Starting phenix.real_space_refine on Sat Aug 8 13:38:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujx_64229/08_2026/9ujx_64229.cif" } resolution = 4.02 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= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17607 2.51 5 N 4882 2.21 5 O 5138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 27747 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2342 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain breaks: 1 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2319 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "C" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2319 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "E" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2343 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2225 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Chain: "a" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2342 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain breaks: 1 Chain: "b" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2319 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "c" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "d" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2318 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "e" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "f" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2218 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 11, 'TRANS': 267} Chain breaks: 2 Time building chain proxies: 6.16, per 1000 atoms: 0.22 Number of scatterers: 27747 At special positions: 0 Unit cell: (165.426, 159.842, 131.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5138 8.00 N 4882 7.00 C 17607 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 36 sheets defined 47.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.762A pdb=" N HIS A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.518A pdb=" N SER A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.617A pdb=" N VAL A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.732A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 4.258A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.767A pdb=" N ARG A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 239 through 261 removed outlier: 4.305A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.704A pdb=" N ALA B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.833A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 78 through 88 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.619A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.556A pdb=" N TRP C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 231 removed outlier: 3.683A pdb=" N VAL C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 262 removed outlier: 3.849A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 258 " --> pdb=" O MET C 254 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.519A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.748A pdb=" N PHE C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 4.444A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.703A pdb=" N ILE D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 238 through 262 removed outlier: 3.573A pdb=" N ARG D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.668A pdb=" N ARG D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 315 removed outlier: 4.009A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.928A pdb=" N ILE E 154 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 211 removed outlier: 4.056A pdb=" N ARG E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 Processing helix chain 'E' and resid 241 through 262 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.579A pdb=" N PHE E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 315 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 56 through 63 Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 149 through 160 removed outlier: 3.850A pdb=" N ARG F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 241 through 261 Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 292 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 302 through 314 Processing helix chain 'a' and resid 18 through 23 Processing helix chain 'a' and resid 53 through 64 Processing helix chain 'a' and resid 76 through 88 removed outlier: 3.689A pdb=" N HIS a 80 " --> pdb=" O GLY a 76 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 126 through 133 Processing helix chain 'a' and resid 142 through 146 removed outlier: 3.580A pdb=" N GLY a 146 " --> pdb=" O TYR a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 153 through 160 removed outlier: 4.127A pdb=" N VAL a 157 " --> pdb=" O VAL a 153 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER a 160 " --> pdb=" O ARG a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 210 Processing helix chain 'a' and resid 221 through 233 Processing helix chain 'a' and resid 238 through 261 Processing helix chain 'a' and resid 269 through 284 Processing helix chain 'a' and resid 286 through 294 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 Processing helix chain 'b' and resid 18 through 23 removed outlier: 3.514A pdb=" N GLY b 23 " --> pdb=" O ARG b 19 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 63 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 102 through 107 Processing helix chain 'b' and resid 126 through 133 Processing helix chain 'b' and resid 152 through 160 Processing helix chain 'b' and resid 205 through 211 Processing helix chain 'b' and resid 221 through 233 Processing helix chain 'b' and resid 234 through 237 Processing helix chain 'b' and resid 238 through 262 removed outlier: 3.532A pdb=" N ARG b 242 " --> pdb=" O ASN b 238 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU b 243 " --> pdb=" O ALA b 239 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE b 244 " --> pdb=" O GLU b 240 " (cutoff:3.500A) Processing helix chain 'b' and resid 271 through 284 Processing helix chain 'b' and resid 285 through 294 Processing helix chain 'b' and resid 299 through 315 removed outlier: 3.997A pdb=" N ALA b 304 " --> pdb=" O GLU b 300 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR b 305 " --> pdb=" O LEU b 301 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 23 removed outlier: 3.531A pdb=" N GLY c 23 " --> pdb=" O ARG c 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 64 Processing helix chain 'c' and resid 76 through 88 removed outlier: 4.321A pdb=" N ILE c 81 " --> pdb=" O LYS c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 102 through 107 Processing helix chain 'c' and resid 126 through 134 Processing helix chain 'c' and resid 147 through 159 removed outlier: 4.489A pdb=" N VAL c 153 " --> pdb=" O ASP c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 204 through 209 Processing helix chain 'c' and resid 221 through 232 removed outlier: 4.112A pdb=" N VAL c 226 " --> pdb=" O HIS c 222 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN c 227 " --> pdb=" O ASP c 223 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL c 229 " --> pdb=" O GLU c 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS c 232 " --> pdb=" O ILE c 228 " (cutoff:3.500A) Processing helix chain 'c' and resid 238 through 261 removed outlier: 3.596A pdb=" N GLU c 243 " --> pdb=" O ALA c 239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE c 244 " --> pdb=" O GLU c 240 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL c 251 " --> pdb=" O LYS c 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA c 258 " --> pdb=" O MET c 254 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE c 259 " --> pdb=" O THR c 255 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE c 260 " --> pdb=" O ARG c 256 " (cutoff:3.500A) Processing helix chain 'c' and resid 269 through 284 removed outlier: 3.577A pdb=" N GLU c 278 " --> pdb=" O ILE c 274 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA c 281 " --> pdb=" O ALA c 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE c 282 " --> pdb=" O GLU c 278 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 294 removed outlier: 3.787A pdb=" N LEU c 292 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE c 294 " --> pdb=" O PHE c 290 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 314 removed outlier: 3.742A pdb=" N PHE c 309 " --> pdb=" O THR c 305 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 23 Processing helix chain 'd' and resid 50 through 63 Processing helix chain 'd' and resid 76 through 89 removed outlier: 3.554A pdb=" N HIS d 80 " --> pdb=" O GLY d 76 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 134 Processing helix chain 'd' and resid 152 through 159 Processing helix chain 'd' and resid 207 through 211 Processing helix chain 'd' and resid 221 through 232 Processing helix chain 'd' and resid 233 through 237 Processing helix chain 'd' and resid 238 through 261 removed outlier: 4.294A pdb=" N GLU d 243 " --> pdb=" O ALA d 239 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE d 244 " --> pdb=" O GLU d 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 269 through 284 Processing helix chain 'd' and resid 285 through 292 Processing helix chain 'd' and resid 294 through 298 removed outlier: 4.164A pdb=" N CYS d 298 " --> pdb=" O LEU d 295 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 315 removed outlier: 3.688A pdb=" N ALA d 304 " --> pdb=" O GLU d 300 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR d 305 " --> pdb=" O LEU d 301 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 23 Processing helix chain 'e' and resid 50 through 64 Processing helix chain 'e' and resid 77 through 88 Processing helix chain 'e' and resid 102 through 107 Processing helix chain 'e' and resid 126 through 134 Processing helix chain 'e' and resid 150 through 160 removed outlier: 3.736A pdb=" N ILE e 154 " --> pdb=" O VAL e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 221 through 231 Processing helix chain 'e' and resid 239 through 262 removed outlier: 4.316A pdb=" N GLU e 243 " --> pdb=" O ALA e 239 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE e 244 " --> pdb=" O GLU e 240 " (cutoff:3.500A) Processing helix chain 'e' and resid 269 through 284 Processing helix chain 'e' and resid 286 through 295 Processing helix chain 'e' and resid 302 through 315 Processing helix chain 'f' and resid 18 through 23 Processing helix chain 'f' and resid 56 through 64 Processing helix chain 'f' and resid 76 through 88 removed outlier: 3.777A pdb=" N ILE f 81 " --> pdb=" O LYS f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 108 Processing helix chain 'f' and resid 126 through 134 Processing helix chain 'f' and resid 149 through 160 removed outlier: 3.758A pdb=" N ARG f 156 " --> pdb=" O PHE f 152 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL f 157 " --> pdb=" O VAL f 153 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER f 160 " --> pdb=" O ARG f 156 " (cutoff:3.500A) Processing helix chain 'f' and resid 221 through 232 Processing helix chain 'f' and resid 233 through 237 Processing helix chain 'f' and resid 241 through 261 Processing helix chain 'f' and resid 269 through 283 Processing helix chain 'f' and resid 285 through 292 Processing helix chain 'f' and resid 294 through 298 Processing helix chain 'f' and resid 299 through 314 removed outlier: 4.170A pdb=" N ALA f 304 " --> pdb=" O GLU f 300 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR f 305 " --> pdb=" O LEU f 301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.390A pdb=" N VAL A 67 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA A 185 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 69 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N MET A 68 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.194A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 67 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA B 185 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 69 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU B 217 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER B 70 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.780A pdb=" N VAL C 93 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP C 141 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 95 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N MET C 68 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 114 Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.158A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 67 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.107A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 108 through 115 Processing sheet with id=AB7, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'F' and resid 92 through 96 removed outlier: 3.804A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET F 68 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 14 through 17 Processing sheet with id=AC1, first strand: chain 'a' and resid 92 through 96 removed outlier: 6.490A pdb=" N VAL a 93 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ASP a 141 " --> pdb=" O VAL a 93 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL a 95 " --> pdb=" O ASP a 141 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL a 67 " --> pdb=" O ALA a 183 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA a 185 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL a 69 " --> pdb=" O ALA a 185 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET a 68 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 108 through 109 Processing sheet with id=AC3, first strand: chain 'a' and resid 112 through 114 Processing sheet with id=AC4, first strand: chain 'b' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'b' and resid 92 through 96 removed outlier: 6.387A pdb=" N VAL b 93 " --> pdb=" O VAL b 139 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP b 141 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL b 95 " --> pdb=" O ASP b 141 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL b 67 " --> pdb=" O ALA b 183 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA b 185 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL b 69 " --> pdb=" O ALA b 185 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET b 68 " --> pdb=" O THR b 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 108 through 112 Processing sheet with id=AC7, first strand: chain 'c' and resid 14 through 17 Processing sheet with id=AC8, first strand: chain 'c' and resid 92 through 96 removed outlier: 3.726A pdb=" N VAL c 67 " --> pdb=" O LEU c 181 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 108 through 112 Processing sheet with id=AD1, first strand: chain 'd' and resid 14 through 17 Processing sheet with id=AD2, first strand: chain 'd' and resid 92 through 96 removed outlier: 6.180A pdb=" N LEU d 138 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR d 184 " --> pdb=" O LEU d 138 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE d 140 " --> pdb=" O THR d 184 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL d 67 " --> pdb=" O LEU d 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 108 through 112 Processing sheet with id=AD4, first strand: chain 'e' and resid 14 through 17 Processing sheet with id=AD5, first strand: chain 'e' and resid 92 through 96 removed outlier: 5.698A pdb=" N LEU e 138 " --> pdb=" O PHE e 182 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR e 184 " --> pdb=" O LEU e 138 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE e 140 " --> pdb=" O THR e 184 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL e 67 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 108 through 110 Processing sheet with id=AD7, first strand: chain 'e' and resid 113 through 115 Processing sheet with id=AD8, first strand: chain 'f' and resid 14 through 17 Processing sheet with id=AD9, first strand: chain 'f' and resid 92 through 96 removed outlier: 6.546A pdb=" N VAL f 67 " --> pdb=" O ALA f 183 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA f 185 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL f 69 " --> pdb=" O ALA f 185 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3408 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: 4.59 Time building geometry restraints manager: 3.50 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: 9309 1.34 - 1.46: 3966 1.46 - 1.57: 14841 1.57 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 28333 