Starting phenix.real_space_refine on Sat Aug 8 07:52:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukc_64234/08_2026/9ukc_64234.cif" } resolution = 4.26 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 16344 2.51 5 N 4624 2.21 5 O 4889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25970 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2456 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2409 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Chain: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2404 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2503 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "E" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2555 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "F" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2555 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "G" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2511 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain: "a" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "N" Number of atoms: 6919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 6919 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 58, 'TRANS': 841} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.92, per 1000 atoms: 0.23 Number of scatterers: 25970 At special positions: 0 Unit cell: (120.056, 133.318, 166.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 9 15.00 Mg 3 11.99 O 4889 8.00 N 4624 7.00 C 16344 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: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 32 sheets defined 50.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.786A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 107' Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.803A pdb=" N TRP A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.517A pdb=" N VAL A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.633A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 4.196A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.781A pdb=" N ASN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.502A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.183A pdb=" N ARG A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 292' Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.956A pdb=" N CYS A 298 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.919A pdb=" N PHE A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 4.043A pdb=" N ILE A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 62 removed outlier: 4.234A pdb=" N ALA B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.945A pdb=" N LEU B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.637A pdb=" N ILE B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.544A pdb=" N VAL B 226 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 262 removed outlier: 3.950A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.715A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.954A pdb=" N PHE B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 4.061A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.866A pdb=" N ALA C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.323A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.914A pdb=" N TRP C 211 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.711A pdb=" N VAL C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 262 removed outlier: 4.194A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.655A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 4.108A pdb=" N PHE C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 removed outlier: 3.693A pdb=" N CYS C 298 " --> pdb=" O LEU C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 298' Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.800A pdb=" N GLU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.567A pdb=" N TRP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 154 through 159 removed outlier: 4.533A pdb=" N GLU D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.604A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 238 removed outlier: 