLU cc_start: 0.7978 (mp0) cc_final: 0.7713 (mp0) REVERT: C 66 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (mtt-85) REVERT: C 80 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7870 (m90) REVERT: C 100 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7119 (m90) REVERT: C 302 GLU cc_start: 0.7493 (mp0) cc_final: 0.7245 (mp0) REVERT: C 308 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: D 25 ASP cc_start: 0.8409 (t0) cc_final: 0.8198 (t0) REVERT: D 44 ASP cc_start: 0.7477 (t0) cc_final: 0.6954 (t0) REVERT: D 133 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: D 231 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8753 (p) REVERT: D 237 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: D 243 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6681 (tm-30) REVERT: E 25 ASP cc_start: 0.7558 (t0) cc_final: 0.7253 (t0) REVERT: E 44 ASP cc_start: 0.7677 (t0) cc_final: 0.7390 (t0) REVERT: E 285 ASP cc_start: 0.7418 (t0) cc_final: 0.6901 (t70) REVERT: F 51 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7041 (ttp-170) REVERT: F 132 TYR cc_start: 0.8686 (t80) cc_final: 0.8386 (t80) REVERT: F 250 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7216 (mtm-85) REVERT: F 302 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7495 (mt-10) outliers start: 62 outliers final: 50 residues processed: 556 average time/residue: 0.1338 time to fit residues: 104.4137 Evaluate side-chains 581 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 520 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS B 186 ASN C 227 ASN D 133 GLN E 64 ASN E 80 HIS E 96 ASN E 186 ASN F 80 HIS F 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106538 restraints weight = 22346.756| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.39 r_work: 0.3205 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15320 Z= 0.164 Angle : 0.546 12.150 20869 Z= 0.284 Chirality : 0.042 0.164 2370 Planarity : 0.004 0.049 2708 Dihedral : 5.710 72.503 2164 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.24 % Allowed : 32.04 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1863 helix: 0.82 (0.19), residues: 765 sheet: -0.30 (0.33), residues: 267 loop : -0.66 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 66 TYR 0.017 0.001 TYR B 63 PHE 0.010 0.001 PHE A 259 TRP 0.009 0.001 TRP C 90 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (15320) covalent geometry : angle 0.54554 / 0.28 (20869) hydrogen bonds : bond 0.03687 / 2.46 ( 649) hydrogen bonds : angle 5.11432 / 3.56 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 525 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8539 (mtm-85) REVERT: A 135 ASN cc_start: 0.8357 (p0) cc_final: 0.8142 (p0) REVERT: A 168 ASP cc_start: 0.7725 (t0) cc_final: 0.7497 (t0) REVERT: A 271 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6917 (ttm-80) REVERT: B 27 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: B 163 ARG cc_start: 0.7604 (mtt-85) cc_final: 0.7370 (mtt-85) REVERT: B 254 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: C 19 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: C 20 GLU cc_start: 0.7975 (mp0) cc_final: 0.7721 (mp0) REVERT: C 66 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8072 (mtt-85) REVERT: C 80 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.7805 (m90) REVERT: C 100 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.7174 (m90) REVERT: C 302 GLU cc_start: 0.7486 (mp0) cc_final: 0.7264 (mp0) REVERT: C 308 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: D 25 ASP cc_start: 0.8415 (t0) cc_final: 0.8205 (t0) REVERT: D 44 ASP cc_start: 0.7502 (t0) cc_final: 0.6973 (t0) REVERT: D 133 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: D 231 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8763 (p) REVERT: D 237 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: D 243 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6708 (tm-30) REVERT: E 25 ASP cc_start: 0.7569 (t0) cc_final: 0.7264 (t0) REVERT: E 44 ASP cc_start: 0.7683 (t0) cc_final: 0.7399 (t0) REVERT: E 285 ASP cc_start: 0.7413 (t0) cc_final: 0.6891 (t70) REVERT: F 51 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7052 (ttp-170) REVERT: F 132 TYR cc_start: 0.8699 (t80) cc_final: 0.8406 (t80) REVERT: F 210 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7461 (mmm160) REVERT: F 250 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7232 (mtm-85) REVERT: F 302 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7496 (mt-10) outliers start: 68 outliers final: 55 residues processed: 560 average time/residue: 0.1408 time to fit residues: 110.3556 Evaluate side-chains 584 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 517 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS C 227 ASN D 133 GLN E 64 ASN E 96 ASN E 186 ASN F 80 HIS F 83 GLN F 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107201 restraints weight = 22212.312| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.38 r_work: 0.3213 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15320 Z= 0.134 Angle : 0.543 12.796 20869 Z= 0.282 Chirality : 0.042 0.154 2370 Planarity : 0.004 0.049 2708 Dihedral : 5.656 73.649 2164 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.18 % Allowed : 32.42 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1863 helix: 0.85 (0.19), residues: 768 sheet: -0.36 (0.32), residues: 277 loop : -0.63 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 163 TYR 0.014 0.001 TYR B 63 PHE 0.010 0.001 PHE A 259 TRP 0.008 0.001 TRP C 90 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (15320) covalent geometry : angle 0.54343 / 0.28 (20869) hydrogen bonds : bond 0.03507 / 2.34 ( 649) hydrogen bonds : angle 5.06943 / 3.52 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.06 seconds wall clock time: 67 minutes 56.87 seconds (4076.87 seconds total)