Sorted by residual: bond pdb=" N VAL a 172 " pdb=" CA VAL a 172 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.30e+01 bond pdb=" N ILE a 173 " pdb=" CA ILE a 173 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N ASN c 218 " pdb=" CA ASN c 218 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.06e-02 8.90e+03 9.20e+00 bond pdb=" N TYR c 219 " pdb=" CA TYR c 219 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N TYR b 219 " pdb=" CA TYR b 219 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.01e+00 ... (remaining 28328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 38040 2.31 - 4.63: 433 4.63 - 6.94: 44 6.94 - 9.26: 9 9.26 - 11.57: 3 Bond angle restraints: 38529 Sorted by residual: angle pdb=" C ILE a 173 " pdb=" N ARG a 174 " pdb=" CA ARG a 174 " ideal model delta sigma weight residual 120.49 128.53 -8.04 1.42e+00 4.96e-01 3.20e+01 angle pdb=" C ILE a 81 " pdb=" N GLU a 82 " pdb=" CA GLU a 82 " ideal model delta sigma weight residual 121.14 113.80 7.34 1.75e+00 3.27e-01 1.76e+01 angle pdb=" CB MET d 248 " pdb=" CG MET d 248 " pdb=" SD MET d 248 " ideal model delta sigma weight residual 112.70 124.27 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CB MET F 248 " pdb=" CG MET F 248 " pdb=" SD MET F 248 " ideal model delta sigma weight residual 112.70 101.36 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CA THR F 54 " pdb=" CB THR F 54 " pdb=" OG1 THR F 54 " ideal model delta sigma weight residual 109.60 104.23 5.37 1.50e+00 4.44e-01 1.28e+01 ... (remaining 38524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 15143 16.87 - 33.75: 1347 33.75 - 50.62: 298 50.62 - 67.49: 37 67.49 - 84.36: 34 Dihedral angle restraints: 16859 sinusoidal: 6643 harmonic: 10216 Sorted by residual: dihedral pdb=" CA MET D 151 " pdb=" C MET D 151 " pdb=" N PHE D 152 " pdb=" CA PHE D 152 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA MET d 151 " pdb=" C MET d 151 " pdb=" N PHE d 152 " pdb=" CA PHE d 152 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TYR C 219 " pdb=" C TYR C 219 " pdb=" N LEU C 220 " pdb=" CA LEU C 220 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 16856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3347 0.047 - 0.094: 823 0.094 - 0.140: 191 0.140 - 0.187: 7 0.187 - 0.234: 4 Chirality restraints: 4372 Sorted by residual: chirality pdb=" CG LEU b 217 " pdb=" CB LEU b 217 " pdb=" CD1 LEU b 217 " pdb=" CD2 LEU b 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL a 172 " pdb=" N VAL a 172 " pdb=" C VAL a 172 " pdb=" CB VAL a 172 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR b 165 " pdb=" CA THR b 165 " pdb=" OG1 THR b 165 " pdb=" CG2 THR b 165 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 4369 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP f 211 " -0.027 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP f 211 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP f 211 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP f 211 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP f 211 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP f 211 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP f 211 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 211 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 211 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP f 211 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 40 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO E 41 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 276 " -0.020 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP F 276 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP F 276 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP F 276 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 276 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP F 276 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 276 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 276 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 276 " -0.010 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2114 2.74 - 3.28: 28630 3.28 - 3.82: 46114 3.82 - 4.36: 51407 4.36 - 4.90: 87458 Nonbonded interactions: 215723 Sorted by model distance: nonbonded pdb=" OD1 ASN e 10 " pdb=" OH TYR e 33 " model vdw 2.197 3.040 nonbonded pdb=" O SER e 269 " pdb=" OG1 THR e 272 " model vdw 2.199 3.040 nonbonded pdb=" O SER E 269 " pdb=" OG1 THR E 272 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG f 147 " pdb=" OD1 ASP f 149 " model vdw 2.210 3.120 nonbonded pdb=" O SER D 269 " pdb=" OG1 THR D 272 " model vdw 2.210 3.040 ... (remaining 215718 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 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'B' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'C' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'D' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'E' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'F' and (resid 10 through 187 or resid 205 through 315)) selection = (chain 'a' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'b' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'c' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'd' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'e' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'f' and (resid 10 through 187 or resid 205 through 315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.690 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28333 Z= 0.135 Angle : 0.591 11.571 38529 Z= 0.315 Chirality : 0.042 0.234 4372 Planarity : 0.004 0.103 5022 Dihedral : 13.916 84.364 10231 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 0.34 % Allowed : 0.30 % Favored : 99.36 % 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 (0.15), residues: 3442 helix: 0.75 (0.14), residues: 1450 sheet: 0.34 (0.22), residues: 532 loop : -0.84 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 312 TYR 0.017 0.001 TYR B 47 PHE 0.030 0.001 PHE a 309 TRP 0.072 0.003 TRP f 211 HIS 0.016 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (28333) covalent geometry : angle 0.59108 / 0.32 (38529) hydrogen bonds : bond 0.14775 / 9.97 ( 1173) hydrogen bonds : angle 6.27329 / 4.36 ( 3408) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 956 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6475 (p0) cc_final: 0.5993 (p0) REVERT: A 98 ASP cc_start: 0.7705 (m-30) cc_final: 0.7190 (m-30) REVERT: A 106 LEU cc_start: 0.7883 (mt) cc_final: 0.7528 (mt) REVERT: A 140 PHE cc_start: 0.7233 (m-10) cc_final: 0.6925 (m-10) REVERT: A 152 PHE cc_start: 0.7732 (m-10) cc_final: 0.7440 (m-10) REVERT: B 10 ASN cc_start: 0.8651 (m-40) cc_final: 0.8345 (m-40) REVERT: B 28 MET cc_start: 0.7469 (tmm) cc_final: 0.7211 (tmm) REVERT: B 63 TYR cc_start: 0.7321 (m-80) cc_final: 0.6832 (m-80) REVERT: B 123 PHE cc_start: 0.7768 (t80) cc_final: 0.7366 (t80) REVERT: C 102 SER cc_start: 0.8074 (p) cc_final: 0.7305 (p) REVERT: C 109 LYS cc_start: 0.7338 (pptt) cc_final: 0.7138 (pptt) REVERT: C 135 ASN cc_start: 0.8268 (p0) cc_final: 0.7614 (p0) REVERT: C 139 VAL cc_start: 0.8373 (t) cc_final: 0.8147 (t) REVERT: C 151 MET cc_start: 0.7301 (mpp) cc_final: 0.7029 (mpp) REVERT: C 254 MET cc_start: 0.8382 (ttp) cc_final: 0.8176 (ttp) REVERT: D 10 ASN cc_start: 0.7993 (t0) cc_final: 0.7421 (t0) REVERT: D 29 MET cc_start: 0.5026 (mmp) cc_final: 0.4565 (mmp) REVERT: D 82 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 125 ASP cc_start: 0.8111 (m-30) cc_final: 0.7910 (m-30) REVERT: D 279 ASN cc_start: 0.8719 (m110) cc_final: 0.8181 (m110) REVERT: E 52 GLN cc_start: 0.8430 (mt0) cc_final: 0.7915 (mt0) REVERT: E 89 ASN cc_start: 0.7515 (t0) cc_final: 0.7155 (t0) REVERT: E 119 GLN cc_start: 0.7849 (pm20) cc_final: 0.7569 (pm20) REVERT: E 123 PHE cc_start: 0.6910 (p90) cc_final: 0.6686 (p90) REVERT: E 151 MET cc_start: 0.8159 (tpp) cc_final: 0.7909 (tpp) REVERT: E 208 MET cc_start: 0.7938 (tmm) cc_final: 0.7681 (tmm) REVERT: E 209 ASP cc_start: 0.8157 (t0) cc_final: 0.7946 (t0) REVERT: E 223 ASP cc_start: 0.8245 (m-30) cc_final: 0.7873 (m-30) REVERT: E 235 HIS cc_start: 0.8055 (t-90) cc_final: 0.7803 (t-90) REVERT: E 248 MET cc_start: 0.8155 (mtp) cc_final: 0.7717 (mtp) REVERT: E 253 ASP cc_start: 0.8102 (t0) cc_final: 0.7750 (t0) REVERT: E 254 MET cc_start: 0.8366 (mmp) cc_final: 0.7593 (mmp) REVERT: E 303 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7939 (ttm110) REVERT: F 46 ASP cc_start: 0.7830 (p0) cc_final: 0.7622 (p0) REVERT: F 48 LEU cc_start: 0.8677 (tt) cc_final: 0.8404 (tt) REVERT: F 83 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7907 (mm-40) REVERT: F 89 ASN cc_start: 0.8283 (m110) cc_final: 0.7996 (m-40) REVERT: F 130 TRP cc_start: 0.8259 (t60) cc_final: 0.7972 (t60) REVERT: F 238 ASN cc_start: 0.6882 (p0) cc_final: 0.6454 (p0) REVERT: a 50 ASP cc_start: 0.6589 (p0) cc_final: 0.6141 (p0) REVERT: a 98 ASP cc_start: 0.7664 (m-30) cc_final: 0.7363 (m-30) REVERT: a 182 PHE cc_start: 0.8067 (m-80) cc_final: 0.7348 (m-80) REVERT: a 244 ILE cc_start: 0.8274 (mp) cc_final: 0.7719 (mp) REVERT: a 248 MET cc_start: 0.7986 (mmp) cc_final: 0.7766 (mmp) REVERT: a 302 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7815 (mt-10) REVERT: b 10 ASN cc_start: 0.8746 (m-40) cc_final: 0.8494 (m-40) REVERT: b 69 VAL cc_start: 0.7627 (m) cc_final: 0.7384 (m) REVERT: b 77 LYS cc_start: 0.8294 (mtmt) cc_final: 0.8004 (mtmt) REVERT: b 151 MET cc_start: 0.6690 (tmm) cc_final: 0.6258 (tmm) REVERT: b 248 MET cc_start: 0.7320 (mpp) cc_final: 0.6957 (mpp) REVERT: b 254 MET cc_start: 0.7773 (ptp) cc_final: 0.7509 (ptp) REVERT: c 10 ASN cc_start: 0.7889 (m110) cc_final: 0.7445 (m110) REVERT: c 100 HIS cc_start: 0.6544 (m-70) cc_final: 0.5735 (m-70) REVERT: c 135 ASN cc_start: 0.8165 (p0) cc_final: 0.7416 (p0) REVERT: c 155 GLN cc_start: 0.7911 (mt0) cc_final: 0.7427 (mt0) REVERT: c 208 MET cc_start: 0.6998 (mtm) cc_final: 0.6181 (mtm) REVERT: c 254 MET cc_start: 0.8422 (ttp) cc_final: 0.7946 (ttp) REVERT: d 10 ASN cc_start: 0.8841 (t0) cc_final: 0.8352 (t0) REVERT: d 29 MET cc_start: 0.4985 (mmp) cc_final: 0.4736 (mmp) REVERT: d 68 MET cc_start: 0.6505 (tmm) cc_final: 0.5924 (tmm) REVERT: d 140 PHE cc_start: 0.8700 (m-80) cc_final: 0.8399 (m-10) REVERT: d 152 PHE cc_start: 0.7994 (t80) cc_final: 0.7765 (t80) REVERT: d 214 VAL cc_start: 0.7427 (t) cc_final: 0.6869 (t) REVERT: d 218 ASN cc_start: 0.8217 (m-40) cc_final: 0.8008 (m-40) REVERT: d 276 TRP cc_start: 0.8042 (t60) cc_final: 0.7782 (t60) REVERT: d 279 ASN cc_start: 0.8756 (m-40) cc_final: 0.8343 (m-40) REVERT: e 22 PHE cc_start: 0.8578 (m-10) cc_final: 0.8272 (m-10) REVERT: e 80 HIS cc_start: 0.8534 (t-170) cc_final: 0.8280 (t-170) REVERT: e 83 GLN cc_start: 0.7811 (tp-100) cc_final: 0.6889 (tp-100) REVERT: e 155 GLN cc_start: 0.8171 (tp40) cc_final: 0.7895 (tp40) REVERT: e 156 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8186 (mmm-85) REVERT: e 166 LEU cc_start: 0.8199 (mm) cc_final: 0.7908 (mm) REVERT: e 235 HIS cc_start: 0.7958 (t-90) cc_final: 0.7700 (t-90) REVERT: e 248 MET cc_start: 0.8009 (mpp) cc_final: 0.7706 (mpp) REVERT: e 257 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7685 (tp-100) REVERT: f 47 TYR cc_start: 0.7351 (t80) cc_final: 0.7000 (t80) REVERT: f 48 LEU cc_start: 0.8239 (tt) cc_final: 0.7907 (tt) REVERT: f 49 PHE cc_start: 0.7846 (m-10) cc_final: 0.7280 (m-80) REVERT: f 54 THR cc_start: 0.7645 (p) cc_final: 0.6506 (p) REVERT: f 65 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7573 (mmm-85) REVERT: f 68 MET cc_start: 0.7247 (mtt) cc_final: 0.6237 (mtt) REVERT: f 75 THR cc_start: 0.7273 (m) cc_final: 0.7003 (m) REVERT: f 105 ASP cc_start: 0.7753 (t0) cc_final: 0.7505 (t0) REVERT: f 144 ASP cc_start: 0.7933 (p0) cc_final: 0.7658 (p0) REVERT: f 230 LEU cc_start: 0.8472 (mt) cc_final: 0.8243 (mt) REVERT: f 257 GLN cc_start: 0.8521 (mt0) cc_final: 0.8050 (mt0) outliers start: 10 outliers final: 7 residues processed: 966 average time/residue: 0.1827 time to fit residues: 271.6151 Evaluate side-chains 940 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 933 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN E 83 GLN F 80 HIS F 100 HIS ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 311 GLN d 155 GLN e 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122581 restraints weight = 53258.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127566 restraints weight = 29497.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.131018 restraints weight = 19567.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133300 restraints weight = 14564.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134965 restraints weight = 11800.689| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28333 Z= 0.220 Angle : 0.597 11.199 38529 Z= 0.320 Chirality : 0.043 0.164 4372 Planarity : 0.005 0.074 5022 Dihedral : 4.516 22.885 3840 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.26 % Rotamer: Outliers : 0.40 % Allowed : 6.00 % Favored : 93.59 % 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: -0.27 (0.14), residues: 3442 helix: 0.51 (0.13), residues: 1516 sheet: 0.33 (0.22), residues: 510 loop : -1.06 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 65 TYR 0.018 0.002 TYR C 143 PHE 0.030 0.002 PHE a 288 TRP 0.054 0.003 TRP f 211 HIS 0.018 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (28333) covalent geometry : angle 0.59686 / 0.32 (38529) hydrogen bonds : bond 0.03986 / 2.64 ( 1173) hydrogen bonds : angle 5.23394 / 3.69 ( 3408) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 997 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.8044 (m) cc_final: 0.7641 (p) REVERT: A 98 ASP cc_start: 0.7822 (m-30) cc_final: 0.7278 (m-30) REVERT: A 102 SER cc_start: 0.7815 (p) cc_final: 0.7614 (p) REVERT: A 106 LEU cc_start: 0.8024 (mt) cc_final: 0.7680 (mt) REVERT: A 140 PHE cc_start: 0.7402 (m-10) cc_final: 0.7169 (m-10) REVERT: A 152 PHE cc_start: 0.7789 (m-10) cc_final: 0.7363 (m-10) REVERT: A 180 ARG cc_start: 0.7323 (mpt180) cc_final: 0.7089 (mpt180) REVERT: A 253 ASP cc_start: 0.8247 (m-30) cc_final: 0.7960 (m-30) REVERT: A 268 MET cc_start: 0.6852 (mmp) cc_final: 0.6615 (mmm) REVERT: A 272 THR cc_start: 0.9072 (p) cc_final: 0.7308 (p) REVERT: A 279 ASN cc_start: 0.8453 (m-40) cc_final: 0.7757 (m-40) REVERT: A 311 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7364 (tp-100) REVERT: B 10 ASN cc_start: 0.8811 (m-40) cc_final: 0.8521 (m-40) REVERT: B 28 MET cc_start: 0.7384 (tmm) cc_final: 0.6756 (tmm) REVERT: B 63 TYR cc_start: 0.7433 (m-80) cc_final: 0.6993 (m-80) REVERT: B 68 MET cc_start: 0.7790 (mtt) cc_final: 0.7550 (mtt) REVERT: B 80 HIS cc_start: 0.8226 (m90) cc_final: 0.7850 (m90) REVERT: B 88 LEU cc_start: 0.8879 (mp) cc_final: 0.8665 (mp) REVERT: B 100 HIS cc_start: 0.8429 (m90) cc_final: 0.8203 (m-70) REVERT: B 123 PHE cc_start: 0.7980 (t80) cc_final: 0.7595 (t80) REVERT: B 166 LEU cc_start: 0.8018 (mt) cc_final: 0.7816 (mt) REVERT: C 100 HIS cc_start: 0.6832 (m-70) cc_final: 0.6163 (m-70) REVERT: C 130 TRP cc_start: 0.8715 (t-100) cc_final: 0.8440 (t-100) REVERT: C 135 ASN cc_start: 0.8386 (p0) cc_final: 0.7784 (p0) REVERT: C 138 LEU cc_start: 0.8487 (tt) cc_final: 0.8265 (tt) REVERT: C 142 GLU cc_start: 0.7110 (mp0) cc_final: 0.6591 (mp0) REVERT: C 144 ASP cc_start: 0.7554 (p0) cc_final: 0.7216 (p0) REVERT: C 147 ARG cc_start: 0.7252 (mpp80) cc_final: 0.6385 (mpt180) REVERT: C 151 MET cc_start: 0.7173 (mpp) cc_final: 0.6512 (mpp) REVERT: C 158 LEU cc_start: 0.8824 (tp) cc_final: 0.8515 (tp) REVERT: C 159 GLU cc_start: 0.7418 (mp0) cc_final: 0.7038 (mp0) REVERT: C 169 GLN cc_start: 0.8192 (mm110) cc_final: 0.7920 (mm-40) REVERT: C 211 TRP cc_start: 0.8305 (m100) cc_final: 0.7500 (m100) REVERT: C 248 MET cc_start: 0.8170 (ttt) cc_final: 0.7965 (ttt) REVERT: D 10 ASN cc_start: 0.8468 (t0) cc_final: 0.7901 (t0) REVERT: D 29 MET cc_start: 0.5027 (mmp) cc_final: 0.4576 (mmp) REVERT: D 44 ASP cc_start: 0.8088 (t0) cc_final: 0.7736 (t0) REVERT: D 69 VAL cc_start: 0.8180 (t) cc_final: 0.7771 (m) REVERT: D 79 THR cc_start: 0.8430 (p) cc_final: 0.7980 (t) REVERT: D 89 ASN cc_start: 0.8155 (m-40) cc_final: 0.7943 (m-40) REVERT: D 106 LEU cc_start: 0.7606 (mm) cc_final: 0.7297 (mp) REVERT: D 135 ASN cc_start: 0.7149 (p0) cc_final: 0.6017 (p0) REVERT: D 138 LEU cc_start: 0.8339 (tp) cc_final: 0.8106 (tp) REVERT: D 174 ARG cc_start: 0.7390 (mmp80) cc_final: 0.6818 (mmp80) REVERT: D 218 ASN cc_start: 0.8312 (m-40) cc_final: 0.8104 (m-40) REVERT: D 268 MET cc_start: 0.7302 (tpt) cc_final: 0.7056 (mmm) REVERT: D 279 ASN cc_start: 0.8790 (m110) cc_final: 0.8221 (m110) REVERT: E 10 ASN cc_start: 0.8080 (t0) cc_final: 0.7872 (t0) REVERT: E 47 TYR cc_start: 0.6945 (t80) cc_final: 0.6655 (t80) REVERT: E 52 GLN cc_start: 0.8519 (mt0) cc_final: 0.8015 (mt0) REVERT: E 80 HIS cc_start: 0.8681 (t-170) cc_final: 0.8436 (t-170) REVERT: E 89 ASN cc_start: 0.7712 (t0) cc_final: 0.7109 (t0) REVERT: E 105 ASP cc_start: 0.7549 (t0) cc_final: 0.7346 (t0) REVERT: E 123 PHE cc_start: 0.6919 (p90) cc_final: 0.6705 (p90) REVERT: E 181 LEU cc_start: 0.8490 (tt) cc_final: 0.8192 (tt) REVERT: E 208 MET cc_start: 0.7875 (tmm) cc_final: 0.7582 (tmm) REVERT: E 223 ASP cc_start: 0.8359 (m-30) cc_final: 0.8000 (m-30) REVERT: E 235 HIS cc_start: 0.8139 (t-90) cc_final: 0.7904 (t-90) REVERT: E 253 ASP cc_start: 0.8172 (t0) cc_final: 0.7830 (t0) REVERT: E 254 MET cc_start: 0.8383 (mmp) cc_final: 0.7655 (mmp) REVERT: E 276 TRP cc_start: 0.7977 (t-100) cc_final: 0.7757 (t-100) REVERT: F 54 THR cc_start: 0.8333 (m) cc_final: 0.7898 (p) REVERT: F 83 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7911 (mm-40) REVERT: F 87 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7272 (ttp-110) REVERT: F 89 ASN cc_start: 0.8379 (m110) cc_final: 0.8054 (m-40) REVERT: F 105 ASP cc_start: 0.8304 (t0) cc_final: 0.7956 (t0) REVERT: F 135 ASN cc_start: 0.8848 (p0) cc_final: 0.8253 (p0) REVERT: F 141 ASP cc_start: 0.7609 (t0) cc_final: 0.7395 (t0) REVERT: F 144 ASP cc_start: 0.7659 (p0) cc_final: 0.7396 (p0) REVERT: F 210 ARG cc_start: 0.7174 (ttm170) cc_final: 0.6793 (ttm-80) REVERT: F 230 LEU cc_start: 0.8396 (mt) cc_final: 0.8142 (mt) REVERT: F 238 ASN cc_start: 0.7057 (p0) cc_final: 0.6608 (p0) REVERT: F 257 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8210 (mm-40) REVERT: a 19 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7489 (mtm110) REVERT: a 50 ASP cc_start: 0.6985 (p0) cc_final: 0.6547 (p0) REVERT: a 98 ASP cc_start: 0.7725 (m-30) cc_final: 0.7433 (m-30) REVERT: a 106 LEU cc_start: 0.7950 (mt) cc_final: 0.7635 (mt) REVERT: a 152 PHE cc_start: 0.7617 (m-10) cc_final: 0.7355 (m-10) REVERT: a 182 PHE cc_start: 0.8161 (m-80) cc_final: 0.7321 (m-80) REVERT: a 244 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7583 (mp) REVERT: a 248 MET cc_start: 0.7986 (mmp) cc_final: 0.7609 (mmt) REVERT: a 302 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7953 (mt-10) REVERT: a 305 THR cc_start: 0.8497 (p) cc_final: 0.8241 (p) REVERT: a 309 PHE cc_start: 0.7444 (m-80) cc_final: 0.7208 (m-80) REVERT: b 10 ASN cc_start: 0.8895 (m-40) cc_final: 0.8633 (m-40) REVERT: b 68 MET cc_start: 0.8047 (mtt) cc_final: 0.7819 (mtt) REVERT: b 77 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7972 (mtmt) REVERT: b 82 GLU cc_start: 0.8269 (pt0) cc_final: 0.7463 (pt0) REVERT: b 83 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7664 (mm-40) REVERT: b 95 VAL cc_start: 0.8662 (t) cc_final: 0.8397 (m) REVERT: b 100 HIS cc_start: 0.8303 (m90) cc_final: 0.7856 (m90) REVERT: b 122 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6768 (tm-30) REVERT: b 147 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7269 (mmt-90) REVERT: b 186 ASN cc_start: 0.6710 (m110) cc_final: 0.6320 (m110) REVERT: b 254 MET cc_start: 0.7868 (ptp) cc_final: 0.7636 (ptp) REVERT: b 268 MET cc_start: 0.8398 (tmm) cc_final: 0.8079 (tmm) REVERT: c 10 ASN cc_start: 0.7808 (m110) cc_final: 0.7386 (m110) REVERT: c 75 THR cc_start: 0.7952 (p) cc_final: 0.7722 (p) REVERT: c 135 ASN cc_start: 0.8241 (p0) cc_final: 0.7504 (p0) REVERT: c 138 LEU cc_start: 0.8319 (tt) cc_final: 0.8061 (tt) REVERT: c 139 VAL cc_start: 0.8592 (t) cc_final: 0.8253 (t) REVERT: c 141 ASP cc_start: 0.7761 (m-30) cc_final: 0.7401 (m-30) REVERT: c 142 GLU cc_start: 0.7791 (mp0) cc_final: 0.7466 (mp0) REVERT: c 155 GLN cc_start: 0.8061 (mt0) cc_final: 0.7537 (mt0) REVERT: c 174 ARG cc_start: 0.8003 (mmp-170) cc_final: 0.7777 (mmp-170) REVERT: c 208 MET cc_start: 0.6974 (mtm) cc_final: 0.6195 (mtm) REVERT: c 254 MET cc_start: 0.8508 (ttp) cc_final: 0.8073 (ttp) REVERT: c 256 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8451 (mtp-110) REVERT: d 10 ASN cc_start: 0.8696 (t0) cc_final: 0.8194 (t0) REVERT: d 58 LEU cc_start: 0.8435 (mm) cc_final: 0.8215 (mm) REVERT: d 68 MET cc_start: 0.6528 (tmm) cc_final: 0.6077 (tmm) REVERT: d 73 HIS cc_start: 0.8774 (t-90) cc_final: 0.8569 (t-90) REVERT: d 105 ASP cc_start: 0.7126 (t0) cc_final: 0.6801 (t0) REVERT: d 128 LEU cc_start: 0.8190 (mm) cc_final: 0.7955 (mm) REVERT: d 138 LEU cc_start: 0.8305 (tp) cc_final: 0.8010 (tp) REVERT: d 140 PHE cc_start: 0.8793 (m-80) cc_final: 0.8562 (m-80) REVERT: d 159 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7401 (tm-30) REVERT: d 163 ARG cc_start: 0.7159 (mmt90) cc_final: 0.6565 (mmt90) REVERT: d 171 ARG cc_start: 0.7829 (tpt90) cc_final: 0.7610 (tpt90) REVERT: d 218 ASN cc_start: 0.8252 (m-40) cc_final: 0.8041 (m-40) REVERT: d 279 ASN cc_start: 0.8834 (m-40) cc_final: 0.8369 (m-40) REVERT: e 28 MET cc_start: 0.8154 (tpp) cc_final: 0.7828 (tpp) REVERT: e 77 LYS cc_start: 0.8211 (pttt) cc_final: 0.7772 (pttt) REVERT: e 83 GLN cc_start: 0.7735 (tp-100) cc_final: 0.6844 (tp-100) REVERT: e 133 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: e 135 ASN cc_start: 0.8064 (p0) cc_final: 0.7583 (p0) REVERT: e 155 GLN cc_start: 0.8327 (tp40) cc_final: 0.7712 (tp40) REVERT: e 158 LEU cc_start: 0.8567 (tp) cc_final: 0.8323 (tp) REVERT: e 184 THR cc_start: 0.8512 (t) cc_final: 0.8057 (t) REVERT: e 235 HIS cc_start: 0.8060 (t-90) cc_final: 0.7813 (t-90) REVERT: e 248 MET cc_start: 0.8020 (mpp) cc_final: 0.7708 (mpp) REVERT: e 257 GLN cc_start: 0.8530 (tp-100) cc_final: 0.7877 (tp-100) REVERT: f 54 THR cc_start: 0.8283 (p) cc_final: 0.7507 (p) REVERT: f 68 MET cc_start: 0.7511 (mtt) cc_final: 0.7007 (mtt) REVERT: f 73 HIS cc_start: 0.7178 (t-90) cc_final: 0.6909 (t-90) REVERT: f 75 THR cc_start: 0.7612 (m) cc_final: 0.7290 (m) REVERT: f 105 ASP cc_start: 0.8155 (t0) cc_final: 0.7755 (t0) REVERT: f 141 ASP cc_start: 0.7062 (t0) cc_final: 0.6755 (t0) REVERT: f 150 VAL cc_start: 0.8544 (p) cc_final: 0.8279 (m) REVERT: f 227 ASN cc_start: 0.8582 (m-40) cc_final: 0.8251 (m-40) REVERT: f 230 LEU cc_start: 0.8606 (mt) cc_final: 0.8342 (mt) REVERT: f 257 GLN cc_start: 0.8512 (mt0) cc_final: 0.8081 (mt0) REVERT: f 309 PHE cc_start: 0.8364 (m-80) cc_final: 0.8092 (m-80) outliers start: 12 outliers final: 1 residues processed: 1001 average time/residue: 0.1841 time to fit residues: 282.1117 Evaluate side-chains 969 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 966 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 312 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 240 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN B 169 GLN B 222 HIS C 83 GLN D 155 GLN ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 246 ASN c 296 ASN d 222 HIS e 52 GLN ** e 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 GLN f 83 GLN f 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126546 restraints weight = 52720.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131227 restraints weight = 29846.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134454 restraints weight = 19991.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136633 restraints weight = 14979.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138062 restraints weight = 12206.549| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28333 Z= 0.191 Angle : 0.578 10.180 38529 Z= 0.308 Chirality : 0.043 0.155 4372 Planarity : 0.005 0.125 5022 Dihedral : 4.535 23.283 3840 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.04 % Favored : 93.81 % Rotamer: Outliers : 0.27 % Allowed : 4.26 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3442 helix: 0.41 (0.13), residues: 1512 sheet: 0.11 (0.22), residues: 510 loop : -1.16 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 65 TYR 0.018 0.002 TYR a 132 PHE 0.026 0.002 PHE E 182 TRP 0.045 0.002 TRP a 276 HIS 0.005 0.001 HIS F 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (28333) covalent geometry : angle 0.57828 / 0.31 (38529) hydrogen bonds : bond 0.03830 / 2.56 ( 1173) hydrogen bonds : angle 5.15714 / 3.63 ( 3408) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1002 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7363 (m-10) cc_final: 0.7162 (m-10) REVERT: A 152 PHE cc_start: 0.7749 (m-10) cc_final: 0.7330 (m-10) REVERT: A 158 LEU cc_start: 0.8309 (mp) cc_final: 0.8030 (mp) REVERT: A 180 ARG cc_start: 0.7386 (mpt180) cc_final: 0.7047 (mpt180) REVERT: A 245 VAL cc_start: 0.8580 (t) cc_final: 0.8337 (t) REVERT: A 248 MET cc_start: 0.7705 (ptt) cc_final: 0.7105 (ptt) REVERT: A 253 ASP cc_start: 0.8209 (m-30) cc_final: 0.7919 (m-30) REVERT: A 268 MET cc_start: 0.6499 (mmp) cc_final: 0.6244 (mpp) REVERT: A 279 ASN cc_start: 0.8353 (m-40) cc_final: 0.7703 (m-40) REVERT: B 10 ASN cc_start: 0.8809 (m-40) cc_final: 0.8480 (m-40) REVERT: B 28 MET cc_start: 0.7455 (tmm) cc_final: 0.6837 (tmm) REVERT: B 47 TYR cc_start: 0.6811 (t80) cc_final: 0.6483 (t80) REVERT: B 63 TYR cc_start: 0.7320 (m-80) cc_final: 0.6868 (m-80) REVERT: B 80 HIS cc_start: 0.8136 (m90) cc_final: 0.7725 (m90) REVERT: B 88 LEU cc_start: 0.8834 (mp) cc_final: 0.8619 (mp) REVERT: B 100 HIS cc_start: 0.8434 (m90) cc_final: 0.8137 (m-70) REVERT: B 122 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 149 ASP cc_start: 0.7560 (t0) cc_final: 0.7298 (t0) REVERT: B 166 LEU cc_start: 0.8004 (mt) cc_final: 0.7790 (mt) REVERT: B 210 ARG cc_start: 0.8047 (mmp80) cc_final: 0.7829 (mmp80) REVERT: B 238 ASN cc_start: 0.7639 (p0) cc_final: 0.7243 (p0) REVERT: B 268 MET cc_start: 0.8529 (tmm) cc_final: 0.8164 (tmm) REVERT: C 130 TRP cc_start: 0.8538 (t-100) cc_final: 0.8312 (t-100) REVERT: C 135 ASN cc_start: 0.8315 (p0) cc_final: 0.7378 (p0) REVERT: C 138 LEU cc_start: 0.8413 (tt) cc_final: 0.8166 (tt) REVERT: C 142 GLU cc_start: 0.7141 (mp0) cc_final: 0.6731 (mp0) REVERT: C 147 ARG cc_start: 0.7353 (mpp80) cc_final: 0.6344 (mpt-90) REVERT: C 151 MET cc_start: 0.7081 (mpp) cc_final: 0.6463 (mpp) REVERT: C 158 LEU cc_start: 0.8814 (tp) cc_final: 0.8474 (tp) REVERT: C 159 GLU cc_start: 0.7422 (mp0) cc_final: 0.6995 (mp0) REVERT: C 169 GLN cc_start: 0.8033 (mm110) cc_final: 0.7832 (mm110) REVERT: C 248 MET cc_start: 0.8161 (ttt) cc_final: 0.7939 (ttt) REVERT: D 10 ASN cc_start: 0.8454 (t0) cc_final: 0.7819 (t0) REVERT: D 29 MET cc_start: 0.5063 (mmp) cc_final: 0.4604 (mmp) REVERT: D 82 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 140 PHE cc_start: 0.8442 (m-80) cc_final: 0.8216 (m-80) REVERT: D 154 ILE cc_start: 0.8957 (mm) cc_final: 0.8755 (mm) REVERT: D 174 ARG cc_start: 0.7407 (mmp80) cc_final: 0.6833 (mmp80) REVERT: D 268 MET cc_start: 0.7306 (tpt) cc_final: 0.7048 (mmm) REVERT: D 279 ASN cc_start: 0.8738 (m110) cc_final: 0.8188 (m110) REVERT: E 10 ASN cc_start: 0.8071 (t0) cc_final: 0.7860 (t0) REVERT: E 52 GLN cc_start: 0.8503 (mt0) cc_final: 0.8006 (mt0) REVERT: E 89 ASN cc_start: 0.7717 (t0) cc_final: 0.6946 (t0) REVERT: E 105 ASP cc_start: 0.7590 (t0) cc_final: 0.7324 (t0) REVERT: E 123 PHE cc_start: 0.6866 (p90) cc_final: 0.6627 (p90) REVERT: E 135 ASN cc_start: 0.7693 (p0) cc_final: 0.6557 (p0) REVERT: E 141 ASP cc_start: 0.7229 (t0) cc_final: 0.7001 (t0) REVERT: E 181 LEU cc_start: 0.8420 (tt) cc_final: 0.8186 (tt) REVERT: E 208 MET cc_start: 0.7936 (tmm) cc_final: 0.7565 (tmm) REVERT: E 209 ASP cc_start: 0.8063 (t0) cc_final: 0.7855 (t0) REVERT: E 223 ASP cc_start: 0.8347 (m-30) cc_final: 0.7983 (m-30) REVERT: E 248 MET cc_start: 0.8140 (mtp) cc_final: 0.7809 (mtp) REVERT: E 253 ASP cc_start: 0.8142 (t0) cc_final: 0.7802 (t0) REVERT: E 254 MET cc_start: 0.8308 (mmp) cc_final: 0.7580 (mmp) REVERT: E 268 MET cc_start: 0.7648 (tpt) cc_final: 0.7071 (tpt) REVERT: E 303 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7970 (ttm110) REVERT: F 54 THR cc_start: 0.8276 (m) cc_final: 0.7870 (p) REVERT: F 83 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7856 (mm-40) REVERT: F 87 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7155 (ttp-110) REVERT: F 89 ASN cc_start: 0.8382 (m110) cc_final: 0.8075 (m-40) REVERT: F 130 TRP cc_start: 0.8660 (t60) cc_final: 0.8045 (t60) REVERT: F 135 ASN cc_start: 0.8858 (p0) cc_final: 0.8055 (p0) REVERT: F 138 LEU cc_start: 0.8333 (tp) cc_final: 0.8096 (tp) REVERT: F 141 ASP cc_start: 0.7593 (t0) cc_final: 0.7176 (t0) REVERT: F 230 LEU cc_start: 0.8411 (mt) cc_final: 0.8163 (mt) REVERT: F 238 ASN cc_start: 0.7052 (p0) cc_final: 0.6691 (p0) REVERT: a 19 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7469 (mtm110) REVERT: a 50 ASP cc_start: 0.6965 (p0) cc_final: 0.6594 (p0) REVERT: a 68 MET cc_start: 0.6864 (ttp) cc_final: 0.6547 (ttp) REVERT: a 98 ASP cc_start: 0.7686 (m-30) cc_final: 0.7413 (m-30) REVERT: a 106 LEU cc_start: 0.7975 (mt) cc_final: 0.7657 (mt) REVERT: a 152 PHE cc_start: 0.7523 (m-10) cc_final: 0.7206 (m-10) REVERT: a 158 LEU cc_start: 0.8602 (mp) cc_final: 0.8220 (mp) REVERT: a 244 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8140 (mp) REVERT: a 302 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8040 (mt-10) REVERT: a 305 THR cc_start: 0.8605 (p) cc_final: 0.8300 (p) REVERT: a 306 VAL cc_start: 0.9046 (t) cc_final: 0.8728 (p) REVERT: a 309 PHE cc_start: 0.7509 (m-80) cc_final: 0.7269 (m-80) REVERT: b 10 ASN cc_start: 0.8862 (m-40) cc_final: 0.8611 (m-40) REVERT: b 77 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8045 (mtmt) REVERT: b 82 GLU cc_start: 0.8336 (pt0) cc_final: 0.7876 (pt0) REVERT: b 95 VAL cc_start: 0.8714 (t) cc_final: 0.8339 (m) REVERT: b 100 HIS cc_start: 0.8343 (m90) cc_final: 0.7853 (m90) REVERT: b 122 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6973 (tm-30) REVERT: b 130 TRP cc_start: 0.8340 (t60) cc_final: 0.8091 (t60) REVERT: b 147 ARG cc_start: 0.7628 (mmt-90) cc_final: 0.7236 (mmt-90) REVERT: b 159 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7109 (tm-30) REVERT: b 186 ASN cc_start: 0.6631 (m110) cc_final: 0.6255 (m110) REVERT: b 268 MET cc_start: 0.8377 (tmm) cc_final: 0.8008 (tmm) REVERT: c 10 ASN cc_start: 0.7809 (m110) cc_final: 0.7388 (m110) REVERT: c 68 MET cc_start: 0.7446 (ttt) cc_final: 0.7237 (ttt) REVERT: c 75 THR cc_start: 0.7886 (p) cc_final: 0.7633 (p) REVERT: c 121 THR cc_start: 0.8539 (m) cc_final: 0.8146 (t) REVERT: c 135 ASN cc_start: 0.8222 (p0) cc_final: 0.7498 (p0) REVERT: c 138 LEU cc_start: 0.8330 (tt) cc_final: 0.8122 (tt) REVERT: c 141 ASP cc_start: 0.7697 (m-30) cc_final: 0.7355 (m-30) REVERT: c 142 GLU cc_start: 0.7787 (mp0) cc_final: 0.7463 (mp0) REVERT: c 155 GLN cc_start: 0.8004 (mt0) cc_final: 0.7444 (mt0) REVERT: c 156 ARG cc_start: 0.8969 (tpt-90) cc_final: 0.8743 (tpt-90) REVERT: c 174 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7693 (mmp-170) REVERT: c 208 MET cc_start: 0.6969 (mtm) cc_final: 0.6238 (mtm) REVERT: c 244 ILE cc_start: 0.9104 (mm) cc_final: 0.8718 (mm) REVERT: c 254 MET cc_start: 0.8457 (ttp) cc_final: 0.7975 (ttp) REVERT: c 256 ARG cc_start: 0.8685 (mtp180) cc_final: 0.8358 (ttm-80) REVERT: d 10 ASN cc_start: 0.8583 (t0) cc_final: 0.8066 (t0) REVERT: d 58 LEU cc_start: 0.8496 (mm) cc_final: 0.8254 (mm) REVERT: d 68 MET cc_start: 0.6638 (tmm) cc_final: 0.6146 (tmm) REVERT: d 73 HIS cc_start: 0.8773 (t-90) cc_final: 0.8565 (t-90) REVERT: d 128 LEU cc_start: 0.8219 (mm) cc_final: 0.7971 (mm) REVERT: d 138 LEU cc_start: 0.8310 (tp) cc_final: 0.8026 (tp) REVERT: d 140 PHE cc_start: 0.8782 (m-80) cc_final: 0.8554 (m-80) REVERT: d 154 ILE cc_start: 0.9080 (mm) cc_final: 0.8872 (mm) REVERT: d 159 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7073 (tm-30) REVERT: d 163 ARG cc_start: 0.7173 (mmt90) cc_final: 0.6625 (mmt90) REVERT: d 171 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7568 (mmm160) REVERT: d 210 ARG cc_start: 0.7036 (mtm180) cc_final: 0.6788 (mtm180) REVERT: d 279 ASN cc_start: 0.8796 (m-40) cc_final: 0.8327 (m-40) REVERT: e 39 TYR cc_start: 0.8770 (m-80) cc_final: 0.8529 (m-80) REVERT: e 83 GLN cc_start: 0.7744 (tp-100) cc_final: 0.6811 (tp-100) REVERT: e 96 ASN cc_start: 0.8654 (t0) cc_final: 0.8431 (t0) REVERT: e 135 ASN cc_start: 0.8061 (p0) cc_final: 0.7483 (p0) REVERT: e 155 GLN cc_start: 0.8300 (tp40) cc_final: 0.7540 (tp40) REVERT: e 235 HIS cc_start: 0.8014 (t-90) cc_final: 0.7774 (t-90) REVERT: e 257 GLN cc_start: 0.8512 (tp40) cc_final: 0.7895 (tp40) REVERT: f 48 LEU cc_start: 0.8441 (tt) cc_final: 0.8168 (tt) REVERT: f 54 THR cc_start: 0.8246 (p) cc_final: 0.7525 (p) REVERT: f 73 HIS cc_start: 0.7057 (t-90) cc_final: 0.6831 (t-90) REVERT: f 80 HIS cc_start: 0.8263 (m170) cc_final: 0.7920 (m170) REVERT: f 83 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7885 (tp-100) REVERT: f 89 ASN cc_start: 0.7685 (t0) cc_final: 0.7096 (t0) REVERT: f 155 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7865 (mm-40) REVERT: f 227 ASN cc_start: 0.8576 (m-40) cc_final: 0.8241 (m-40) REVERT: f 230 LEU cc_start: 0.8651 (mt) cc_final: 0.8377 (mt) REVERT: f 257 GLN cc_start: 0.8507 (mt0) cc_final: 0.8087 (mt0) REVERT: f 309 PHE cc_start: 0.8387 (m-80) cc_final: 0.8107 (m-80) outliers start: 8 outliers final: 0 residues processed: 1005 average time/residue: 0.1893 time to fit residues: 289.9637 Evaluate side-chains 975 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 974 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 83 GLN f 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.156894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124080 restraints weight = 52194.