4.042A pdb=" N GLN D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN D 238 " --> pdb=" O HIS D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 238' Processing helix chain 'D' and resid 239 through 262 removed outlier: 4.274A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.528A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.943A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.868A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.737A pdb=" N GLY E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 204 through 209 removed outlier: 3.531A pdb=" N MET E 208 " --> pdb=" O ASN E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 238 through 239 No H-bonds generated for 'chain 'E' and resid 238 through 239' Processing helix chain 'E' and resid 240 through 261 removed outlier: 4.253A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.568A pdb=" N ASN F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 88 removed outlier: 3.596A pdb=" N LEU F 88 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.642A pdb=" N GLY F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.813A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 204 through 209 removed outlier: 4.329A pdb=" N MET F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 241 through 261 removed outlier: 3.729A pdb=" N ILE F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN F 261 " --> pdb=" O GLN F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.657A pdb=" N ALA F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.693A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.820A pdb=" N ALA F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 372 removed outlier: 5.499A pdb=" N GLY G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL G 357 " --> pdb=" O ASN G 353 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.944A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 428 removed outlier: 4.412A pdb=" N MET G 427 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 450 removed outlier: 3.623A pdb=" N THR G 433 " --> pdb=" O GLY G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 Processing helix chain 'G' and resid 498 through 507 removed outlier: 3.599A pdb=" N ARG G 503 " --> pdb=" O TRP G 499 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG G 504 " --> pdb=" O ARG G 500 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN G 505 " --> pdb=" O ARG G 501 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY G 507 " --> pdb=" O ARG G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 511 Processing helix chain 'G' and resid 519 through 534 removed outlier: 3.650A pdb=" N ALA G 523 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP G 526 " --> pdb=" O GLU G 522 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 556 Processing helix chain 'G' and resid 561 through 577 Processing helix chain 'G' and resid 606 through 620 removed outlier: 3.852A pdb=" N ALA G 610 " --> pdb=" O GLU G 606 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 615 " --> pdb=" O MET G 611 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA G 616 " --> pdb=" O THR G 612 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU G 618 " --> pdb=" O GLN G 614 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU G 620 " --> pdb=" O ALA G 616 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 38 removed outlier: 3.502A pdb=" N GLY a 38 " --> pdb=" O ARG a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 88 removed outlier: 3.761A pdb=" N GLN a 86 " --> pdb=" O MET a 82 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 98 removed outlier: 4.069A pdb=" N HIS a 94 " --> pdb=" O ASN a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 124 removed outlier: 4.318A pdb=" N GLU a 112 " --> pdb=" O PHE a 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN a 113 " --> pdb=" O ASP a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 142 removed outlier: 3.600A pdb=" N ALA a 136 " --> pdb=" O SER a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 153 Processing helix chain 'a' and resid 154 through 169 removed