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128959 restraints weight = 28768.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132285 restraints weight = 18934.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134484 restraints weight = 14038.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136151 restraints weight = 11363.667| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28333 Z= 0.179 Angle : 0.581 9.848 38529 Z= 0.306 Chirality : 0.043 0.154 4372 Planarity : 0.004 0.063 5022 Dihedral : 4.559 23.577 3840 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 0.23 % Allowed : 3.39 % Favored : 96.38 % 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: -0.59 (0.14), residues: 3442 helix: 0.29 (0.13), residues: 1534 sheet: -0.02 (0.22), residues: 482 loop : -1.20 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 65 TYR 0.020 0.002 TYR E 47 PHE 0.029 0.002 PHE F 294 TRP 0.047 0.002 TRP a 276 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (28333) covalent geometry : angle 0.58065 / 0.31 (38529) hydrogen bonds : bond 0.03642 / 2.42 ( 1173) hydrogen bonds : angle 5.08254 / 3.58 ( 3408) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 988 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7033 (p0) cc_final: 0.6603 (p0) REVERT: A 106 LEU cc_start: 0.7906 (mt) cc_final: 0.7596 (mt) REVERT: A 140 PHE cc_start: 0.7421 (m-10) cc_final: 0.7198 (m-10) REVERT: A 152 PHE cc_start: 0.7775 (m-10) cc_final: 0.7353 (m-10) REVERT: A 211 TRP cc_start: 0.8214 (m100) cc_final: 0.7986 (m100) REVERT: A 248 MET cc_start: 0.7626 (ptt) cc_final: 0.7250 (ptt) REVERT: A 272 THR cc_start: 0.8996 (p) cc_final: 0.7740 (p) REVERT: A 279 ASN cc_start: 0.8359 (m-40) cc_final: 0.7606 (m-40) REVERT: A 284 ASN cc_start: 0.7855 (p0) cc_final: 0.7302 (m110) REVERT: A 311 GLN cc_start: 0.7768 (tp40) cc_final: 0.7511 (tp-100) REVERT: B 10 ASN cc_start: 0.8830 (m-40) cc_final: 0.8524 (m-40) REVERT: B 28 MET cc_start: 0.7627 (tmm) cc_final: 0.7038 (tmm) REVERT: B 47 TYR cc_start: 0.6820 (t80) cc_final: 0.6436 (t80) REVERT: B 63 TYR cc_start: 0.7322 (m-80) cc_final: 0.6883 (m-80) REVERT: B 80 HIS cc_start: 0.8134 (m90) cc_final: 0.7680 (m90) REVERT: B 100 HIS cc_start: 0.8508 (m90) cc_final: 0.8206 (m-70) REVERT: B 123 PHE cc_start: 0.8047 (t80) cc_final: 0.7725 (t80) REVERT: B 149 ASP cc_start: 0.7600 (t0) cc_final: 0.7328 (t0) REVERT: B 238 ASN cc_start: 0.7657 (p0) cc_final: 0.7203 (p0) REVERT: B 296 ASN cc_start: 0.8140 (m110) cc_final: 0.7934 (m110) REVERT: C 10 ASN cc_start: 0.8846 (t0) cc_final: 0.8620 (t0) REVERT: C 83 GLN cc_start: 0.8221 (mt0) cc_final: 0.7962 (tt0) REVERT: C 130 TRP cc_start: 0.8597 (t-100) cc_final: 0.8317 (t-100) REVERT: C 135 ASN cc_start: 0.8345 (p0) cc_final: 0.7436 (p0) REVERT: C 142 GLU cc_start: 0.7146 (mp0) cc_final: 0.6799 (mp0) REVERT: C 147 ARG cc_start: 0.7365 (mpp80) cc_final: 0.6421 (mpt-90) REVERT: C 151 MET cc_start: 0.7098 (mpp) cc_final: 0.6509 (mpp) REVERT: C 158 LEU cc_start: 0.8776 (tp) cc_final: 0.8462 (tp) REVERT: C 248 MET cc_start: 0.8218 (ttt) cc_final: 0.8015 (ttt) REVERT: D 10 ASN cc_start: 0.8418 (t0) cc_final: 0.7801 (t0) REVERT: D 29 MET cc_start: 0.5138 (mmp) cc_final: 0.4714 (mmp) REVERT: D 82 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8331 (mm-30) REVERT: D 125 ASP cc_start: 0.8210 (m-30) cc_final: 0.7985 (m-30) REVERT: D 138 LEU cc_start: 0.8264 (tp) cc_final: 0.8057 (tp) REVERT: D 174 ARG cc_start: 0.7445 (mmp80) cc_final: 0.6889 (mmp80) REVERT: D 279 ASN cc_start: 0.8746 (m110) cc_final: 0.8208 (m110) REVERT: D 288 PHE cc_start: 0.8180 (t80) cc_final: 0.7641 (t80) REVERT: E 47 TYR cc_start: 0.7060 (t80) cc_final: 0.6702 (t80) REVERT: E 52 GLN cc_start: 0.8505 (mt0) cc_final: 0.8009 (mt0) REVERT: E 80 HIS cc_start: 0.8690 (t-170) cc_final: 0.8396 (t-170) REVERT: E 89 ASN cc_start: 0.7806 (t0) cc_final: 0.7085 (t0) REVERT: E 105 ASP cc_start: 0.7536 (t0) cc_final: 0.7287 (t0) REVERT: E 123 PHE cc_start: 0.6869 (p90) cc_final: 0.6629 (p90) REVERT: E 135 ASN cc_start: 0.7750 (p0) cc_final: 0.6552 (p0) REVERT: E 141 ASP cc_start: 0.7233 (t0) cc_final: 0.7006 (t0) REVERT: E 155 GLN cc_start: 0.8104 (tp40) cc_final: 0.7497 (tp40) REVERT: E 181 LEU cc_start: 0.8510 (tt) cc_final: 0.8274 (tt) REVERT: E 208 MET cc_start: 0.7870 (tmm) cc_final: 0.7508 (tmm) REVERT: E 223 ASP cc_start: 0.8337 (m-30) cc_final: 0.8008 (m-30) REVERT: E 235 HIS cc_start: 0.8137 (t-90) cc_final: 0.7919 (t-90) REVERT: E 253 ASP cc_start: 0.8072 (t0) cc_final: 0.7740 (t0) REVERT: E 254 MET cc_start: 0.8329 (mmp) cc_final: 0.7611 (mmp) REVERT: E 257 GLN cc_start: 0.8535 (tp40) cc_final: 0.7939 (tp40) REVERT: E 268 MET cc_start: 0.7686 (tpt) cc_final: 0.7405 (tpt) REVERT: E 303 ARG cc_start: 0.8529 (ttm110) cc_final: 0.8009 (ttm110) REVERT: F 54 THR cc_start: 0.8301 (m) cc_final: 0.7891 (p) REVERT: F 77 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7683 (ptmt) REVERT: F 83 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7790 (mm-40) REVERT: F 89 ASN cc_start: 0.8390 (m110) cc_final: 0.8062 (m-40) REVERT: F 135 ASN cc_start: 0.8756 (p0) cc_final: 0.7969 (p0) REVERT: F 141 ASP cc_start: 0.7601 (t0) cc_final: 0.7024 (t0) REVERT: F 186 ASN cc_start: 0.7457 (m-40) cc_final: 0.7252 (m-40) REVERT: F 230 LEU cc_start: 0.8483 (mt) cc_final: 0.8200 (mt) REVERT: F 245 VAL cc_start: 0.8562 (t) cc_final: 0.8252 (m) REVERT: F 257 GLN cc_start: 0.8355 (tp-100) cc_final: 0.8045 (tp-100) REVERT: a 19 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7487 (mtm110) REVERT: a 50 ASP cc_start: 0.7031 (p0) cc_final: 0.6693 (p0) REVERT: a 68 MET cc_start: 0.6877 (ttp) cc_final: 0.6525 (ttp) REVERT: a 106 LEU cc_start: 0.7973 (mt) cc_final: 0.7631 (mt) REVERT: a 152 PHE cc_start: 0.7540 (m-10) cc_final: 0.7235 (m-10) REVERT: a 158 LEU cc_start: 0.8658 (mp) cc_final: 0.8349 (mp) REVERT: a 244 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7648 (mp) REVERT: a 248 MET cc_start: 0.7949 (mmp) cc_final: 0.7402 (mmp) REVERT: a 256 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7987 (mtp-110) REVERT: a 302 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8058 (mt-10) REVERT: a 305 THR cc_start: 0.8706 (p) cc_final: 0.8316 (p) REVERT: a 306 VAL cc_start: 0.9012 (t) cc_final: 0.8725 (p) REVERT: a 309 PHE cc_start: 0.7567 (m-80) cc_final: 0.6527 (m-80) REVERT: b 10 ASN cc_start: 0.8865 (m-40) cc_final: 0.8619 (m-40) REVERT: b 22 PHE cc_start: 0.7796 (m-10) cc_final: 0.7078 (m-10) REVERT: b 80 HIS cc_start: 0.8421 (m90) cc_final: 0.8167 (m90) REVERT: b 83 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7662 (mm-40) REVERT: b 100 HIS cc_start: 0.8376 (m90) cc_final: 0.7814 (m90) REVERT: b 130 TRP cc_start: 0.8379 (t60) cc_final: 0.8058 (t60) REVERT: b 147 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.7290 (mmt-90) REVERT: b 186 ASN cc_start: 0.6514 (m110) cc_final: 0.6222 (m110) REVERT: c 10 ASN cc_start: 0.7843 (m110) cc_final: 0.7487 (m110) REVERT: c 68 MET cc_start: 0.7447 (ttt) cc_final: 0.7216 (ttt) REVERT: c 75 THR cc_start: 0.7894 (p) cc_final: 0.7633 (p) REVERT: c 102 SER cc_start: 0.8035 (p) cc_final: 0.6999 (p) REVERT: c 105 ASP cc_start: 0.7842 (m-30) cc_final: 0.7621 (m-30) REVERT: c 121 THR cc_start: 0.8547 (m) cc_final: 0.8140 (t) REVERT: c 135 ASN cc_start: 0.8253 (p0) cc_final: 0.7589 (p0) REVERT: c 141 ASP cc_start: 0.7672 (m-30) cc_final: 0.7338 (m-30) REVERT: c 142 GLU cc_start: 0.7768 (mp0) cc_final: 0.7444 (mp0) REVERT: c 155 GLN cc_start: 0.8008 (mt0) cc_final: 0.7105 (mt0) REVERT: c 156 ARG cc_start: 0.8969 (tpt-90) cc_final: 0.8715 (tpt-90) REVERT: c 159 GLU cc_start: 0.7258 (mp0) cc_final: 0.6728 (mp0) REVERT: c 169 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8058 (mm-40) REVERT: c 208 MET cc_start: 0.7010 (mtm) cc_final: 0.6262 (mtm) REVERT: c 244 ILE cc_start: 0.9171 (mm) cc_final: 0.8762 (mm) REVERT: c 254 MET cc_start: 0.8480 (ttp) cc_final: 0.7985 (ttp) REVERT: d 10 ASN cc_start: 0.8516 (t0) cc_final: 0.7954 (t0) REVERT: d 68 MET cc_start: 0.6589 (tmm) cc_final: 0.6100 (tmm) REVERT: d 73 HIS cc_start: 0.8754 (t-90) cc_final: 0.8527 (t-90) REVERT: d 105 ASP cc_start: 0.6930 (t0) cc_final: 0.6619 (t0) REVERT: d 128 LEU cc_start: 0.8184 (mm) cc_final: 0.7911 (mm) REVERT: d 138 LEU cc_start: 0.8322 (tp) cc_final: 0.7971 (tp) REVERT: d 140 PHE cc_start: 0.8798 (m-80) cc_final: 0.8540 (m-80) REVERT: d 154 ILE cc_start: 0.9022 (mm) cc_final: 0.8778 (mm) REVERT: d 163 ARG cc_start: 0.7099 (mmt90) cc_final: 0.6444 (mmt90) REVERT: d 174 ARG cc_start: 0.7702 (mmp80) cc_final: 0.7231 (mmp80) REVERT: d 210 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6882 (mtm180) REVERT: d 279 ASN cc_start: 0.8792 (m-40) cc_final: 0.8336 (m-40) REVERT: e 39 TYR cc_start: 0.8859 (m-80) cc_final: 0.8596 (m-80) REVERT: e 44 ASP cc_start: 0.7791 (t0) cc_final: 0.7573 (t0) REVERT: e 83 GLN cc_start: 0.7763 (tp-100) cc_final: 0.6759 (tp-100) REVERT: e 109 LYS cc_start: 0.8352 (pttp) cc_final: 0.8113 (pttp) REVERT: e 133 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: e 135 ASN cc_start: 0.8167 (p0) cc_final: 0.7794 (p0) REVERT: e 155 GLN cc_start: 0.8303 (tp40) cc_final: 0.7486 (tp40) REVERT: e 235 HIS cc_start: 0.8058 (t-90) cc_final: 0.7756 (t-90) REVERT: e 248 MET cc_start: 0.7816 (mpp) cc_final: 0.7576 (mpp) REVERT: e 257 GLN cc_start: 0.8579 (tp40) cc_final: 0.7964 (tp40) REVERT: f 48 LEU cc_start: 0.8382 (tt) cc_final: 0.8128 (tt) REVERT: f 54 THR cc_start: 0.8269 (p) cc_final: 0.7362 (p) REVERT: f 73 HIS cc_start: 0.7112 (t-90) cc_final: 0.6841 (t-90) REVERT: f 89 ASN cc_start: 0.7641 (t0) cc_final: 0.7043 (t0) REVERT: f 144 ASP cc_start: 0.7949 (p0) cc_final: 0.7747 (p0) REVERT: f 155 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7933 (mm-40) REVERT: f 227 ASN cc_start: 0.8586 (m-40) cc_final: 0.8266 (m-40) REVERT: f 230 LEU cc_start: 0.8684 (mt) cc_final: 0.8403 (mt) REVERT: f 257 GLN cc_start: 0.8511 (mt0) cc_final: 0.8081 (mt0) REVERT: f 309 PHE cc_start: 0.8412 (m-80) cc_final: 0.8131 (m-80) outliers start: 7 outliers final: 0 residues processed: 991 average time/residue: 0.1830 time to fit residues: 276.9885 Evaluate side-chains 962 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 960 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 230 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 307 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 101 optimal weight: 0.0370 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 222 HIS B 169 GLN C 10 ASN C 169 GLN D 100 HIS E 83 GLN ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 134 HIS a 311 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 222 HIS f 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.156636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124163 restraints weight = 52841.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129165 restraints weight = 28784.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132575 restraints weight = 18779.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134799 restraints weight = 13814.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136533 restraints weight = 11089.865| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28333 Z= 0.114 Angle : 0.557 8.980 38529 Z= 0.288 Chirality : 0.042 0.156 4372 Planarity : 0.004 0.060 5022 Dihedral : 4.388 21.338 3840 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3442 helix: 0.42 (0.13), residues: 1527 sheet: 0.03 (0.22), residues: 505 loop : -1.07 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 65 TYR 0.019 0.001 TYR E 47 PHE 0.032 0.002 PHE e 290 TRP 0.045 0.002 TRP f 276 HIS 0.004 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (28333) covalent geometry : angle 0.55704 / 0.29 (38529) hydrogen bonds : bond 0.03134 / 2.07 ( 1173) hydrogen bonds : angle 4.89312 / 3.44 ( 3408) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 984 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6874 (p0) cc_final: 0.6482 (p0) REVERT: A 98 ASP cc_start: 0.7948 (m-30) cc_final: 0.7444 (m-30) REVERT: A 106 LEU cc_start: 0.7850 (mt) cc_final: 0.7548 (mt) REVERT: A 140 PHE cc_start: 0.7447 (m-10) cc_final: 0.7180 (m-10) REVERT: A 152 PHE cc_start: 0.7789 (m-10) cc_final: 0.7379 (m-10) REVERT: A 211 TRP cc_start: 0.8156 (m100) cc_final: 0.7855 (m100) REVERT: A 248 MET cc_start: 0.7589 (ptt) cc_final: 0.7148 (ptt) REVERT: A 279 ASN cc_start: 0.8340 (m-40) cc_final: 0.7583 (m-40) REVERT: A 294 PHE cc_start: 0.7079 (t80) cc_final: 0.6870 (t80) REVERT: A 311 GLN cc_start: 0.7669 (tp40) cc_final: 0.7362 (tp-100) REVERT: B 10 ASN cc_start: 0.8779 (m-40) cc_final: 0.8458 (m-40) REVERT: B 28 MET cc_start: 0.7575 (tmm) cc_final: 0.6995 (tmm) REVERT: B 47 TYR cc_start: 0.6781 (t80) cc_final: 0.6347 (t80) REVERT: B 63 TYR cc_start: 0.7259 (m-80) cc_final: 0.6844 (m-80) REVERT: B 80 HIS cc_start: 0.8130 (m90) cc_final: 0.7628 (m90) REVERT: B 100 HIS cc_start: 0.8463 (m90) cc_final: 0.8166 (m-70) REVERT: B 123 PHE cc_start: 0.8047 (t80) cc_final: 0.7707 (t80) REVERT: B 149 ASP cc_start: 0.7507 (t0) cc_final: 0.7277 (t0) REVERT: B 169 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: B 210 ARG cc_start: 0.7979 (mmp80) cc_final: 0.7675 (mmp80) REVERT: B 238 ASN cc_start: 0.7559 (p0) cc_final: 0.7107 (p0) REVERT: C 10 ASN cc_start: 0.8777 (t160) cc_final: 0.8548 (t0) REVERT: C 65 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.7118 (mmm-85) REVERT: C 83 GLN cc_start: 0.8196 (mt0) cc_final: 0.7943 (tt0) REVERT: C 94 ARG cc_start: 0.8197 (ptt90) cc_final: 0.7967 (ptt90) REVERT: C 100 HIS cc_start: 0.6634 (m-70) cc_final: 0.6031 (m-70) REVERT: C 130 TRP cc_start: 0.8571 (t-100) cc_final: 0.8370 (t-100) REVERT: C 135 ASN cc_start: 0.8288 (p0) cc_final: 0.7407 (p0) REVERT: C 142 GLU cc_start: 0.7128 (mp0) cc_final: 0.6690 (mp0) REVERT: C 147 ARG cc_start: 0.7377 (mpp80) cc_final: 0.6526 (mtt180) REVERT: C 151 MET cc_start: 0.7045 (mpp) cc_final: 0.6478 (mpp) REVERT: C 158 LEU cc_start: 0.8767 (tp) cc_final: 0.8562 (tp) REVERT: C 159 GLU cc_start: 0.7424 (mp0) cc_final: 0.6963 (mp0) REVERT: C 209 ASP cc_start: 0.8339 (t0) cc_final: 0.8135 (t0) REVERT: C 266 THR cc_start: 0.8417 (p) cc_final: 0.8161 (p) REVERT: C 285 ASP cc_start: 0.8460 (p0) cc_final: 0.8248 (p0) REVERT: C 293 THR cc_start: 0.7886 (m) cc_final: 0.7540 (m) REVERT: D 10 ASN cc_start: 0.8506 (t0) cc_final: 0.7843 (t0) REVERT: D 29 MET cc_start: 0.5127 (mmp) cc_final: 0.4731 (mmp) REVERT: D 82 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8271 (mm-30) REVERT: D 106 LEU cc_start: 0.7567 (mm) cc_final: 0.7160 (mp) REVERT: D 125 ASP cc_start: 0.8159 (m-30) cc_final: 0.7938 (m-30) REVERT: D 138 LEU cc_start: 0.8420 (tp) cc_final: 0.8119 (tp) REVERT: D 171 ARG cc_start: 0.7579 (mmm160) cc_final: 0.7245 (mmm-85) REVERT: D 174 ARG cc_start: 0.7396 (mmp80) cc_final: 0.6871 (mmp80) REVERT: D 279 ASN cc_start: 0.8754 (m110) cc_final: 0.8218 (m110) REVERT: D 288 PHE cc_start: 0.8161 (t80) cc_final: 0.7618 (t80) REVERT: E 10 ASN cc_start: 0.7925 (t0) cc_final: 0.7714 (t0) REVERT: E 47 TYR cc_start: 0.7024 (t80) cc_final: 0.6727 (t80) REVERT: E 52 GLN cc_start: 0.8439 (mt0) cc_final: 0.7902 (mt0) REVERT: E 77 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7444 (mtmt) REVERT: E 80 HIS cc_start: 0.8580 (t-170) cc_final: 0.8315 (t-170) REVERT: E 89 ASN cc_start: 0.7696 (t0) cc_final: 0.6965 (t0) REVERT: E 119 GLN cc_start: 0.8077 (pm20) cc_final: 0.7763 (pm20) REVERT: E 123 PHE cc_start: 0.6790 (p90) cc_final: 0.6560 (p90) REVERT: E 135 ASN cc_start: 0.7727 (p0) cc_final: 0.6595 (p0) REVERT: E 141 ASP cc_start: 0.7226 (t0) cc_final: 0.7010 (t0) REVERT: E 155 GLN cc_start: 0.8056 (tp40) cc_final: 0.7420 (tp40) REVERT: E 181 LEU cc_start: 0.8541 (tt) cc_final: 0.8262 (tt) REVERT: E 208 MET cc_start: 0.7764 (tmm) cc_final: 0.7454 (tmm) REVERT: E 223 ASP cc_start: 0.8200 (m-30) cc_final: 0.7897 (m-30) REVERT: E 246 ASN cc_start: 0.8361 (t0) cc_final: 0.8149 (t0) REVERT: E 248 MET cc_start: 0.7912 (mtp) cc_final: 0.7533 (mtp) REVERT: E 253 ASP cc_start: 0.7895 (t0) cc_final: 0.7522 (t0) REVERT: E 254 MET cc_start: 0.8192 (mmp) cc_final: 0.7544 (mmp) REVERT: E 257 GLN cc_start: 0.8427 (tp40) cc_final: 0.7809 (tp40) REVERT: E 268 MET cc_start: 0.7679 (tpt) cc_final: 0.7086 (tpt) REVERT: E 303 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7925 (ttm110) REVERT: F 46 ASP cc_start: 0.8217 (p0) cc_final: 0.8016 (p0) REVERT: F 54 THR cc_start: 0.8354 (m) cc_final: 0.7948 (p) REVERT: F 83 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7779 (mm-40) REVERT: F 89 ASN cc_start: 0.8374 (m110) cc_final: 0.8036 (m-40) REVERT: F 135 ASN cc_start: 0.8734 (p0) cc_final: 0.7963 (p0) REVERT: F 141 ASP cc_start: 0.7576 (t0) cc_final: 0.7076 (t0) REVERT: F 210 ARG cc_start: 0.6939 (ttm-80) cc_final: 0.6561 (ttm-80) REVERT: F 230 LEU cc_start: 0.8429 (mt) cc_final: 0.8160 (mt) REVERT: F 245 VAL cc_start: 0.8383 (t) cc_final: 0.8163 (m) REVERT: F 257 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7975 (tp-100) REVERT: a 19 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7408 (mtm110) REVERT: a 50 ASP cc_start: 0.6848 (p0) cc_final: 0.6466 (p0) REVERT: a 68 MET cc_start: 0.6828 (ttp) cc_final: 0.6535 (ttp) REVERT: a 106 LEU cc_start: 0.7844 (mt) cc_final: 0.7514 (mt) REVERT: a 152 PHE cc_start: 0.7509 (m-10) cc_final: 0.7226 (m-10) REVERT: a 158 LEU cc_start: 0.8659 (mp) cc_final: 0.8392 (mp) REVERT: a 182 PHE cc_start: 0.8091 (m-80) cc_final: 0.7288 (m-80) REVERT: a 244 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7634 (mp) REVERT: a 248 MET cc_start: 0.7847 (mmp) cc_final: 0.7388 (mmt) REVERT: a 256 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7966 (mtp-110) REVERT: a 302 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7984 (mt-10) REVERT: a 306 VAL cc_start: 0.9007 (t) cc_final: 0.8757 (p) REVERT: b 10 ASN cc_start: 0.8797 (m-40) cc_final: 0.8554 (m-40) REVERT: b 69 VAL cc_start: 0.7778 (m) cc_final: 0.7374 (m) REVERT: b 77 LYS cc_start: 0.8300 (mtmt) cc_final: 0.8094 (mtmt) REVERT: b 80 HIS cc_start: 0.8331 (m90) cc_final: 0.8061 (m90) REVERT: b 88 LEU cc_start: 0.8704 (mp) cc_final: 0.8489 (mp) REVERT: b 100 HIS cc_start: 0.8301 (m90) cc_final: 0.7742 (m90) REVERT: b 130 TRP cc_start: 0.8353 (t60) cc_final: 0.8071 (t60) REVERT: b 147 ARG cc_start: 0.7672 (mmt-90) cc_final: 0.7245 (mmt-90) REVERT: b 186 ASN cc_start: 0.6474 (m110) cc_final: 0.6151 (m110) REVERT: b 256 ARG cc_start: 0.8050 (mpt90) cc_final: 0.7609 (mpt90) REVERT: b 291 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7484 (ttt90) REVERT: c 10 ASN cc_start: 0.7775 (m110) cc_final: 0.7429 (m110) REVERT: c 75 THR cc_start: 0.7714 (p) cc_final: 0.7453 (p) REVERT: c 135 ASN cc_start: 0.8196 (p0) cc_final: 0.7537 (p0) REVERT: c 142 GLU cc_start: 0.7687 (mp0) cc_final: 0.7477 (mp0) REVERT: c 151 MET cc_start: 0.7380 (mmm) cc_final: 0.6936 (mmm) REVERT: c 156 ARG cc_start: 0.8979 (tpt-90) cc_final: 0.8670 (tpt-90) REVERT: c 165 THR cc_start: 0.7881 (p) cc_final: 0.7486 (p) REVERT: c 208 MET cc_start: 0.6901 (mtm) cc_final: 0.6224 (mtm) REVERT: c 244 ILE cc_start: 0.9092 (mm) cc_final: 0.8609 (mm) REVERT: c 254 MET cc_start: 0.8455 (ttp) cc_final: 0.8011 (ttp) REVERT: c 256 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.8149 (mtp85) REVERT: d 10 ASN cc_start: 0.8542 (t0) cc_final: 0.7965 (t0) REVERT: d 68 MET cc_start: 0.6615 (tmm) cc_final: 0.6148 (tmm) REVERT: d 73 HIS cc_start: 0.8598 (t-90) cc_final: 0.8364 (t-90) REVERT: d 105 ASP cc_start: 0.6810 (t0) cc_final: 0.6536 (t0) REVERT: d 128 LEU cc_start: 0.8157 (mm) cc_final: 0.7917 (mm) REVERT: d 151 MET cc_start: 0.7551 (tpt) cc_final: 0.7320 (tpt) REVERT: d 156 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8169 (mmm160) REVERT: d 163 ARG cc_start: 0.7033 (mmt90) cc_final: 0.6453 (mmt90) REVERT: d 174 ARG cc_start: 0.7696 (mmp80) cc_final: 0.7278 (mmp80) REVERT: d 210 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6791 (mtm180) REVERT: d 279 ASN cc_start: 0.8810 (m-40) cc_final: 0.8401 (m-40) REVERT: e 28 MET cc_start: 0.8063 (tpt) cc_final: 0.7533 (tpt) REVERT: e 39 TYR cc_start: 0.8822 (m-80) cc_final: 0.8502 (m-80) REVERT: e 44 ASP cc_start: 0.7808 (t0) cc_final: 0.7590 (t0) REVERT: e 83 GLN cc_start: 0.7731 (tp-100) cc_final: 0.6686 (tp-100) REVERT: e 103 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7822 (ttp-110) REVERT: e 135 ASN cc_start: 0.8059 (p0) cc_final: 0.7466 (p0) REVERT: e 154 ILE cc_start: 0.8277 (mm) cc_final: 0.7936 (mm) REVERT: e 155 GLN cc_start: 0.8221 (tp40) cc_final: 0.7443 (tp40) REVERT: e 235 HIS cc_start: 0.8013 (t-90) cc_final: 0.7746 (t-90) REVERT: e 257 GLN cc_start: 0.8519 (tp40) cc_final: 0.7813 (tp40) REVERT: f 48 LEU cc_start: 0.8412 (tt) cc_final: 0.8178 (tt) REVERT: f 54 THR cc_start: 0.8099 (p) cc_final: 0.7118 (p) REVERT: f 69 VAL cc_start: 0.8306 (t) cc_final: 0.7944 (m) REVERT: f 87 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7604 (tpp80) REVERT: f 144 ASP cc_start: 0.7977 (p0) cc_final: 0.7732 (p0) REVERT: f 227 ASN cc_start: 0.8579 (m-40) cc_final: 0.8259 (m-40) REVERT: f 230 LEU cc_start: 0.8648 (mt) cc_final: 0.8362 (mt) REVERT: f 257 GLN cc_start: 0.8468 (mt0) cc_final: 0.7998 (mt0) REVERT: f 309 PHE cc_start: 0.8247 (m-80) cc_final: 0.8035 (m-80) outliers start: 3 outliers final: 0 residues processed: 985 average time/residue: 0.1787 time to fit residues: 268.5426 Evaluate side-chains 951 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 949 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 196 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 173 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS B 169 GLN C 10 ASN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 224 ASN c 73 HIS ** c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127570 restraints weight = 52206.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132540 restraints weight = 28606.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135882 restraints weight = 18813.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138186 restraints weight = 13961.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139839 restraints weight = 11257.440| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28333 Z= 0.115 Angle : 0.554 8.139 38529 Z= 0.286 Chirality : 0.042 0.162 4372 Planarity : 0.004 0.058 5022 Dihedral : 4.323 23.456 3840 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.38 (0.14), residues: 3442 helix: 0.45 (0.13), residues: 1534 sheet: 0.06 (0.22), residues: 498 loop : -1.07 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 87 TYR 0.018 0.001 TYR E 47 PHE 0.028 0.001 PHE e 290 TRP 0.040 0.002 TRP a 276 HIS 0.005 0.001 HIS f 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (28333) covalent geometry : angle 0.55417 / 0.29 (38529) hydrogen bonds : bond 0.03110 / 2.05 ( 1173) hydrogen bonds : angle 4.86613 / 3.42 ( 3408) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 993 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5099 (pmm) cc_final: 0.4835 (pmm) REVERT: A 50 ASP cc_start: 0.6859 (p0) cc_final: 0.6464 (p0) REVERT: A 98 ASP cc_start: 0.8000 (m-30) cc_final: 0.7461 (m-30) REVERT: A 106 LEU cc_start: 0.7884 (mt) cc_final: 0.7590 (mt) REVERT: A 140 PHE cc_start: 0.7398 (m-10) cc_final: 0.7139 (m-10) REVERT: A 152 PHE cc_start: 0.7807 (m-10) cc_final: 0.7366 (m-10) REVERT: A 174 ARG cc_start: 0.8197 (mmp80) cc_final: 0.7974 (mmp80) REVERT: A 248 MET cc_start: 0.7597 (ptt) cc_final: 0.7208 (ptt) REVERT: A 272 THR cc_start: 0.9025 (p) cc_final: 0.7839 (p) REVERT: A 279 ASN cc_start: 0.8273 (m-40) cc_final: 0.7538 (m-40) REVERT: A 303 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7692 (mmt-90) REVERT: A 306 VAL cc_start: 0.8895 (t) cc_final: 0.8498 (m) REVERT: A 311 GLN cc_start: 0.7642 (tp40) cc_final: 0.7341 (tp-100) REVERT: B 10 ASN cc_start: 0.8763 (m-40) cc_final: 0.8458 (m-40) REVERT: B 28 MET cc_start: 0.7590 (tmm) cc_final: 0.7103 (tmm) REVERT: B 47 TYR cc_start: 0.6782 (t80) cc_final: 0.6316 (t80) REVERT: B 63 TYR cc_start: 0.7246 (m-80) cc_final: 0.6674 (m-80) REVERT: B 80 HIS cc_start: 0.8086 (m90) cc_final: 0.7601 (m90) REVERT: B 100 HIS cc_start: 0.8475 (m90) cc_final: 0.8197 (m-70) REVERT: B 123 PHE cc_start: 0.8049 (t80) cc_final: 0.7717 (t80) REVERT: B 210 ARG cc_start: 0.7960 (mmp80) cc_final: 0.7636 (mmp80) REVERT: B 238 ASN cc_start: 0.7546 (p0) cc_final: 0.7079 (p0) REVERT: B 268 MET cc_start: 0.8442 (tmm) cc_final: 0.8216 (tmm) REVERT: C 68 MET cc_start: 0.7539 (ttt) cc_final: 0.7277 (ttt) REVERT: C 83 GLN cc_start: 0.8207 (mt0) cc_final: 0.7931 (tt0) REVERT: C 100 HIS cc_start: 0.6666 (m-70) cc_final: 0.5981 (m-70) REVERT: C 130 TRP cc_start: 0.8530 (t-100) cc_final: 0.8283 (t-100) REVERT: C 135 ASN cc_start: 0.8307 (p0) cc_final: 0.7449 (p0) REVERT: C 141 ASP cc_start: 0.7070 (t0) cc_final: 0.5764 (t0) REVERT: C 142 GLU cc_start: 0.7148 (mp0) cc_final: 0.6046 (mp0) REVERT: C 144 ASP cc_start: 0.7424 (p0) cc_final: 0.7113 (p0) REVERT: C 147 ARG cc_start: 0.7288 (mpp80) cc_final: 0.6476 (mtt180) REVERT: C 151 MET cc_start: 0.7038 (mpp) cc_final: 0.6438 (mpp) REVERT: C 159 GLU cc_start: 0.7357 (mp0) cc_final: 0.6810 (mp0) REVERT: C 168 ASP cc_start: 0.8304 (t0) cc_final: 0.7309 (t0) REVERT: C 209 ASP cc_start: 0.8369 (t0) cc_final: 0.8144 (t0) REVERT: C 266 THR cc_start: 0.8395 (p) cc_final: 0.8065 (p) REVERT: C 293 THR cc_start: 0.7909 (m) cc_final: 0.7567 (m) REVERT: D 10 ASN cc_start: 0.8510 (t0) cc_final: 0.7839 (t0) REVERT: D 29 MET cc_start: 0.5114 (mmp) cc_final: 0.4673 (mmp) REVERT: D 82 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8284 (mm-30) REVERT: D 125 ASP cc_start: 0.8144 (m-30) cc_final: 0.7912 (m-30) REVERT: D 138 LEU cc_start: 0.8419 (tp) cc_final: 0.8113 (tp) REVERT: D 171 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7217 (mmm-85) REVERT: D 174 ARG cc_start: 0.7389 (mmp80) cc_final: 0.6823 (mmp80) REVERT: D 279 ASN cc_start: 0.8762 (m110) cc_final: 0.8199 (m110) REVERT: D 288 PHE cc_start: 0.8163 (t80) cc_final: 0.7646 (t80) REVERT: E 10 ASN cc_start: 0.7956 (t0) cc_final: 0.7715 (t0) REVERT: E 47 TYR cc_start: 0.7018 (t80) cc_final: 0.6774 (t80) REVERT: E 52 GLN cc_start: 0.8422 (mt0) cc_final: 0.7900 (mt0) REVERT: E 80 HIS cc_start: 0.8545 (t-170) cc_final: 0.8336 (t-170) REVERT: E 83 GLN cc_start: 0.8179 (tt0) cc_final: 0.6385 (tt0) REVERT: E 89 ASN cc_start: 0.7678 (t0) cc_final: 0.7241 (t0) REVERT: E 123 PHE cc_start: 0.6799 (p90) cc_final: 0.6571 (p90) REVERT: E 135 ASN cc_start: 0.7772 (p0) cc_final: 0.6594 (p0) REVERT: E 155 GLN cc_start: 0.8091 (tp40) cc_final: 0.7467 (tp40) REVERT: E 181 LEU cc_start: 0.8493 (tt) cc_final: 0.8235 (tt) REVERT: E 182 PHE cc_start: 0.7675 (m-80) cc_final: 0.7015 (m-80) REVERT: E 208 MET cc_start: 0.7726 (tmm) cc_final: 0.7417 (tmm) REVERT: E 217 LEU cc_start: 0.8544 (tt) cc_final: 0.8292 (tt) REVERT: E 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7942 (m-30) REVERT: E 235 HIS cc_start: 0.8147 (t-90) cc_final: 0.7904 (t-90) REVERT: E 248 MET cc_start: 0.7932 (mtp) cc_final: 0.7590 (mtp) REVERT: E 254 MET cc_start: 0.8264 (mmp) cc_final: 0.7611 (mmp) REVERT: E 257 GLN cc_start: 0.8473 (tp40) cc_final: 0.8220 (tp40) REVERT: E 268 MET cc_start: 0.7691 (tpt) cc_final: 0.7148 (tpt) REVERT: E 303 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7952 (ttm110) REVERT: F 77 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7556 (ptmt) REVERT: F 83 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7752 (mm-40) REVERT: F 89 ASN cc_start: 0.8339 (m110) cc_final: 0.8000 (m-40) REVERT: F 135 ASN cc_start: 0.8723 (p0) cc_final: 0.7946 (p0) REVERT: F 141 ASP cc_start: 0.7637 (t0) cc_final: 0.6516 (t0) REVERT: F 210 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6567 (ttm-80) REVERT: F 230 LEU cc_start: 0.8469 (mt) cc_final: 0.8199 (mt) REVERT: F 238 ASN cc_start: 0.7770 (p0) cc_final: 0.7183 (p0) REVERT: F 245 VAL cc_start: 0.8394 (t) cc_final: 0.8114 (m) REVERT: F 257 GLN cc_start: 0.8327 (tp-100) cc_final: 0.8037 (tp-100) REVERT: F 268 MET cc_start: 0.7299 (mmp) cc_final: 0.6936 (mmp) REVERT: a 19 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7420 (mtm110) REVERT: a 50 ASP cc_start: 0.6829 (p0) cc_final: 0.6444 (p0) REVERT: a 68 MET cc_start: 0.6831 (ttp) cc_final: 0.6597 (ttp) REVERT: a 106 LEU cc_start: 0.7873 (mt) cc_final: 0.7561 (mt) REVERT: a 152 PHE cc_start: 0.7521 (m-10) cc_final: 0.7295 (m-10) REVERT: a 182 PHE cc_start: 0.8080 (m-80) cc_final: 0.7324 (m-80) REVERT: a 244 ILE cc_start: 0.8354 (mp) cc_final: 0.7691 (mp) REVERT: a 248 MET cc_start: 0.7823 (mmp) cc_final: 0.7333 (mmt) REVERT: a 256 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: a 302 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7998 (mt-10) REVERT: a 306 VAL cc_start: 0.9020 (t) cc_final: 0.8789 (p) REVERT: b 10 ASN cc_start: 0.8777 (m-40) cc_final: 0.8549 (m-40) REVERT: b 69 VAL cc_start: 0.7738 (m) cc_final: 0.7331 (m) REVERT: b 77 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8072 (mtmt) REVERT: b 80 HIS cc_start: 0.8345 (m90) cc_final: 0.8055 (m90) REVERT: b 83 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7367 (mm-40) REVERT: b 100 HIS cc_start: 0.8285 (m90) cc_final: 0.7703 (m90) REVERT: b 130 TRP cc_start: 0.8357 (t60) cc_final: 0.8117 (t60) REVERT: b 147 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7170 (mmt-90) REVERT: b 168 ASP cc_start: 0.8346 (t0) cc_final: 0.6651 (t0) REVERT: b 186 ASN cc_start: 0.6479 (m110) cc_final: 0.6144 (m110) REVERT: b 208 MET cc_start: 0.8002 (tpp) cc_final: 0.7774 (mmm) REVERT: b 256 ARG cc_start: 0.8099 (mpt90) cc_final: 0.7719 (mpt90) REVERT: b 291 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7523 (ttt90) REVERT: c 10 ASN cc_start: 0.7773 (m110) cc_final: 0.7426 (m110) REVERT: c 28 MET cc_start: 0.5086 (mtm) cc_final: 0.4884 (mtm) REVERT: c 75 THR cc_start: 0.7587 (p) cc_final: 0.7357 (p) REVERT: c 100 HIS cc_start: 0.6556 (m-70) cc_final: 0.5776 (m-70) REVERT: c 102 SER cc_start: 0.7914 (p) cc_final: 0.6824 (p) REVERT: c 130 TRP cc_start: 0.8765 (t60) cc_final: 0.8424 (t60) REVERT: c 135 ASN cc_start: 0.8256 (p0) cc_final: 0.7589 (p0) REVERT: c 136 VAL cc_start: 0.8685 (p) cc_final: 0.8448 (p) REVERT: c 156 ARG cc_start: 0.8981 (tpt-90) cc_final: 0.8647 (tpp80) REVERT: c 159 GLU cc_start: 0.7095 (mp0) cc_final: 0.6723 (mp0) REVERT: c 165 THR cc_start: 0.7738 (p) cc_final: 0.7455 (p) REVERT: c 208 MET cc_start: 0.6976 (mtm) cc_final: 0.6257 (mtm) REVERT: c 244 ILE cc_start: 0.9126 (mm) cc_final: 0.8687 (mm) REVERT: c 254 MET cc_start: 0.8445 (ttp) cc_final: 0.7954 (ttp) REVERT: d 10 ASN cc_start: 0.8518 (t0) cc_final: 0.7918 (t0) REVERT: d 68 MET cc_start: 0.6618 (tmm) cc_final: 0.6109 (tmm) REVERT: d 69 VAL cc_start: 0.7612 (m) cc_final: 0.7385 (t) REVERT: d 73 HIS cc_start: 0.8569 (t-90) cc_final: 0.8329 (t-90) REVERT: d 105 ASP cc_start: 0.6818 (t0) cc_final: 0.6562 (t0) REVERT: d 151 MET cc_start: 0.7535 (tpt) cc_final: 0.7306 (tpt) REVERT: d 156 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8137 (mmm160) REVERT: d 163 ARG cc_start: 0.7024 (mmt90) cc_final: 0.6370 (mmt90) REVERT: d 166 LEU cc_start: 0.7509 (mm) cc_final: 0.7302 (mm) REVERT: d 174 ARG cc_start: 0.7723 (mmp80) cc_final: 0.7203 (mmp80) REVERT: d 210 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6733 (mtm180) REVERT: d 279 ASN cc_start: 0.8783 (m-40) cc_final: 0.8379 (m-40) REVERT: e 28 MET cc_start: 0.8142 (tpt) cc_final: 0.7581 (tpt) REVERT: e 39 TYR cc_start: 0.8842 (m-80) cc_final: 0.8516 (m-80) REVERT: e 44 ASP cc_start: 0.7841 (t0) cc_final: 0.7623 (t0) REVERT: e 77 LYS cc_start: 0.7985 (pttm) cc_final: 0.7465 (pttm) REVERT: e 83 GLN cc_start: 0.7712 (tp-100) cc_final: 0.6643 (tp-100) REVERT: e 103 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7762 (ttp-170) REVERT: e 135 ASN cc_start: 0.8056 (p0) cc_final: 0.7398 (p0) REVERT: e 155 GLN cc_start: 0.8286 (tp40) cc_final: 0.7490 (tp40) REVERT: e 166 LEU cc_start: 0.8279 (mm) cc_final: 0.7940 (mm) REVERT: e 235 HIS cc_start: 0.8046 (t-90) cc_final: 0.7747 (t-90) REVERT: e 248 MET cc_start: 0.7765 (mpp) cc_final: 0.7544 (mpp) REVERT: e 257 GLN cc_start: 0.8533 (tp40) cc_final: 0.7804 (tp40) REVERT: f 54 THR cc_start: 0.8054 (p) cc_final: 0.7208 (p) REVERT: f 77 LYS cc_start: 0.8650 (pttm) cc_final: 0.8201 (pttm) REVERT: f 141 ASP cc_start: 0.7161 (t0) cc_final: 0.5944 (t0) REVERT: f 144 ASP cc_start: 0.7952 (p0) cc_final: 0.7680 (p0) REVERT: f 217 LEU cc_start: 0.6906 (tt) cc_final: 0.6601 (mt) REVERT: f 227 ASN cc_start: 0.8587 (m-40) cc_final: 0.8269 (m-40) REVERT: f 230 LEU cc_start: 0.8671 (mt) cc_final: 0.8383 (mt) REVERT: f 254 MET cc_start: 0.8258 (ttm) cc_final: 0.8057 (ttm) REVERT: f 257 GLN cc_start: 0.8511 (mt0) cc_final: 0.8043 (mt0) outliers start: 0 outliers final: 0 residues processed: 993 average time/residue: 0.1859 time to fit residues: 281.2284 Evaluate side-chains 955 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 955 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 184 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS A 284 ASN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN d 100 HIS ** e 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121576 restraints weight = 52571.