outlier: 4.129A pdb=" N SER a 160 " --> pdb=" O GLU a 156 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR a 168 " --> pdb=" O ARG a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 177 Processing helix chain 'a' and resid 178 through 191 removed outlier: 4.280A pdb=" N LEU a 182 " --> pdb=" O GLN a 178 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP a 183 " --> pdb=" O VAL a 179 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP a 185 " --> pdb=" O GLU a 181 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP a 186 " --> pdb=" O LEU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 198 removed outlier: 3.629A pdb=" N ARG a 197 " --> pdb=" O ASP a 194 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU a 198 " --> pdb=" O ILE a 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 194 through 198' Processing helix chain 'a' and resid 199 through 204 removed outlier: 4.366A pdb=" N GLU a 203 " --> pdb=" O GLU a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 219 Processing helix chain 'N' and resid 357 through 374 removed outlier: 3.829A pdb=" N VAL N 361 " --> pdb=" O ARG N 357 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA N 362 " --> pdb=" O VAL N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 375 through 379 removed outlier: 3.644A pdb=" N ARG N 379 " --> pdb=" O PRO N 376 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 395 Processing helix chain 'N' and resid 403 through 418 Processing helix chain 'N' and resid 427 through 436 removed outlier: 3.738A pdb=" N ALA N 434 " --> pdb=" O ALA N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 464 removed outlier: 3.973A pdb=" N LYS N 464 " --> pdb=" O ALA N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 466 through 476 removed outlier: 3.862A pdb=" N ARG N 476 " --> pdb=" O GLU N 472 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 541 Processing helix chain 'N' and resid 555 through 560 Processing helix chain 'N' and resid 571 through 578 removed outlier: 3.647A pdb=" N ALA N 575 " --> pdb=" O CYS N 571 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 601 removed outlier: 4.548A pdb=" N GLY N 594 " --> pdb=" O ASP N 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 620 through 631 removed outlier: 3.913A pdb=" N ASP N 624 " --> pdb=" O GLY N 620 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU N 631 " --> pdb=" O ALA N 627 " (cutoff:3.500A) Processing helix chain 'N' and resid 639 through 657 Processing helix chain 'N' and resid 659 through 664 removed outlier: 3.635A pdb=" N ALA N 663 " --> pdb=" O LEU N 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 670 through 687 Processing helix chain 'N' and resid 704 through 714 removed outlier: 3.642A pdb=" N LEU N 710 " --> pdb=" O LEU N 706 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL N 711 " --> pdb=" O THR N 707 " (cutoff:3.500A) Processing helix chain 'N' and resid 727 through 731 Processing helix chain 'N' and resid 732 through 741 removed outlier: 3.596A pdb=" N ALA N 736 " --> pdb=" O SER N 732 " (cutoff:3.500A) Processing helix chain 'N' and resid 748 through 752 Processing helix chain 'N' and resid 776 through 793 Processing helix chain 'N' and resid 802 through 836 removed outlier: 4.089A pdb=" N GLN N 815 " --> pdb=" O SER N 811 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG N 817 " --> pdb=" O GLU N 813 " (cutoff:3.500A) Proline residue: N 818 - end of helix removed outlier: 4.512A pdb=" N GLY N 824 " --> pdb=" O VAL N 820 " (cutoff:3.500A) Proline residue: N 825 - end of helix removed outlier: 4.218A pdb=" N PHE N 831 " --> pdb=" O GLU N 827 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU N 832 " --> pdb=" O ILE N 828 " (cutoff:3.500A) Processing helix chain 'N' and resid 872 through 894 removed outlier: 3.731A pdb=" N LEU N 885 " --> pdb=" O LYS N 881 " (cutoff:3.500A) Processing helix chain 'N' and resid 909 through 914 removed outlier: 4.296A pdb=" N THR N 913 " --> pdb=" O SER N 909 " (cutoff:3.500A) Processing helix chain 'N' and resid 915 through 926 removed outlier: 3.557A pdb=" N ALA N 923 " --> pdb=" O ALA N 919 " (cutoff:3.500A) Processing helix chain 'N' and resid 945 through 950 removed outlier: 4.412A pdb=" N LEU N 949 " --> pdb=" O PRO N 945 " (cutoff:3.500A) Processing helix chain 'N' and resid 961 through 968 removed outlier: 3.646A pdb=" N ARG N 965 " --> pdb=" O SER N 961 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP N 966 " --> pdb=" O GLY N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 970 through 985 removed outlier: 4.115A pdb=" N LEU N 974 " --> pdb=" O GLU N 970 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE N 975 " --> pdb=" O GLN N 971 " (cutoff:3.500A) Processing helix chain 'N' and resid 992 through 1008 Processing helix chain 'N' and resid 1011 through 1020 Processing helix chain 'N' and resid 1034 through 1041 removed outlier: 3.604A pdb=" N LEU N1038 " --> pdb=" O GLY N1034 " (cutoff:3.500A) Processing helix chain 'N' and resid 1046 through 1058 removed outlier: 3.749A pdb=" N LEU N1050 " --> pdb=" O GLY N1046 " (cutoff:3.500A) Processing helix chain 'N' and resid 1072 through 1082 removed outlier: 3.871A pdb=" N GLU N1077 " --> pdb=" O GLY N1073 " (cutoff:3.500A) Processing helix chain 'N' and resid 1095 through 1098 Processing helix chain 'N' and resid 1099 through 1107 removed outlier: 4.571A pdb=" N TYR N1103 " --> pdb=" O SER N1099 " (cutoff:3.500A) Processing helix chain 'N' and resid 1107 through 1117 removed outlier: 4.017A pdb=" N ALA N1111 " --> pdb=" O GLY N1107 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR N1112 " --> pdb=" O GLY N1108 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU N1114 " --> pdb=" O ALA N1110 " (cutoff:3.500A) Processing helix chain 'N' and resid 1139 through 1149 removed outlier: 4.304A pdb=" N VAL N1146 " --> pdb=" O GLU N1142 " (cutoff:3.500A) Processing helix chain 'N' and resid 1153 through 1161 removed outlier: 3.588A pdb=" N ILE N1157 " --> pdb=" O ASN N1153 " (cutoff:3.500A) Processing helix chain 'N' and resid 1162 through 1164 No H-bonds generated for 'chain 'N' and resid 1162 through 1164' Processing helix chain 'N' and resid 1165 through 1186 removed outlier: 3.867A pdb=" N ALA N1169 " --> pdb=" O TYR N1165 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE N1171 " --> pdb=" O GLY N1167 " (cutoff:3.500A) Processing helix chain 'N' and resid 1189 through 1201 removed outlier: 4.021A pdb=" N PHE N1193 " --> pdb=" O GLY N1189 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL N1196 " --> pdb=" O HIS N1192 " (cutoff:3.500A) Processing helix chain 'N' and resid 1203 through 1214 Processing helix chain 'N' and resid 1214 through 1231 removed outlier: 3.614A pdb=" N ARG N1231 " --> pdb=" O GLU N1227 " (cutoff:3.500A) Processing helix chain 'N' and resid 1241 through 1255 removed outlier: 4.244A pdb=" N GLU N1246 " --> pdb=" O ARG N1242 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN N1247 " --> pdb=" O PHE N1243 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU N1252 " --> pdb=" O LEU N1248 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN N1253 " --> pdb=" O SER N1249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.526A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.296A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 67 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 114 Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 96 removed outlier: 3.724A pdb=" N ASP C 141 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 215 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.905A pdb=" N LEU C 166 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.425A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.290A pdb=" N VAL E 93 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP E 141 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL E 95 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 113 Processing sheet with id=AB9, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.777A pdb=" N LEU E 164 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 173 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU E 166 " --> pdb=" O ARG E 171 