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126477 restraints weight = 28894.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129747 restraints weight = 19044.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131962 restraints weight = 14147.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133251 restraints weight = 11436.945| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28333 Z= 0.227 Angle : 0.630 12.312 38529 Z= 0.334 Chirality : 0.044 0.194 4372 Planarity : 0.005 0.082 5022 Dihedral : 4.641 25.085 3840 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.71 % Favored : 93.17 % Rotamer: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.05 % 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: -0.65 (0.14), residues: 3442 helix: 0.28 (0.13), residues: 1537 sheet: -0.17 (0.22), residues: 480 loop : -1.24 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 65 TYR 0.028 0.002 TYR f 132 PHE 0.029 0.002 PHE f 309 TRP 0.064 0.003 TRP F 276 HIS 0.006 0.001 HIS F 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 (28333) covalent geometry : angle 0.63022 / 0.33 (38529) hydrogen bonds : bond 0.03872 / 2.55 ( 1173) hydrogen bonds : angle 5.15042 / 3.64 ( 3408) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1016 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8088 (t) cc_final: 0.7737 (m) REVERT: A 50 ASP cc_start: 0.7131 (p0) cc_final: 0.6786 (p0) REVERT: A 95 VAL cc_start: 0.8250 (p) cc_final: 0.8045 (t) REVERT: A 98 ASP cc_start: 0.8121 (m-30) cc_final: 0.7679 (m-30) REVERT: A 106 LEU cc_start: 0.7939 (mt) cc_final: 0.7622 (mt) REVERT: A 152 PHE cc_start: 0.7821 (m-10) cc_final: 0.7367 (m-10) REVERT: A 248 MET cc_start: 0.7727 (ptt) cc_final: 0.7250 (ptt) REVERT: A 279 ASN cc_start: 0.8321 (m-40) cc_final: 0.7590 (m-40) REVERT: A 306 VAL cc_start: 0.8940 (t) cc_final: 0.8610 (m) REVERT: A 311 GLN cc_start: 0.7639 (tp40) cc_final: 0.7326 (tp-100) REVERT: B 10 ASN cc_start: 0.8848 (m-40) cc_final: 0.8553 (m-40) REVERT: B 28 MET cc_start: 0.7601 (tmm) cc_final: 0.6950 (tmm) REVERT: B 47 TYR cc_start: 0.6898 (t80) cc_final: 0.6378 (t80) REVERT: B 63 TYR cc_start: 0.7061 (m-80) cc_final: 0.6737 (m-80) REVERT: B 65 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6099 (ttp80) REVERT: B 77 LYS cc_start: 0.8624 (ptpt) cc_final: 0.8180 (ptpt) REVERT: B 80 HIS cc_start: 0.8118 (m90) cc_final: 0.7600 (m90) REVERT: B 100 HIS cc_start: 0.8574 (m90) cc_final: 0.8323 (m-70) REVERT: B 123 PHE cc_start: 0.8123 (t80) cc_final: 0.7591 (t80) REVERT: B 171 ARG cc_start: 0.7167 (ptt180) cc_final: 0.6457 (ptt180) REVERT: B 213 ILE cc_start: 0.7324 (mp) cc_final: 0.6889 (mp) REVERT: B 238 ASN cc_start: 0.7711 (p0) cc_final: 0.7213 (p0) REVERT: B 296 ASN cc_start: 0.8157 (m110) cc_final: 0.7939 (m110) REVERT: C 68 MET cc_start: 0.7594 (ttt) cc_final: 0.7306 (ttt) REVERT: C 83 GLN cc_start: 0.8268 (mt0) cc_final: 0.7989 (tt0) REVERT: C 94 ARG cc_start: 0.8263 (ptt90) cc_final: 0.8047 (ptt90) REVERT: C 130 TRP cc_start: 0.8658 (t-100) cc_final: 0.8364 (t-100) REVERT: C 135 ASN cc_start: 0.8302 (p0) cc_final: 0.7460 (p0) REVERT: C 142 GLU cc_start: 0.7241 (mp0) cc_final: 0.6908 (mp0) REVERT: C 144 ASP cc_start: 0.7527 (p0) cc_final: 0.7315 (p0) REVERT: C 169 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7919 (mm110) REVERT: C 209 ASP cc_start: 0.8469 (t0) cc_final: 0.8216 (t0) REVERT: D 10 ASN cc_start: 0.8457 (t0) cc_final: 0.7859 (t0) REVERT: D 29 MET cc_start: 0.5107 (mmp) cc_final: 0.4665 (mmp) REVERT: D 82 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 125 ASP cc_start: 0.8195 (m-30) cc_final: 0.7993 (m-30) REVERT: D 138 LEU cc_start: 0.8403 (tp) cc_final: 0.8105 (tp) REVERT: D 174 ARG cc_start: 0.7457 (mmp80) cc_final: 0.6958 (mmp80) REVERT: D 279 ASN cc_start: 0.8789 (m110) cc_final: 0.8266 (m110) REVERT: D 288 PHE cc_start: 0.8179 (t80) cc_final: 0.7664 (t80) REVERT: E 10 ASN cc_start: 0.8166 (t0) cc_final: 0.7929 (t0) REVERT: E 22 PHE cc_start: 0.8638 (m-10) cc_final: 0.8383 (m-10) REVERT: E 47 TYR cc_start: 0.7039 (t80) cc_final: 0.6767 (t80) REVERT: E 52 GLN cc_start: 0.8495 (mt0) cc_final: 0.7990 (mt0) REVERT: E 80 HIS cc_start: 0.8654 (t-170) cc_final: 0.8401 (t-170) REVERT: E 89 ASN cc_start: 0.7602 (t0) cc_final: 0.7212 (t0) REVERT: E 123 PHE cc_start: 0.6847 (p90) cc_final: 0.6619 (p90) REVERT: E 135 ASN cc_start: 0.7826 (p0) cc_final: 0.6677 (p0) REVERT: E 155 GLN cc_start: 0.8134 (tp40) cc_final: 0.7475 (tp40) REVERT: E 181 LEU cc_start: 0.8488 (tt) cc_final: 0.8168 (tt) REVERT: E 217 LEU cc_start: 0.8610 (tt) cc_final: 0.8398 (tt) REVERT: E 223 ASP cc_start: 0.8293 (m-30) cc_final: 0.8026 (m-30) REVERT: E 235 HIS cc_start: 0.8233 (t-90) cc_final: 0.7976 (t-90) REVERT: E 246 ASN cc_start: 0.8415 (t0) cc_final: 0.8174 (t0) REVERT: E 253 ASP cc_start: 0.7967 (t0) cc_final: 0.7748 (t0) REVERT: E 254 MET cc_start: 0.8352 (mmp) cc_final: 0.7681 (mmp) REVERT: E 257 GLN cc_start: 0.8508 (tp40) cc_final: 0.7875 (tp40) REVERT: E 268 MET cc_start: 0.7769 (tpt) cc_final: 0.7488 (tpt) REVERT: E 294 PHE cc_start: 0.8880 (t80) cc_final: 0.8643 (t80) REVERT: E 303 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8033 (ttm110) REVERT: F 58 LEU cc_start: 0.8651 (mt) cc_final: 0.8377 (mt) REVERT: F 83 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7806 (mm-40) REVERT: F 89 ASN cc_start: 0.8378 (m110) cc_final: 0.8014 (m-40) REVERT: F 135 ASN cc_start: 0.8722 (p0) cc_final: 0.7852 (p0) REVERT: F 141 ASP cc_start: 0.7715 (t0) cc_final: 0.7295 (t0) REVERT: F 144 ASP cc_start: 0.7668 (p0) cc_final: 0.7282 (p0) REVERT: F 230 LEU cc_start: 0.8507 (mt) cc_final: 0.8258 (mt) REVERT: F 245 VAL cc_start: 0.8588 (t) cc_final: 0.8288 (m) REVERT: F 257 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8029 (tp-100) REVERT: a 19 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7464 (mtm110) REVERT: a 50 ASP cc_start: 0.7160 (p0) cc_final: 0.6859 (p0) REVERT: a 68 MET cc_start: 0.6875 (ttp) cc_final: 0.6570 (ttp) REVERT: a 106 LEU cc_start: 0.8028 (mt) cc_final: 0.7687 (mt) REVERT: a 152 PHE cc_start: 0.7548 (m-10) cc_final: 0.7343 (m-10) REVERT: a 244 ILE cc_start: 0.8372 (mp) cc_final: 0.7620 (mp) REVERT: a 248 MET cc_start: 0.7895 (mmp) cc_final: 0.7481 (mmt) REVERT: a 256 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8028 (mtp-110) REVERT: a 302 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8078 (mt-10) REVERT: a 306 VAL cc_start: 0.9054 (t) cc_final: 0.8769 (p) REVERT: b 10 ASN cc_start: 0.8843 (m-40) cc_final: 0.8637 (m-40) REVERT: b 63 TYR cc_start: 0.7718 (m-80) cc_final: 0.7314 (m-80) REVERT: b 69 VAL cc_start: 0.7842 (m) cc_final: 0.7344 (m) REVERT: b 77 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8055 (mtmt) REVERT: b 80 HIS cc_start: 0.8454 (m90) cc_final: 0.8181 (m90) REVERT: b 83 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7621 (mm-40) REVERT: b 100 HIS cc_start: 0.8415 (m90) cc_final: 0.7830 (m90) REVERT: b 104 ILE cc_start: 0.8779 (mt) cc_final: 0.8494 (mm) REVERT: b 127 ILE cc_start: 0.8758 (pt) cc_final: 0.8550 (pt) REVERT: b 130 TRP cc_start: 0.8424 (t60) cc_final: 0.8130 (t60) REVERT: b 141 ASP cc_start: 0.6682 (t70) cc_final: 0.6159 (t70) REVERT: b 147 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7390 (mmt-90) REVERT: b 168 ASP cc_start: 0.8464 (t0) cc_final: 0.6664 (t0) REVERT: b 214 VAL cc_start: 0.7291 (p) cc_final: 0.7079 (m) REVERT: b 248 MET cc_start: 0.7143 (mpp) cc_final: 0.6933 (mpp) REVERT: b 256 ARG cc_start: 0.8064 (mpt90) cc_final: 0.7756 (mpt90) REVERT: b 291 ARG cc_start: 0.8110 (ttt90) cc_final: 0.7645 (ttt90) REVERT: c 10 ASN cc_start: 0.7875 (m110) cc_final: 0.7529 (m110) REVERT: c 65 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7248 (mmm-85) REVERT: c 75 THR cc_start: 0.8026 (p) cc_final: 0.7710 (p) REVERT: c 100 HIS cc_start: 0.6584 (m-70) cc_final: 0.5723 (m-70) REVERT: c 130 TRP cc_start: 0.8904 (t60) cc_final: 0.8590 (t60) REVERT: c 135 ASN cc_start: 0.8334 (p0) cc_final: 0.7722 (p0) REVERT: c 136 VAL cc_start: 0.8742 (p) cc_final: 0.8529 (p) REVERT: c 141 ASP cc_start: 0.7786 (m-30) cc_final: 0.7500 (m-30) REVERT: c 142 GLU cc_start: 0.7822 (mp0) cc_final: 0.7518 (mp0) REVERT: c 147 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6856 (mtt180) REVERT: c 149 ASP cc_start: 0.7105 (t0) cc_final: 0.6865 (t0) REVERT: c 156 ARG cc_start: 0.8984 (tpt-90) cc_final: 0.8650 (tpt-90) REVERT: c 159 GLU cc_start: 0.7233 (mp0) cc_final: 0.6643 (mp0) REVERT: c 165 THR cc_start: 0.7978 (p) cc_final: 0.7524 (p) REVERT: c 208 MET cc_start: 0.7034 (mtm) cc_final: 0.6311 (mtm) REVERT: c 209 ASP cc_start: 0.8068 (t0) cc_final: 0.7756 (t0) REVERT: c 244 ILE cc_start: 0.9134 (mm) cc_final: 0.8709 (mm) REVERT: c 254 MET cc_start: 0.8454 (ttp) cc_final: 0.7964 (ttp) REVERT: d 10 ASN cc_start: 0.8421 (t0) cc_final: 0.7853 (t0) REVERT: d 68 MET cc_start: 0.6612 (tmm) cc_final: 0.6110 (tmm) REVERT: d 154 ILE cc_start: 0.9039 (mm) cc_final: 0.8644 (mm) REVERT: d 156 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8138 (mmm160) REVERT: d 159 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6939 (tm-30) REVERT: d 163 ARG cc_start: 0.7073 (mmt90) cc_final: 0.6417 (mmt90) REVERT: d 174 ARG cc_start: 0.7753 (mmp80) cc_final: 0.7218 (mmp80) REVERT: d 182 PHE cc_start: 0.8158 (m-80) cc_final: 0.7835 (m-10) REVERT: d 210 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6875 (mtm180) REVERT: d 276 TRP cc_start: 0.8212 (t60) cc_final: 0.7595 (t60) REVERT: d 279 ASN cc_start: 0.8825 (m-40) cc_final: 0.8401 (m-40) REVERT: e 28 MET cc_start: 0.8252 (tpt) cc_final: 0.7739 (tpt) REVERT: e 39 TYR cc_start: 0.8913 (m-80) cc_final: 0.8661 (m-80) REVERT: e 44 ASP cc_start: 0.7876 (t0) cc_final: 0.7633 (t0) REVERT: e 83 GLN cc_start: 0.7770 (tp-100) cc_final: 0.6697 (tp-100) REVERT: e 96 ASN cc_start: 0.8729 (t0) cc_final: 0.8515 (t0) REVERT: e 109 LYS cc_start: 0.8357 (pttp) cc_final: 0.8154 (pttp) REVERT: e 135 ASN cc_start: 0.8201 (p0) cc_final: 0.7549 (p0) REVERT: e 151 MET cc_start: 0.8124 (mmm) cc_final: 0.7806 (tpp) REVERT: e 155 GLN cc_start: 0.8349 (tp40) cc_final: 0.7539 (tp40) REVERT: e 166 LEU cc_start: 0.8331 (mm) cc_final: 0.8053 (mm) REVERT: e 235 HIS cc_start: 0.8116 (t-90) cc_final: 0.7809 (t-90) REVERT: e 248 MET cc_start: 0.7835 (mpp) cc_final: 0.7588 (mpp) REVERT: e 253 ASP cc_start: 0.8240 (t0) cc_final: 0.8010 (t0) REVERT: e 257 GLN cc_start: 0.8590 (tp40) cc_final: 0.7900 (tp40) REVERT: f 54 THR cc_start: 0.8241 (p) cc_final: 0.7456 (p) REVERT: f 77 LYS cc_start: 0.8666 (pttm) cc_final: 0.8213 (pttm) REVERT: f 89 ASN cc_start: 0.7624 (t0) cc_final: 0.7035 (t0) REVERT: f 98 ASP cc_start: 0.6313 (t0) cc_final: 0.6042 (t0) REVERT: f 141 ASP cc_start: 0.7451 (t0) cc_final: 0.6026 (t0) REVERT: f 144 ASP cc_start: 0.8018 (p0) cc_final: 0.7770 (p0) REVERT: f 227 ASN cc_start: 0.8620 (m-40) cc_final: 0.8319 (m-40) REVERT: f 230 LEU cc_start: 0.8740 (mt) cc_final: 0.8456 (mt) REVERT: f 254 MET cc_start: 0.8375 (ttm) cc_final: 0.8116 (ttm) REVERT: f 257 GLN cc_start: 0.8564 (mt0) cc_final: 0.8194 (mt0) REVERT: f 268 MET cc_start: 0.8114 (mmp) cc_final: 0.7599 (mmp) REVERT: f 294 PHE cc_start: 0.6987 (t80) cc_final: 0.6771 (t80) REVERT: f 309 PHE cc_start: 0.8356 (m-80) cc_final: 0.8113 (m-80) outliers start: 1 outliers final: 0 residues processed: 1016 average time/residue: 0.1776 time to fit residues: 276.3961 Evaluate side-chains 983 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 983 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 276 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 344 optimal weight: 0.6980 chunk 204 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 326 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS B 169 GLN C 296 ASN D 155 GLN E 83 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS a 133 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 GLN b 222 HIS d 222 HIS f 52 GLN ** f 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.158942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127225 restraints weight = 52395.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131865 restraints weight = 29748.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135012 restraints weight = 19948.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137120 restraints weight = 14970.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138516 restraints weight = 12243.009| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28333 Z= 0.117 Angle : 0.587 9.395 38529 Z= 0.302 Chirality : 0.043 0.180 4372 Planarity : 0.004 0.058 5022 Dihedral : 4.441 21.194 3840 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -0.46 (0.14), residues: 3442 helix: 0.42 (0.13), residues: 1529 sheet: -0.12 (0.22), residues: 502 loop : -1.10 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG f 250 TYR 0.018 0.001 TYR f 132 PHE 0.037 0.002 PHE a 288 TRP 0.048 0.002 TRP a 276 HIS 0.006 0.001 HIS c 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (28333) covalent geometry : angle 0.58729 / 0.30 (38529) hydrogen bonds : bond 0.03221 / 2.12 ( 1173) hydrogen bonds : angle 4.90465 / 3.46 ( 3408) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1007 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5036 (pmm) cc_final: 0.4830 (pmm) REVERT: A 50 ASP cc_start: 0.6902 (p0) cc_final: 0.6540 (p0) REVERT: A 95 VAL cc_start: 0.8251 (p) cc_final: 0.7644 (m) REVERT: A 98 ASP cc_start: 0.8101 (m-30) cc_final: 0.7637 (m-30) REVERT: A 106 LEU cc_start: 0.7918 (mt) cc_final: 0.7590 (mt) REVERT: A 140 PHE cc_start: 0.7411 (m-10) cc_final: 0.7196 (m-10) REVERT: A 152 PHE cc_start: 0.7787 (m-10) cc_final: 0.7366 (m-10) REVERT: A 174 ARG cc_start: 0.8197 (mmp80) cc_final: 0.7948 (mmp80) REVERT: A 211 TRP cc_start: 0.8016 (m100) cc_final: 0.7786 (m100) REVERT: A 248 MET cc_start: 0.7618 (ptt) cc_final: 0.7110 (ptt) REVERT: A 249 VAL cc_start: 0.7910 (t) cc_final: 0.7662 (p) REVERT: A 272 THR cc_start: 0.9006 (p) cc_final: 0.8029 (p) REVERT: A 279 ASN cc_start: 0.8247 (m-40) cc_final: 0.7484 (m-40) REVERT: A 311 GLN cc_start: 0.7621 (tp40) cc_final: 0.7351 (tp-100) REVERT: B 10 ASN cc_start: 0.8787 (m-40) cc_final: 0.8488 (m-40) REVERT: B 28 MET cc_start: 0.7574 (tmm) cc_final: 0.7070 (tmm) REVERT: B 63 TYR cc_start: 0.6944 (m-80) cc_final: 0.6688 (m-80) REVERT: B 65 ARG cc_start: 0.7329 (ttp80) cc_final: 0.6715 (ttp80) REVERT: B 77 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8187 (ptpt) REVERT: B 80 HIS cc_start: 0.7897 (m90) cc_final: 0.7507 (m90) REVERT: B 123 PHE cc_start: 0.8088 (t80) cc_final: 0.7609 (t80) REVERT: B 171 ARG cc_start: 0.7018 (ptt180) cc_final: 0.6401 (ptt180) REVERT: B 213 ILE cc_start: 0.7104 (mp) cc_final: 0.6662 (mp) REVERT: B 238 ASN cc_start: 0.7592 (p0) cc_final: 0.7166 (p0) REVERT: B 244 ILE cc_start: 0.7830 (mp) cc_final: 0.7539 (mp) REVERT: C 68 MET cc_start: 0.7540 (ttt) cc_final: 0.7286 (ttt) REVERT: C 83 GLN cc_start: 0.8150 (mt0) cc_final: 0.7867 (tt0) REVERT: C 94 ARG cc_start: 0.8192 (ptt90) cc_final: 0.7922 (ptt90) REVERT: C 95 VAL cc_start: 0.8621 (m) cc_final: 0.8385 (t) REVERT: C 130 TRP cc_start: 0.8597 (t-100) cc_final: 0.8350 (t-100) REVERT: C 135 ASN cc_start: 0.8227 (p0) cc_final: 0.7522 (p0) REVERT: C 138 LEU cc_start: 0.8381 (tt) cc_final: 0.8171 (tt) REVERT: C 141 ASP cc_start: 0.7116 (t0) cc_final: 0.5966 (t0) REVERT: C 142 GLU cc_start: 0.7203 (mp0) cc_final: 0.6202 (mp0) REVERT: C 144 ASP cc_start: 0.7377 (p0) cc_final: 0.7122 (p0) REVERT: C 159 GLU cc_start: 0.7412 (mp0) cc_final: 0.6972 (mp0) REVERT: C 209 ASP cc_start: 