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG E 171 " --> pdb=" O LEU E 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'F' and resid 93 through 96 removed outlier: 5.849A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 67 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA F 185 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL F 69 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 110 through 115 Processing sheet with id=AC4, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.658A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS G 539 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE G 583 " --> pdb=" O LYS G 539 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU G 541 " --> pdb=" O ILE G 583 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE G 585 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER G 545 " --> pdb=" O ILE G 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.658A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS G 539 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE G 583 " --> pdb=" O LYS G 539 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU G 541 " --> pdb=" O ILE G 583 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE G 585 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG G 597 " --> pdb=" O LEU G 582 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 584 " --> pdb=" O ARG G 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 377 through 381 removed outlier: 5.089A pdb=" N PHE G 379 " --> pdb=" O GLN G 406 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN G 406 " --> pdb=" O PHE G 379 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 381 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 43 through 47 Processing sheet with id=AC8, first strand: chain 'N' and resid 497 through 500 removed outlier: 6.729A pdb=" N VAL N 381 " --> pdb=" O PHE N 504 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY N 506 " --> pdb=" O VAL N 381 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU N 383 " --> pdb=" O GLY N 506 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA N 382 " --> pdb=" O VAL N 549 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 401 through 402 Processing sheet with id=AD1, first strand: chain 'N' and resid 451 through 454 removed outlier: 3.849A pdb=" N GLU N 451 " --> pdb=" O LEU N 495 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 613 through 614 Processing sheet with id=AD3, first strand: chain 'N' and resid 900 through 905 removed outlier: 6.299A pdb=" N PHE N 901 " --> pdb=" O THR N 957 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG N 959 " --> pdb=" O PHE N 901 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU N 903 " --> pdb=" O ARG N 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 1023 through 1025 removed outlier: 4.578A pdb=" N VAL N1023 " --> pdb=" O TYR N1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 1085 through 1089 removed outlier: 3.667A pdb=" N ASP N1127 " --> pdb=" O VAL N1135 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL N1135 " --> pdb=" O ASP N1127 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 3033 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: 5.34 Time building geometry restraints manager: 3.43 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: 8849 1.34 - 1.46: 3612 1.46 - 1.57: 13849 1.57 - 1.69: 16 1.69 - 1.81: 181 Bond restraints: 26507 Sorted by residual: bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 26502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 35922 3.91 - 7.82: 112 7.82 - 11.73: 10 11.73 - 15.64: 1 15.64 - 19.55: 3 Bond angle restraints: 36048 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 107.40 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 108.26 18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.98 16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" CD PRO A 129 " ideal model delta sigma weight residual 112.00 106.70 5.30 1.40e+00 5.10e-01 1.44e+01 angle pdb=" CA ASN C 218 " pdb=" C ASN C 218 " pdb=" O ASN C 218 " ideal model delta sigma weight