0.8395 (t0) cc_final: 0.8109 (t0) REVERT: C 285 ASP cc_start: 0.8465 (p0) cc_final: 0.8263 (p0) REVERT: C 293 THR cc_start: 0.7976 (m) cc_final: 0.7603 (m) REVERT: D 10 ASN cc_start: 0.8506 (t0) cc_final: 0.7755 (t0) REVERT: D 29 MET cc_start: 0.5126 (mmp) cc_final: 0.4684 (mmp) REVERT: D 82 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 125 ASP cc_start: 0.8158 (m-30) cc_final: 0.7919 (m-30) REVERT: D 138 LEU cc_start: 0.8426 (tp) cc_final: 0.8108 (tp) REVERT: D 171 ARG cc_start: 0.7546 (mmm160) cc_final: 0.7182 (mmm-85) REVERT: D 174 ARG cc_start: 0.7375 (mmp80) cc_final: 0.6781 (mmp80) REVERT: D 279 ASN cc_start: 0.8736 (m110) cc_final: 0.8172 (m110) REVERT: D 288 PHE cc_start: 0.8126 (t80) cc_final: 0.7631 (t80) REVERT: E 52 GLN cc_start: 0.8404 (mt0) cc_final: 0.7883 (mt0) REVERT: E 68 MET cc_start: 0.7250 (ttp) cc_final: 0.7019 (ttp) REVERT: E 77 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7527 (mtmt) REVERT: E 89 ASN cc_start: 0.7575 (t0) cc_final: 0.7161 (t0) REVERT: E 96 ASN cc_start: 0.8670 (t0) cc_final: 0.8446 (t0) REVERT: E 119 GLN cc_start: 0.8150 (pm20) cc_final: 0.7849 (pm20) REVERT: E 123 PHE cc_start: 0.6751 (p90) cc_final: 0.6522 (p90) REVERT: E 135 ASN cc_start: 0.7807 (p0) cc_final: 0.6725 (p0) REVERT: E 155 GLN cc_start: 0.8045 (tp40) cc_final: 0.7452 (tp40) REVERT: E 182 PHE cc_start: 0.7565 (m-10) cc_final: 0.7232 (m-80) REVERT: E 186 ASN cc_start: 0.7391 (t0) cc_final: 0.7150 (t0) REVERT: E 223 ASP cc_start: 0.8271 (m-30) cc_final: 0.7923 (m-30) REVERT: E 235 HIS cc_start: 0.8149 (t-90) cc_final: 0.7913 (t-90) REVERT: E 246 ASN cc_start: 0.8345 (t0) cc_final: 0.8144 (t0) REVERT: E 254 MET cc_start: 0.8262 (mmp) cc_final: 0.7599 (mmp) REVERT: E 257 GLN cc_start: 0.8364 (tp40) cc_final: 0.7714 (tp40) REVERT: E 268 MET cc_start: 0.7674 (tpt) cc_final: 0.7115 (tpt) REVERT: E 303 ARG cc_start: 0.8450 (ttm110) cc_final: 0.7940 (ttm110) REVERT: F 83 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7785 (mm-40) REVERT: F 89 ASN cc_start: 0.8376 (m110) cc_final: 0.8027 (m-40) REVERT: F 130 TRP cc_start: 0.8568 (t60) cc_final: 0.8352 (t60) REVERT: F 135 ASN cc_start: 0.8658 (p0) cc_final: 0.7905 (p0) REVERT: F 141 ASP cc_start: 0.7644 (t0) cc_final: 0.7209 (t0) REVERT: F 210 ARG cc_start: 0.6851 (ttm-80) cc_final: 0.6543 (ttm-80) REVERT: F 230 LEU cc_start: 0.8463 (mt) cc_final: 0.8203 (mt) REVERT: F 245 VAL cc_start: 0.8393 (t) cc_final: 0.8082 (m) REVERT: F 257 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8026 (tp-100) REVERT: a 19 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7420 (mtm110) REVERT: a 50 ASP cc_start: 0.6856 (p0) cc_final: 0.6512 (p0) REVERT: a 68 MET cc_start: 0.6841 (ttp) cc_final: 0.6569 (ttp) REVERT: a 106 LEU cc_start: 0.7850 (mt) cc_final: 0.7533 (mt) REVERT: a 152 PHE cc_start: 0.7494 (m-10) cc_final: 0.7278 (m-10) REVERT: a 174 ARG cc_start: 0.8265 (mmp-170) cc_final: 0.7960 (mmp-170) REVERT: a 182 PHE cc_start: 0.8106 (m-80) cc_final: 0.7522 (m-80) REVERT: a 240 GLU cc_start: 0.7702 (tp30) cc_final: 0.7328 (tp30) REVERT: a 244 ILE cc_start: 0.8250 (mp) cc_final: 0.7566 (mp) REVERT: a 248 MET cc_start: 0.7655 (mmp) cc_final: 0.7286 (mmt) REVERT: a 256 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7956 (mtp-110) REVERT: a 302 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7999 (mt-10) REVERT: a 306 VAL cc_start: 0.8980 (t) cc_final: 0.8713 (p) REVERT: a 309 PHE cc_start: 0.7574 (m-80) cc_final: 0.7084 (m-80) REVERT: b 10 ASN cc_start: 0.8747 (m-40) cc_final: 0.8522 (m-40) REVERT: b 61 PHE cc_start: 0.6998 (m-80) cc_final: 0.6691 (m-80) REVERT: b 69 VAL cc_start: 0.7834 (m) cc_final: 0.7318 (m) REVERT: b 77 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7952 (mtmt) REVERT: b 80 HIS cc_start: 0.8370 (m90) cc_final: 0.8120 (m90) REVERT: b 83 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7485 (mm-40) REVERT: b 96 ASN cc_start: 0.7506 (t0) cc_final: 0.7266 (t0) REVERT: b 100 HIS cc_start: 0.8336 (m90) cc_final: 0.7667 (m90) REVERT: b 130 TRP cc_start: 0.8331 (t60) cc_final: 0.8043 (t60) REVERT: b 141 ASP cc_start: 0.6485 (t70) cc_final: 0.6211 (t0) REVERT: b 147 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7279 (mmt-90) REVERT: b 168 ASP cc_start: 0.8369 (t0) cc_final: 0.6530 (t0) REVERT: b 248 MET cc_start: 0.7025 (mpp) cc_final: 0.6733 (mpp) REVERT: b 291 ARG cc_start: 0.7988 (ttt90) cc_final: 0.7522 (ttt90) REVERT: c 10 ASN cc_start: 0.7763 (m110) cc_final: 0.7430 (m110) REVERT: c 29 MET cc_start: 0.6069 (mmp) cc_final: 0.5868 (mmp) REVERT: c 100 HIS cc_start: 0.6542 (m-70) cc_final: 0.5620 (m-70) REVERT: c 102 SER cc_start: 0.7931 (p) cc_final: 0.7054 (p) REVERT: c 105 ASP cc_start: 0.7848 (m-30) cc_final: 0.7625 (m-30) REVERT: c 135 ASN cc_start: 0.8235 (p0) cc_final: 0.7634 (p0) REVERT: c 141 ASP cc_start: 0.7630 (m-30) cc_final: 0.7360 (m-30) REVERT: c 156 ARG cc_start: 0.8940 (tpt-90) cc_final: 0.8647 (tpt-90) REVERT: c 159 GLU cc_start: 0.7065 (mp0) cc_final: 0.6469 (mp0) REVERT: c 165 THR cc_start: 0.7874 (p) cc_final: 0.7419 (p) REVERT: c 208 MET cc_start: 0.6951 (mtm) cc_final: 0.6248 (mtm) REVERT: c 244 ILE cc_start: 0.9076 (mm) cc_final: 0.8636 (mm) REVERT: c 254 MET cc_start: 0.8272 (ttp) cc_final: 0.7890 (ttp) REVERT: c 268 MET cc_start: 0.6723 (mmp) cc_final: 0.5678 (mmp) REVERT: c 294 PHE cc_start: 0.6853 (t80) cc_final: 0.6622 (t80) REVERT: d 10 ASN cc_start: 0.8465 (t0) cc_final: 0.7854 (t0) REVERT: d 68 MET cc_start: 0.6565 (tmm) cc_final: 0.6081 (tmm) REVERT: d 73 HIS cc_start: 0.8622 (t-90) cc_final: 0.8401 (t-90) REVERT: d 154 ILE cc_start: 0.9010 (mm) cc_final: 0.8763 (mm) REVERT: d 156 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8104 (mmm160) REVERT: d 163 ARG cc_start: 0.6997 (mmt90) cc_final: 0.6374 (mmt90) REVERT: d 174 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7144 (mmp80) REVERT: d 182 PHE cc_start: 0.8038 (m-80) cc_final: 0.7731 (m-10) REVERT: d 210 ARG cc_start: 0.7026 (mtm180) cc_final: 0.6721 (mtm180) REVERT: d 279 ASN cc_start: 0.8751 (m-40) cc_final: 0.8354 (m-40) REVERT: e 28 MET cc_start: 0.8173 (tpt) cc_final: 0.7674 (tpt) REVERT: e 39 TYR cc_start: 0.8866 (m-80) cc_final: 0.8612 (m-80) REVERT: e 44 ASP cc_start: 0.7816 (t0) cc_final: 0.7600 (t0) REVERT: e 47 TYR cc_start: 0.7414 (t80) cc_final: 0.7208 (t80) REVERT: e 77 LYS cc_start: 0.7927 (pttm) cc_final: 0.7435 (pttm) REVERT: e 83 GLN cc_start: 0.7706 (tp-100) cc_final: 0.6633 (tp-100) REVERT: e 103 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7881 (ttp-170) REVERT: e 135 ASN cc_start: 0.8059 (p0) cc_final: 0.7402 (p0) REVERT: e 151 MET cc_start: 0.8059 (mmm) cc_final: 0.7742 (tpp) REVERT: e 155 GLN cc_start: 0.8247 (tp40) cc_final: 0.7440 (tp40) REVERT: e 158 LEU cc_start: 0.8488 (tp) cc_final: 0.7863 (tp) REVERT: e 166 LEU cc_start: 0.8301 (mm) cc_final: 0.7950 (mm) REVERT: e 210 ARG cc_start: 0.8475 (mmm160) cc_final: 0.7841 (mmm160) REVERT: e 235 HIS cc_start: 0.8041 (t-90) cc_final: 0.7758 (t-90) REVERT: e 253 ASP cc_start: 0.8199 (t0) cc_final: 0.7944 (t0) REVERT: e 257 GLN cc_start: 0.8490 (tp40) cc_final: 0.7809 (tp40) REVERT: f 54 THR cc_start: 0.8149 (p) cc_final: 0.7133 (p) REVERT: f 77 LYS cc_start: 0.8594 (pttm) cc_final: 0.8097 (pttm) REVERT: f 144 ASP cc_start: 0.7971 (p0) cc_final: 0.7660 (p0) REVERT: f 227 ASN cc_start: 0.8553 (m-40) cc_final: 0.8236 (m-40) REVERT: f 230 LEU cc_start: 0.8691 (mt) cc_final: 0.8401 (mt) REVERT: f 240 GLU cc_start: 0.7656 (tp30) cc_final: 0.7416 (tp30) REVERT: f 248 MET cc_start: 0.7860 (mtt) cc_final: 0.7450 (mmm) REVERT: f 254 MET cc_start: 0.8330 (ttm) cc_final: 0.8096 (ttm) REVERT: f 257 GLN cc_start: 0.8531 (mt0) cc_final: 0.8112 (mt0) REVERT: f 302 GLU cc_start: 0.8312 (mp0) cc_final: 0.7895 (mp0) REVERT: f 309 PHE cc_start: 0.8255 (m-80) cc_final: 0.7991 (m-80) outliers start: 0 outliers final: 0 residues processed: 1007 average time/residue: 0.1710 time to fit residues: 262.5989 Evaluate side-chains 974 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 974 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 110 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 301 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN E 83 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** a 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 GLN b 186 ASN b 222 HIS ** c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.159313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126550 restraints weight = 52549.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131524 restraints weight = 28740.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134911 restraints weight = 18871.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137170 restraints weight = 13936.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138520 restraints weight = 11240.927| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28333 Z= 0.112 Angle : 0.592 10.500 38529 Z= 0.303 Chirality : 0.042 0.187 4372 Planarity : 0.005 0.080 5022 Dihedral : 4.393 25.482 3840 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.02 % Rotamer: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % 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: -0.42 (0.14), residues: 3442 helix: 0.41 (0.13), residues: 1535 sheet: -0.18 (0.22), residues: 542 loop : -1.01 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 87 TYR 0.028 0.001 TYR a 47 PHE 0.034 0.002 PHE F 294 TRP 0.057 0.002 TRP a 276 HIS 0.008 0.001 HIS a 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (28333) covalent geometry : angle 0.59193 / 0.30 (38529) hydrogen bonds : bond 0.03100 / 2.04 ( 1173) hydrogen bonds : angle 4.85808 / 3.42 ( 3408) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 995 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5038 (pmm) cc_final: 0.4772 (pmm) REVERT: A 50 ASP cc_start: 0.6893 (p0) cc_final: 0.6554 (p0) REVERT: A 95 VAL cc_start: 0.8224 (p) cc_final: 0.7589 (m) REVERT: A 98 ASP cc_start: 0.8120 (m-30) cc_final: 0.7638 (m-30) REVERT: A 106 LEU cc_start: 0.7914 (mt) cc_final: 0.7563 (mt) REVERT: A 140 PHE cc_start: 0.7454 (m-10) cc_final: 0.7212 (m-10) REVERT: A 152 PHE cc_start: 0.7806 (m-10) cc_final: 0.7383 (m-10) REVERT: A 174 ARG cc_start: 0.8185 (mmp80) cc_final: 0.7863 (mmp80) REVERT: A 249 VAL cc_start: 0.7870 (t) cc_final: 0.7651 (p) REVERT: A 272 THR cc_start: 0.8853 (p) cc_final: 0.7941 (p) REVERT: A 279 ASN cc_start: 0.8269 (m-40) cc_final: 0.7544 (m-40) REVERT: A 311 GLN cc_start: 0.7623 (tp40) cc_final: 0.7373 (tp-100) REVERT: B 10 ASN cc_start: 0.8753 (m-40) cc_final: 0.8453 (m-40) REVERT: B 28 MET cc_start: 0.7529 (tmm) cc_final: 0.7115 (tmm) REVERT: B 63 TYR cc_start: 0.6914 (m-80) cc_final: 0.6650 (m-80) REVERT: B 77 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8217 (ptpt) REVERT: B 80 HIS cc_start: 0.7892 (m90) cc_final: 0.7484 (m90) REVERT: B 123 PHE cc_start: 0.8092 (t80) cc_final: 0.7679 (t80) REVERT: B 151 MET cc_start: 0.6648 (tmm) cc_final: 0.6330 (tmm) REVERT: B 210 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7633 (mmp80) REVERT: B 238 ASN cc_start: 0.7585 (p0) cc_final: 0.7150 (p0) REVERT: B 244 ILE cc_start: 0.7798 (mp) cc_final: 0.7524 (mp) REVERT: C 68 MET cc_start: 0.7568 (ttt) cc_final: 0.7294 (ttt) REVERT: C 83 GLN cc_start: 0.8134 (mt0) cc_final: 0.7883 (tt0) REVERT: C 94 ARG cc_start: 0.8161 (ptt90) cc_final: 0.7936 (ptt90) REVERT: C 100 HIS cc_start: 0.6701 (m-70) cc_final: 0.5560 (m-70) REVERT: C 130 TRP cc_start: 0.8575 (t-100) cc_final: 0.8354 (t-100) REVERT: C 135 ASN cc_start: 0.8225 (p0) cc_final: 0.7536 (p0) REVERT: C 138 LEU cc_start: 0.8404 (tt) cc_final: 0.8192 (tt) REVERT: C 142 GLU cc_start: 0.7161 (mp0) cc_final: 0.6761 (mp0) REVERT: C 144 ASP cc_start: 0.7379 (p0) cc_final: 0.7108 (p0) REVERT: C 159 GLU cc_start: 0.7384 (mp0) cc_final: 0.6884 (mp0) REVERT: C 209 ASP cc_start: 0.8419 (t0) cc_final: 0.8114 (t0) REVERT: C 266 THR cc_start: 0.8338 (p) cc_final: 0.8003 (p) REVERT: C 268 MET cc_start: 0.7409 (tpt) cc_final: 0.7035 (tpt) REVERT: C 293 THR cc_start: 0.7896 (m) cc_final: 0.7472 (m) REVERT: D 10 ASN cc_start: 0.8518 (t0) cc_final: 0.7801 (t0) REVERT: D 29 MET cc_start: 0.5145 (mmp) cc_final: 0.4706 (mmp) REVERT: D 69 VAL cc_start: 0.7848 (t) cc_final: 0.7580 (t) REVERT: D 82 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 125 ASP cc_start: 0.8131 (m-30) cc_final: 0.7893 (m-30) REVERT: D 138 LEU cc_start: 0.8455 (tp) cc_final: 0.8152 (tp) REVERT: D 171 ARG cc_start: 0.7544 (mmm160) cc_final: 0.7109 (mmm-85) REVERT: D 174 ARG cc_start: 0.7378 (mmp80) cc_final: 0.6757 (mmp80) REVERT: D 279 ASN cc_start: 0.8751 (m110) cc_final: 0.8208 (m110) REVERT: D 288 PHE cc_start: 0.8113 (t80) cc_final: 0.7624 (t80) REVERT: E 10 ASN cc_start: 0.7991 (t0) cc_final: 0.7690 (t0) REVERT: E 50 ASP cc_start: 0.7119 (t70) cc_final: 0.6652 (t0) REVERT: E 52 GLN cc_start: 0.8412 (mt0) cc_final: 0.7857 (mt0) REVERT: E 68 MET cc_start: 0.7198 (ttp) cc_final: 0.6907 (ttp) REVERT: E 77 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7539 (mtmt) REVERT: E 89 ASN cc_start: 0.7566 (t0) cc_final: 0.7096 (t0) REVERT: E 96 ASN cc_start: 0.8621 (t0) cc_final: 0.8420 (t0) REVERT: E 103 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7905 (ttp-110) REVERT: E 123 PHE cc_start: 0.6759 (p90) cc_final: 0.6546 (p90) REVERT: E 135 ASN cc_start: 0.7785 (p0) cc_final: 0.6657 (p0) REVERT: E 155 GLN cc_start: 0.8151 (tp40) cc_final: 0.7457 (tp40) REVERT: E 181 LEU cc_start: 0.8404 (tp) cc_final: 0.8060 (tt) REVERT: E 186 ASN cc_start: 0.7401 (t0) cc_final: 0.7161 (t0) REVERT: E 223 ASP cc_start: 0.8260 (m-30) cc_final: 0.7994 (m-30) REVERT: E 235 HIS cc_start: 0.8197 (t-90) cc_final: 0.7928 (t-90) REVERT: E 246 ASN cc_start: 0.8370 (t0) cc_final: 0.8163 (t0) REVERT: E 253 ASP cc_start: 0.7807 (t0) cc_final: 0.7599 (t0) REVERT: E 254 MET cc_start: 0.8321 (mmp) cc_final: 0.7657 (mmp) REVERT: E 257 GLN cc_start: 0.8373 (tp40) cc_final: 0.7715 (tp40) REVERT: E 268 MET cc_start: 0.7715 (tpt) cc_final: 0.7135 (tpt) REVERT: E 303 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7963 (ttm110) REVERT: F 83 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7797 (mm-40) REVERT: F 89 ASN cc_start: 0.8336 (m110) cc_final: 0.7995 (m-40) REVERT: F 130 TRP cc_start: 0.8503 (t60) cc_final: 0.8284 (t60) REVERT: F 135 ASN cc_start: 0.8683 (p0) cc_final: 0.7922 (p0) REVERT: F 141 ASP cc_start: 0.7578 (t0) cc_final: 0.7258 (t0) REVERT: F 210 ARG cc_start: 0.6832 (ttm-80) cc_final: 0.6539 (ttm-80) REVERT: F 230 LEU cc_start: 0.8473 (mt) cc_final: 0.8221 (mt) REVERT: F 245 VAL cc_start: 0.8255 (t) cc_final: 0.8025 (m) REVERT: F 257 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8016 (tp-100) REVERT: a 19 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7431 (mtm110) REVERT: a 50 ASP cc_start: 0.6670 (p0) cc_final: 0.6323 (p0) REVERT: a 68 MET cc_start: 0.6778 (ttp) cc_final: 0.6528 (ttp) REVERT: a 80 HIS cc_start: 0.8025 (m90) cc_final: 0.7714 (m90) REVERT: a 152 PHE cc_start: 0.7537 (m-10) cc_final: 0.7282 (m-10) REVERT: a 158 LEU cc_start: 0.8502 (mp) cc_final: 0.8301 (mp) REVERT: a 182 PHE cc_start: 0.8135 (m-80) cc_final: 0.7535 (m-80) REVERT: a 240 GLU cc_start: 0.7710 (tp30) cc_final: 0.7368 (tp30) REVERT: a 244 ILE cc_start: 0.8298 (mp) cc_final: 0.7660 (mp) REVERT: a 248 MET cc_start: 0.7766 (mmp) cc_final: 0.7406 (mmt) REVERT: a 256 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.7982 (mtp-110) REVERT: a 302 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7948 (mt-10) REVERT: a 306 VAL cc_start: 0.8998 (t) cc_final: 0.8733 (p) REVERT: a 309 PHE cc_start: 0.7493 (m-80) cc_final: 0.7026 (m-80) REVERT: b 10 ASN cc_start: 0.8728 (m-40) cc_final: 0.8425 (m-40) REVERT: b 68 MET cc_start: 0.8075 (mtt) cc_final: 0.7750 (mtt) REVERT: b 80 HIS cc_start: 0.8442 (m90) cc_final: 0.8075 (m90) REVERT: b 83 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7511 (mm-40) REVERT: b 100 HIS cc_start: 0.8258 (m90) cc_final: 0.7601 (m90) REVERT: b 130 TRP cc_start: 0.8350 (t60) cc_final: 0.8085 (t60) REVERT: b 147 ARG cc_start: 0.7707 (mmt-90) cc_final: 0.7205 (mmt-90) REVERT: b 159 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7117 (tm-30) REVERT: b 168 ASP cc_start: 0.8388 (t0) cc_final: 0.6580 (t0) REVERT: b 248 MET cc_start: 0.7041 (mpp) cc_final: 0.6753 (mpp) REVERT: b 291 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7536 (ttt90) REVERT: c 10 ASN cc_start: 0.7767 (m110) cc_final: 0.7431 (m110) REVERT: c 28 MET cc_start: 0.5051 (mtm) cc_final: 0.4839 (mtm) REVERT: c 100 HIS cc_start: 0.6439 (m-70) cc_final: 0.5757 (m-70) REVERT: c 102 SER cc_start: 0.7784 (p) cc_final: 0.7029 (p) REVERT: c 121 THR cc_start: 0.8484 (m) cc_final: 0.8075 (t) REVERT: c 135 ASN cc_start: 0.8249 (p0) cc_final: 0.7654 (p0) REVERT: c 150 VAL cc_start: 0.8890 (m) cc_final: 0.8631 (m) REVERT: c 153 VAL cc_start: 0.9229 (t) cc_final: 0.8994 (p) REVERT: c 156 ARG cc_start: 0.8920 (tpt-90) cc_final: 0.8708 (tpt-90) REVERT: c 159 GLU cc_start: 0.7089 (mp0) cc_final: 0.6480 (mp0) REVERT: c 165 THR cc_start: 0.7952 (p) cc_final: 0.7619 (p) REVERT: c 208 MET cc_start: 0.6973 (mtm) cc_final: 0.6239 (mtm) REVERT: c 244 ILE cc_start: 0.9111 (mm) cc_final: 0.8697 (mm) REVERT: c 254 MET cc_start: 0.8327 (ttp) cc_final: 0.7911 (ttp) REVERT: d 10 ASN cc_start: 0.8446 (t0) cc_final: 0.7816 (t0) REVERT: d 68 MET cc_start: 0.6540 (tmm) cc_final: 0.6019 (tmm) REVERT: d 154 ILE cc_start: 0.9015 (mm) cc_final: 0.8763 (mm) REVERT: d 156 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8111 (mmm160) REVERT: d 163 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6302 (mmt90) REVERT: d 174 ARG cc_start: 0.7714 (mmp80) cc_final: 0.7121 (mmp80) REVERT: d 182 PHE cc_start: 0.8015 (m-80) cc_final: 0.7668 (m-10) REVERT: d 210 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6717 (mtm180) REVERT: d 279 ASN cc_start: 0.8767 (m-40) cc_final: 0.8358 (m-40) REVERT: e 28 MET cc_start: 0.8228 (tpt) cc_final: 0.7653 (tpt) REVERT: e 39 TYR cc_start: 0.8869 (m-80) cc_final: 0.8592 (m-80) REVERT: e 44 ASP cc_start: 0.7829 (t0) cc_final: 0.7613 (t0) REVERT: e 77 LYS cc_start: 0.7959 (pttm) cc_final: 0.7455 (pttm) REVERT: e 83 GLN cc_start: 0.7724 (tp-100) cc_final: 0.6632 (tp-100) REVERT: e 103 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7854 (ttp-170) REVERT: e 135 ASN cc_start: 0.8057 (p0) cc_final: 0.7474 (p0) REVERT: e 155 GLN cc_start: 0.8250 (tp40) cc_final: 0.7491 (tp40) REVERT: e 166 LEU cc_start: 0.8244 (mm) cc_final: 0.7906 (mm) REVERT: e 235 HIS cc_start: 0.8060 (t-90) cc_final: 0.7764 (t-90) REVERT: e 253 ASP cc_start: 0.8199 (t0) cc_final: 0.7949 (t0) REVERT: e 257 GLN cc_start: 0.8506 (tp40) cc_final: 0.7820 (tp40) REVERT: f 54 THR cc_start: 0.7957 (p) cc_final: 0.6779 (p) REVERT: f 141 ASP cc_start: 0.7330 (t0) cc_final: 0.6797 (t0) REVERT: f 144 ASP cc_start: 0.7964 (p0) cc_final: 0.7657 (p0) REVERT: f 227 ASN cc_start: 0.8590 (m-40) cc_final: 0.8293 (m-40) REVERT: f 230 LEU cc_start: 0.8658 (mt) cc_final: 0.8396 (mt) REVERT: f 240 GLU cc_start: 0.7704 (tp30) cc_final: 0.7499 (tp30) REVERT: f 243 GLU cc_start: 0.7917 (pm20) cc_final: 0.7582 (pm20) REVERT: f 248 MET cc_start: 0.7813 (mtt) cc_final: 0.7604 (mtt) REVERT: f 254 MET cc_start: 0.8341 (ttm) cc_final: 0.8102 (ttm) REVERT: f 257 GLN cc_start: 0.8527 (mt0) cc_final: 0.8044 (mt0) REVERT: f 302 GLU cc_start: 0.8330 (mp0) cc_final: 0.7911 (mp0) REVERT: f 309 PHE cc_start: 0.8251 (m-80) cc_final: 0.8029 (m-80) outliers start: 1 outliers final: 0 residues processed: 996 average time/residue: 0.1715 time to fit residues: 262.8319 Evaluate side-chains 963 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 963 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 113 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 222 HIS C 279 ASN E 83 GLN E 169 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 222 HIS ** f 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.158220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126367 restraints weight = 52239.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130912 restraints weight = 29895.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133956 restraints weight = 20105.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136096 restraints weight = 15188.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137448 restraints weight = 12391.031| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28333 Z= 0.145 Angle : 0.619 12.499 38529 Z= 0.320 Chirality : 0.043 0.196 4372 Planarity : 0.004 0.058 5022 Dihedral : 4.489 24.872 3840 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.19 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.47 (0.14), residues: 3442 helix: 0.37 (0.13), residues: 1536 sheet: -0.13 (0.22), residues: 512 loop : -1.07 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 87 TYR 0.025 0.001 TYR E 63 PHE 0.036 0.002 PHE a 288 TRP 0.051 0.002 TRP E 276 HIS 0.005 0.001 HIS f 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (28333) covalent geometry : angle 0.61903 / 0.32 (38529) hydrogen bonds : bond 0.03442 / 2.27 ( 1173) hydrogen bonds : angle 4.97288 / 3.50 ( 3408) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1000 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.5034 (pmm) cc_final: 0.4822 (pmm) REVERT: A 50 ASP cc_start: 0.6969 (p0) cc_final: 0.6630 (p0) REVERT: A 95 VAL cc_start: 0.8249 (p) cc_final: 0.7655 (m) REVERT: A 106 LEU cc_start: 0.7899 (mt) cc_final: 0.7524 (mt) REVERT: A 152 PHE cc_start: 0.7776 (m-10) cc_final: 0.7372 (m-10) REVERT: A 174 ARG cc_start: 0.8176 (mmp80) cc_final: 0.7901 (mmp80) REVERT: A 248 MET cc_start: 0.7694 (ptm) cc_final: 0.7169 (ptm) REVERT: A 279 ASN cc_start: 0.8270 (m-40) cc_final: 0.7532 (m-40) REVERT: A 311 GLN cc_start: 0.7607 (tp40) cc_final: 0.7335 (tp-100) REVERT: B 10 ASN cc_start: 0.8807 (m-40) cc_final: 0.8518 (m-40) REVERT: B 28 MET cc_start: 0.7613 (tmm) cc_final: 0.7172 (tmm) REVERT: B 63 TYR cc_start: 0.7041 (m-80) cc_final: 0.6748 (m-80) REVERT: B 77 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8213 (ptpt) REVERT: B 80 HIS cc_start: 0.7863 (m90) cc_final: 0.7473 (m90) REVERT: B 123 PHE cc_start: 0.8103 (t80) cc_final: 0.7611 (t80) REVERT: B 171 ARG cc_start: 0.7091 (ptt180) cc_final: 0.6422 (ptt180) REVERT: B 210 ARG cc_start: 0.7974 (mmp80) cc_final: 0.7678 (mmp80) REVERT: B 238 ASN cc_start: 0.7622 (p0) cc_final: 0.7143 (p0) REVERT: B 244 ILE cc_start: 0.7787 (mp) cc_final: 0.7512 (mp) REVERT: C 68 MET cc_start: 0.7558 (ttt) cc_final: 0.7295 (ttt) REVERT: C 77 LYS cc_start: 0.7724 (ptmt) cc_final: 0.7307 (ptmt) REVERT: C 83 GLN cc_start: 0.8183 (mt0) cc_final: 0.7903 (tt0) REVERT: C 94 ARG cc_start: 0.8158 (ptt90) cc_final: 0.7889 (ptt90) REVERT: C 130 TRP cc_start: 0.8603 (t-100) cc_final: 0.8391 (t-100) REVERT: C 135 ASN cc_start: 0.8277 (p0) cc_final: 0.7568 (p0) REVERT: C 141 ASP cc_start: 0.7155 (t0) cc_final: 0.5754 (t0) REVERT: C 142 GLU cc_start: 0.7193 (mp0) cc_final: 0.6105 (mp0) REVERT: C 144 ASP cc_start: 0.7407 (p0) cc_final: 0.7197 (p0) REVERT: C 151 MET cc_start: 0.7004 (mpp) cc_final: 0.6775 (mpp) REVERT: C 159 GLU cc_start: 0.7459 (mp0) cc_final: 0.6973 (mp0) REVERT: C 184 THR cc_start: 0.7868 (t) cc_final: 0.7316 (t) REVERT: C 209 ASP cc_start: 0.8398 (t0) cc_final: 0.8102 (t0) REVERT: C 266 THR cc_start: 0.8389 (p) cc_final: 0.7974 (p) REVERT: C 268 MET cc_start: 0.7400 (tpt) cc_final: 0.6739 (tpt) REVERT: D 10 ASN cc_start: 0.8516 (t0) cc_final: 0.7831 (t0) REVERT: D 29 MET cc_start: 0.5148 (mmp) cc_final: 0.4708 (mmp) REVERT: D 82 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8221 (mm-30) REVERT: D 125 ASP cc_start: 0.8160 (m-30) cc_final: 0.7918 (m-30) REVERT: D 138 LEU cc_start: 0.8430 (tp) cc_final: 0.8130 (tp) REVERT: D 171 ARG cc_start: 0.7568 (mmm160) cc_final: 0.7195 (mmm-85) REVERT: D 174 ARG cc_start: 0.7393 (mmp80) cc_final: 0.6763 (mmp80) REVERT: D 217 LEU cc_start: 0.8044 (mm) cc_final: 0.7756 (mm) REVERT: D 279 ASN cc_start: 0.8739 (m110) cc_final: 0.8201 (m110) REVERT: D 288 PHE cc_start: 0.8140 (t80) cc_final: 0.7635 (t80) REVERT: E 50 ASP cc_start: 0.7160 (t70) cc_final: 0.6668 (t0) REVERT: E 52 GLN cc_start: 0.8377 (mt0) cc_final: 0.7821 (mt0) REVERT: E 68 MET cc_start: 0.7216 (ttp) cc_final: 0.6927 (ttp) REVERT: E 77 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7664 (mtmt) REVERT: E 89 ASN cc_start: 0.7686 (t0) cc_final: 0.7177 (t0) REVERT: E 123 PHE cc_start: 0.6725 (p90) cc_final: 0.6514 (p90) REVERT: E 135 ASN cc_start: 0.7836 (p0) cc_final: 0.6795 (p0) REVERT: E 155 GLN cc_start: 0.8198 (tp40) cc_final: 0.7469 (tp40) REVERT: E 186 ASN cc_start: 0.7405 (t0) cc_final: 0.7153 (t0) REVERT: E 223 ASP cc_start: 0.8305 (m-30) cc_final: 0.7973 (m-30) REVERT: E 235 HIS cc_start: 0.8138 (t-90) cc_final: 0.7899 (t-90) REVERT: E 253 ASP cc_start: 0.7822 (t0) cc_final: 0.7612 (t0) REVERT: E 254 MET cc_start: 0.8315 (mmp) cc_final: 0.7640 (mmp) REVERT: E 257 GLN cc_start: 0.8350 (tp40) cc_final: 0.7685 (tp40) REVERT: E 268 MET cc_start: 0.7732 (tpt) cc_final: 0.7335 (tpt) REVERT: E 303 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7966 (ttm110) REVERT: F 65 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8108 (mtp85) REVERT: F 77 LYS cc_start: 0.8312 (ptpt) cc_final: 0.8010 (ptpt) REVERT: F 83 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7762 (mm-40) REVERT: F 89 ASN cc_start: 0.8369 (m110) cc_final: 0.8037 (m-40) REVERT: F 135 ASN cc_start: 0.8680 (p0) cc_final: 0.7904 (p0) REVERT: F 141 ASP cc_start: 0.7665 (t0) cc_final: 0.7254 (t0) REVERT: F 210 ARG cc_start: 0.6882 (ttm-80) cc_final: 0.6559 (ttm-80) REVERT: F 230 LEU cc_start: 0.8482 (mt) cc_final: 0.8227 (mt) REVERT: F 257 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8044 (tp-100) REVERT: a 19 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7303 (mtm110) REVERT: a 50 ASP cc_start: 0.6836 (p0) cc_final: 0.6599 (p0) REVERT: a 68 MET cc_start: 0.6807 (ttp) cc_final: 0.6497 (ttp) REVERT: a 80 HIS cc_start: 0.8020 (m90) cc_final: 0.7745 (m90) REVERT: a 82 GLU cc_start: 0.8699 (pm20) cc_final: 0.8427 (pm20) REVERT: a 152 PHE cc_start: 0.7489 (m-10) cc_final: 0.7281 (m-10) REVERT: a 240 GLU cc_start: 0.7742 (tp30) cc_final: 0.7437 (tp30) REVERT: a 244 ILE cc_start: 0.8255 (mp) cc_final: 0.7579 (mp) REVERT: a 248 MET cc_start: 0.7629 (mmp) cc_final: 0.7168 (mmt) REVERT: a 256 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.7939 (mtp-110) REVERT: a 302 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7992 (mt-10) REVERT: a 306 VAL cc_start: 0.8999 (t) cc_final: 0.8709 (p) REVERT: a 309 PHE cc_start: 0.7486 (m-80) cc_final: 0.7022 (m-80) REVERT: b 10 ASN cc_start: 0.8740 (m-40) cc_final: 0.8452 (m-40) REVERT: b 68 MET cc_start: 0.8069 (mtt) cc_final: 0.7841 (mtt) REVERT: b 77 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8061 (mtmt) REVERT: b 80 HIS cc_start: 0.8351 (m90) cc_final: 0.8052 (m90) REVERT: b 83 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7516 (mm-40) REVERT: b 98 ASP cc_start: 0.6981 (p0) cc_final: 0.6641 (p0) REVERT: b 100 HIS cc_start: 0.8330 (m90) cc_final: 0.7698 (m90) REVERT: b 130 TRP cc_start: 0.8350 (t60) cc_final: 0.8072 (t60) REVERT: b 147 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7183 (mmt-90) REVERT: b 151 MET cc_start: 0.6726 (tmm) cc_final: 0.6404 (tmm) REVERT: b 168 ASP cc_start: 0.8390 (t0) cc_final: 0.6444 (t0) REVERT: b 181 LEU cc_start: 0.8079 (tp) cc_final: 0.7858 (tp) REVERT: b 208 MET cc_start: 0.8047 (mmm) cc_final: 0.7827 (mmt) REVERT: b 248 MET cc_start: 0.6953 (mpp) cc_final: 0.6654 (mpp) REVERT: b 254 MET cc_start: 0.8028 (ptm) cc_final: 0.7787 (ptm) REVERT: b 256 ARG cc_start: 0.8069 (mpt90) cc_final: 0.7682 (mpt90) REVERT: b 291 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7519 (ttt90) REVERT: c 10 ASN cc_start: 0.7779 (m110) cc_final: 0.7429 (m110) REVERT: c 100 HIS cc_start: 0.6575 (m-70) cc_final: 0.5990 (m-70) REVERT: c 102 SER cc_start: 0.7939 (p) cc_final: 0.7023 (p) REVERT: c 105 ASP cc_start: 0.7876 (m-30) cc_final: 0.7606 (m-30) REVERT: c 121 THR cc_start: 0.8499 (m) cc_final: 0.8157 (t) REVERT: c 141 ASP cc_start: 0.7683 (m-30) cc_final: 0.7435 (m-30) REVERT: c 150 VAL cc_start: 0.8875 (m) cc_final: 0.8622 (m) REVERT: c 151 MET cc_start: 0.7273 (mmm) cc_final: 0.6696 (mmm) REVERT: c 156 ARG cc_start: 0.8920 (tpt-90) cc_final: 0.8599 (tpt-90) REVERT: c 159 GLU cc_start: 0.7136 (mp0) cc_final: 0.6511 (mp0) REVERT: c 165 THR cc_start: 0.7824 (p) cc_final: 0.7486 (p) REVERT: c 208 MET cc_start: 0.6990 (mtm) cc_final: 0.6265 (mtm) REVERT: c 244 ILE cc_start: 0.9097 (mm) cc_final: 0.8747 (mm) REVERT: c 254 MET cc_start: 0.8334 (ttp) cc_final: 0.7919 (ttp) REVERT: d 10 ASN cc_start: 0.8421 (t0) cc_final: 0.7835 (t0) REVERT: d 68 MET cc_start: 0.6759 (tmm) cc_final: 0.6254 (tmm) REVERT: d 154 ILE cc_start: 0.8998 (mm) cc_final: 0.8774 (mm) REVERT: d 156 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8144 (mmm160) REVERT: d 163 ARG cc_start: 0.6988 (mmt90) cc_final: 0.6335 (mmt90) REVERT: d 174 ARG cc_start: 0.7709 (mmp80) cc_final: 0.7111 (mmp80) REVERT: d 182 PHE cc_start: 0.8112 (m-80) cc_final: 0.7739 (m-10) REVERT: d 210 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6732 (mtm180) REVERT: d 279 ASN cc_start: 0.8763 (m-40) cc_final: 0.8357 (m-40) REVERT: e 28 MET cc_start: 0.8188 (tpt) cc_final: 0.7637 (tpt) REVERT: e 39 TYR cc_start: 0.8888 (m-80) cc_final: 0.8642 (m-80) REVERT: e 44 ASP cc_start: 0.7811 (t0) cc_final: 0.7595 (t0) REVERT: e 47 TYR cc_start: 0.7458 (t80) cc_final: 0.7239 (t80) REVERT: e 77 LYS cc_start: 0.7990 (pttm) cc_final: 0.7455 (pttm) REVERT: e 83 GLN cc_start: 0.7722 (tp-100) cc_final: 0.6628 (tp-100) REVERT: e 103 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7897 (ttp-170) REVERT: e 123 PHE cc_start: 0.7060 (m-80) cc_final: 0.6773 (m-80) REVERT: e 135 ASN cc_start: 0.8041 (p0) cc_final: 0.7670 (p0) REVERT: e 155 GLN cc_start: 0.8262 (tp40) cc_final: 0.7430 (tp40) REVERT: e 158 LEU cc_start: 0.8511 (tp) cc_final: 0.8309 (tp) REVERT: e 166 LEU cc_start: 0.8326 (mm) cc_final: 0.7997 (mm) REVERT: e 235 HIS cc_start: 0.8064 (t-90) cc_final: 0.7779 (t-90) REVERT: e 253 ASP cc_start: 0.8188 (t0) cc_final: 0.7943 (t0) REVERT: e 257 GLN cc_start: 0.8485 (tp40) cc_final: 0.7806 (tp40) REVERT: f 54 THR cc_start: 0.8032 (p) cc_final: 0.7016 (p) REVERT: f 141 ASP cc_start: 0.7428 (t0) cc_final: 0.7158 (t0) REVERT: f 144 ASP cc_start: 0.7935 (p0) cc_final: 0.7625 (p0) REVERT: f 149 ASP cc_start: 0.8254 (p0) cc_final: 0.8001 (p0) REVERT: f 227 ASN cc_start: 0.8544 (m-40) cc_final: 0.8246 (m-40) REVERT: f 230 LEU cc_start: 0.8676 (mt) cc_final: 0.8421 (mt) REVERT: f 240 GLU cc_start: 0.7688 (tp30) cc_final: 0.7469 (tp30) REVERT: f 243 GLU cc_start: 0.7946 (pm20) cc_final: 0.7607 (pm20) REVERT: f 250 ARG cc_start: 0.7681 (mmt-90) cc_final: 0.7146 (mmt-90) REVERT: f 257 GLN cc_start: 0.8517 (mt0) cc_final: 0.8057 (mt0) REVERT: f 302 GLU cc_start: 0.8308 (mp0) cc_final: 0.7901 (mp0) REVERT: f 309 PHE cc_start: 0.8265 (m-80) cc_final: 0.8010 (m-80) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.1715 time to fit residues: 263.6632 Evaluate side-chains 967 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 967 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 194 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 280 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 250 optimal weight: 0.0970 chunk 174 optimal weight: 0.0980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 155 GLN B 169 GLN B 222 HIS ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** a 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 261 ASN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 296 ASN e 133 GLN e 296 ASN ** f 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN ** f 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.159074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126942 restraints weight = 52267.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131891 restraints weight = 28748.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135232 restraints weight = 18897.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137638 restraints weight = 13964.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.139052 restraints weight = 11106.913| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28333 Z= 0.108 Angle : 0.609 11.475 38529 Z= 0.310 Chirality : 0.043 0.187 4372 Planarity : 0.004 0.080 5022 Dihedral : 4.371 22.465 3840 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3442 helix: 0.33 (0.13), residues: 1551 sheet: -0.13 (0.22), residues: 526 loop : -0.99 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 303 TYR 0.025 0.001 TYR E 47 PHE 0.024 0.001 PHE F 309 TRP 0.059 0.003 TRP a 276 HIS 0.006 0.001 HIS a 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (28333) covalent geometry : angle 0.60886 / 0.31 (38529) hydrogen bonds : bond 0.03081 / 2.05 ( 1173) hydrogen bonds : angle 4.86084 / 3.41 ( 3408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5922.63 seconds wall clock time: 102 minutes 9.48 seconds (6129.48 seconds total)