residual 120.56 116.08 4.48 1.21e+00 6.83e-01 1.37e+01 ... (remaining 36043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14265 17.90 - 35.80: 1355 35.80 - 53.70: 259 53.70 - 71.60: 45 71.60 - 89.49: 19 Dihedral angle restraints: 15943 sinusoidal: 6388 harmonic: 9555 Sorted by residual: dihedral pdb=" CA VAL F 188 " pdb=" C VAL F 188 " pdb=" N GLY F 189 " pdb=" CA GLY F 189 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP E 141 " pdb=" C ASP E 141 " pdb=" N GLU E 142 " pdb=" CA GLU E 142 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP E 50 " pdb=" C ASP E 50 " pdb=" N ARG E 51 " pdb=" CA ARG E 51 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 15940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3240 0.054 - 0.107: 696 0.107 - 0.161: 80 0.161 - 0.214: 7 0.214 - 0.268: 4 Chirality restraints: 4027 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4024 not shown) Planarity restraints: 4746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 129 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 174 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO F 175 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO F 175 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 175 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N1146 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C VAL N1146 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL N1146 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL N1147 " -0.017 2.00e-02 2.50e+03 ... (remaining 4743 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 230 2.48 - 3.09: 18961 3.09 - 3.69: 41414 3.69 - 4.30: 57064 4.30 - 4.90: 90478 Nonbonded interactions: 208147 Sorted by model distance: nonbonded pdb=" O2G ANP D 401 " pdb="MG MG D 402 " model vdw 1.879 2.170 nonbonded pdb=" O2G ANP F 401 " pdb="MG MG F 402 " model vdw 1.932 2.170 nonbonded pdb=" O1B ANP D 401 " pdb="MG MG D 402 " model vdw 1.943 2.170 nonbonded pdb=" N3B ANP F 401 " pdb="MG MG F 402 " model vdw 2.048 2.250 nonbonded pdb=" NH1 ARG E 94 " pdb="MG MG E 402 " model vdw 2.060 2.250 ... (remaining 208142 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 5 through 319) selection = (chain 'B' and resid 5 through 319) selection = (chain 'C' and (resid 5 through 188 or resid 203 through 319)) selection = (chain 'D' and (resid 5 through 188 or resid 203 through 319)) selection = (chain 'E' and (resid 5 through 188 or resid 203 through 319)) selection = (chain 'F' and (resid 5 through 188 or resid 203 through 319)) } 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.630 Find NCS groups from input model: 0.380 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 26507 Z= 0.186 Angle : 0.679 19.549 36048 Z= 0.342 Chirality : 0.044 0.268 4027 Planarity : 0.005 0.100 4746 Dihedral : 14.553 89.494 9775 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 0.04 % Allowed : 0.55 % Favored : 99.41 % 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: -0.82 (0.15), residues: 3275 helix: 0.06 (0.15), residues: 1273 sheet: -0.73 (0.26), residues: 385 loop : -0.91 (0.17), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 271 TYR 0.023 0.001 TYR a 139 PHE 0.034 0.002 PHE D 309 TRP 0.039 0.002 TRP B 130 HIS 0.006 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (26507) covalent geometry : angle 0.67861 / 0.34 (36048) hydrogen bonds : bond 0.15294 / 10.09 ( 1049) hydrogen bonds : angle 6.48362 / 4.61 ( 3033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 754 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7504 (pp30) cc_final: 0.7180 (pp30) REVERT: A 83 GLN cc_start: 0.8459 (mp10) cc_final: 0.7912 (mp10) REVERT: A 138 LEU cc_start: 0.7879 (tp) cc_final: 0.7520 (tp) REVERT: A 176 HIS cc_start: 0.7900 (t-90) cc_final: 0.7520 (t-90) REVERT: A 215 THR cc_start: 0.8681 (t) cc_final: 0.8424 (t) REVERT: A 244 ILE cc_start: 0.7803 (mt) cc_final: 0.7335 (mt) REVERT: A 248 MET cc_start: 0.7604 (mtm) cc_final: 0.7083 (mtm) REVERT: A 268 MET cc_start: 0.6655 (mmm) cc_final: 0.6182 (mmm) REVERT: A 275 THR cc_start: 0.8711 (m) cc_final: 0.8505 (m) REVERT: B 155 GLN cc_start: 0.8549 (tp40) cc_final: 0.7751 (tp40) REVERT: B 230 LEU cc_start: 0.8429 (mt) cc_final: 0.8219 (mt) REVERT: B 288 PHE cc_start: 0.7486 (m-10) cc_final: 0.7197 (m-10) REVERT: C 42 GLU cc_start: 0.7462 (pm20) cc_final: 0.6987 (pm20) REVERT: C 47 TYR cc_start: 0.7840 (t80) cc_final: 0.7331 (t80) REVERT: C 49 PHE cc_start: 0.8149 (m-10) cc_final: 0.7502 (m-10) REVERT: C 89 ASN cc_start: 0.8569 (m110) cc_final: 0.8284 (m110) REVERT: C 240 GLU cc_start: 0.8073 (tp30) cc_final: 0.7601 (tp30) REVERT: C 278 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6592 (tm-30) REVERT: C 302 GLU cc_start: 0.7742 (mp0) cc_final: 0.7062 (mp0) REVERT: D 11 LEU cc_start: 0.8171 (mm) cc_final: 0.7946 (mm) REVERT: D 93 VAL cc_start: 0.8442 (t) cc_final: 0.8116 (p) REVERT: D 96 ASN cc_start: 0.8475 (m-40) cc_final: 0.8247 (m-40) REVERT: D 151 MET cc_start: 0.7316 (tmm) cc_final: 0.7059 (tmm) REVERT: D 168 ASP cc_start: 0.7255 (t0) cc_final: 0.6844 (t0) REVERT: D 186 ASN cc_start: 0.7835 (p0) cc_final: 0.7598 (p0) REVERT: D 207 GLN cc_start: 0.7402 (pt0) cc_final: 0.7084 (pt0) REVERT: D 248 MET cc_start: 0.7652 (mtp) cc_final: 0.7078 (mtp) REVERT: D 254 MET cc_start: 0.7971 (ppp) cc_final: 0.7751 (ppp) REVERT: E 77 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7621 (ptpp) REVERT: E 158 LEU cc_start: 0.8083 (tp) cc_final: 0.7759 (tp) REVERT: E 202 GLN cc_start: 0.7831 (pp30) cc_final: 0.7260 (pp30) REVERT: E 288 PHE cc_start: 0.8181 (t80) cc_final: 0.7878 (t80) REVERT: E 290 PHE cc_start: 0.8024 (t80) cc_final: 0.7806 (t80) REVERT: F 25 ASP cc_start: 0.5608 (t0) cc_final: 0.4784 (t0) REVERT: F 48 LEU cc_start: 0.7554 (tp) cc_final: 0.7305 (tp) REVERT: F 98 ASP cc_start: 0.6659 (m-30) cc_final: 0.6438 (m-30) REVERT: F 103 ARG cc_start: 0.7891 (ptt-90) cc_final: 0.7659 (ptt-90) REVERT: F 123 PHE cc_start: 0.7580 (t80) cc_final: 0.7343 (t80) REVERT: F 124 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8390 (mtmt) REVERT: F 135 ASN cc_start: 0.8374 (p0) cc_final: 0.7917 (p0) REVERT: F 151 MET cc_start: 0.7401 (mmp) cc_final: 0.7108 (mmp) REVERT: F 171 ARG cc_start: 0.7432 (tpt90) cc_final: 0.7138 (tpt90) REVERT: F 201 GLN cc_start: 0.8049 (mm110) cc_final: 0.7829 (mm110) REVERT: F 227 ASN cc_start: 0.8199 (m110) cc_final: 0.7871 (m110) REVERT: F 279 ASN cc_start: 0.8087 (m110) cc_final: 0.7703 (m110) REVERT: F 290 PHE cc_start: 0.7899 (t80) cc_final: 0.7605 (t80) REVERT: G 323 ARG cc_start: 0.7747 (tpm170) cc_final: 0.7545 (tpm170) REVERT: G 387 ASP cc_start: 0.7062 (t70) cc_final: 0.6710 (t70) REVERT: G 446 LEU cc_start: 0.8571 (mt) cc_final: 0.8236 (mt) REVERT: G 463 TRP cc_start: 0.7169 (m-90) cc_final: 0.6648 (m-90) REVERT: G 489 HIS cc_start: 0.6180 (t70) cc_final: 0.5569 (t-170) REVERT: G 526 TRP cc_start: 0.7792 (t60) cc_final: 0.7316 (t60) REVERT: G 544 ILE cc_start: 0.8295 (mp) cc_final: 0.7604 (mp) REVERT: G 561 ASN cc_start: 0.8259 (t0) cc_final: 0.8023 (t0) REVERT: a 23 GLU cc_start: 0.7663 (tp30) cc_final: 0.7437 (tp30) REVERT: a 70 HIS cc_start: 0.8140 (t-90) cc_final: 0.7932 (t-90) REVERT: a 131 LEU cc_start: 0.7623 (mt) cc_final: 0.7106 (mt) REVERT: a 134 MET cc_start: 0.7201 (ppp) cc_final: 0.6620 (ppp) REVERT: a 219 MET cc_start: 0.5489 (tmm) cc_final: 0.4877 (tmm) REVERT: N 395 LEU cc_start: 0.8146 (tp) cc_final: 0.7790 (tp) REVERT: N 472 GLU cc_start: 0.8662 (mp0) cc_final: 0.8315 (mp0) REVERT: N 551 MET cc_start: -0.2449 (ttp) cc_final: -0.2820 (ttp) REVERT: N 608 HIS cc_start: 0.8641 (p-80) cc_final: 0.8194 (p90) REVERT: N 782 GLU cc_start: 0.8868 (tt0) cc_final: 0.8569 (tt0) REVERT: N 880 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7950 (mmtt) REVERT: N 881 LYS cc_start: 0.7310 (mtmm) cc_final: 0.6990 (mtmm) REVERT: N 885 LEU cc_start: 0.8281 (tp) cc_final: 0.7943 (tp) REVERT: N 928 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7329 (tp40) REVERT: N 1038 LEU cc_start: 0.7221 (mm) cc_final: 0.6977 (mm) REVERT: N 1054 TRP cc_start: 0.7356 (t60) cc_final: 0.7014 (t60) REVERT: N 1105 PHE cc_start: 0.7155 (m-80) cc_final: 0.6785 (m-80) REVERT: N 1139 LEU cc_start: 0.7906 (tp) cc_final: 0.7560 (tp) REVERT: N 1142 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6777 (tm-30) REVERT: N 1209 PHE cc_start: 0.7218 (t80) cc_final: 0.6698 (t80) REVERT: N 1210 MET cc_start: 0.7604 (mtm) cc_final: 0.7387 (mtm) REVERT: N 1225 LEU cc_start: 0.8500 (mm) cc_final: 0.8260 (mm) REVERT: N 1243 PHE cc_start: 0.7798 (t80) cc_final: 0.7275 (t80) outliers start: 1 outliers final: 0 residues processed: 754 average time/residue: 0.1790 time to fit residues: 208.4824 Evaluate side-chains 735 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 735 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 52 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** N 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 815 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1125 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.169952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135382 restraints weight = 48427.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140602 restraints weight = 29754.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144247 restraints weight = 20467.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147149 restraints weight = 15283.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149055 restraints weight = 11995.669| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26507 Z= 0.179 Angle : 0.598 12.988 36048 Z= 0.314 Chirality : 0.043 0.186 4027 Planarity : 0.005 0.059 4746 Dihedral : 7.029 84.763 3737 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.26 % Allowed : 6.15 % 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: -0.83 (0.15), residues: 3275 helix: 0.06 (0.14), residues: 1331 sheet: -0.48 (0.28), residues: 351 loop : -1.03 (0.17), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N1150 TYR 0.018 0.001 TYR N 538 PHE 0.026 0.002 PHE D 61 TRP 0.015 0.002 TRP N1054 HIS 0.007 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (26507) covalent geometry : angle 0.59792 / 0.31 (36048) hydrogen bonds : bond 0.04272 / 2.86 ( 1049) hydrogen bonds : angle 5.47330 / 3.89 ( 3033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 774 time to evaluate : 0.800 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: A 22 PHE cc_start: 0.7862 (m-10) cc_final: 0.7658 (m-10) REVERT: A 52 GLN cc_start: 0.7674 (pp30) cc_final: 0.7340 (pp30) REVERT: A 68 MET cc_start: 0.6755 (tpt) cc_final: 0.6431 (tpt) REVERT: A 72 TYR cc_start: 0.6768 (m-80) cc_final: 0.6223 (m-80) REVERT: A 138 LEU cc_start: 0.7763 (tp) cc_final: 0.7397 (tp) REVERT: A 176 HIS cc_start: 0.7933 (t-90) cc_final: 0.7497 (t-90) REVERT: A 215 THR cc_start: 0.8749 (t) cc_final: 0.8436 (t) REVERT: A 244 ILE cc_start: 0.8014 (mt) cc_final: 0.7560 (mt) REVERT: A 248 MET cc_start: 0.7806 (mtm) cc_final: 0.7238 (mtm) REVERT: A 268 MET cc_start: 0.7029 (mmm) cc_final: 0.6549 (mmm) REVERT: A 282 ILE cc_start: 0.8265 (mt) cc_final: 0.8060 (mt) REVERT: B 130 TRP cc_start: 0.8398 (t60) cc_final: 0.7746 (t60) REVERT: B 155 GLN cc_start: 0.8566 (tp40) cc_final: 0.7802 (tp40) REVERT: B 230 LEU cc_start: 0.8714 (mt) cc_final: 0.8432 (mt) REVERT: B 253 ASP cc_start: 0.7747 (m-30) cc_final: 0.7489 (m-30) REVERT: C 42 GLU cc_start: 0.7428 (pm20) cc_final: 0.6972 (pm20) REVERT: C 47 TYR cc_start: 0.7862 (t80) cc_final: 0.7385 (t80) REVERT: C 49 PHE cc_start: 0.8178 (m-10) cc_final: 0.7544 (m-10) REVERT: C 89 ASN cc_start: 0.8585 (m110) cc_final: 0.8300 (m110) REVERT: C 98 ASP cc_start: 0.7227 (t0) cc_final: 0.6940 (t0) REVERT: C 135 ASN cc_start: 0.8475 (p0) cc_final: 0.7927 (p0) REVERT: C 150 VAL cc_start: 0.8421 (t) cc_final: 0.8024 (p) REVERT: C 240 GLU cc_start: 0.7812 (tp30) cc_final: 0.7518 (tp30) REVERT: C 302 GLU cc_start: 0.7830 (mp0) cc_final: 0.7188 (mp0) REVERT: D 11 LEU cc_start: 0.8200 (mm) cc_final: 0.7976 (mm) REVERT: D 93 VAL cc_start: 0.8424 (t) cc_final: 0.8112 (p) REVERT: D 151 MET cc_start: 0.7297 (tmm) cc_final: 0.6507 (tmm) REVERT: D 168 ASP cc_start: 0.7202 (t0) cc_final: 0.6882 (t0) REVERT: D 207 GLN cc_start: 0.7463 (pt0) cc_final: 0.7262 (pt0) REVERT: D 246 ASN cc_start: 0.8520 (m-40) cc_final: 0.8266 (m-40) REVERT: D 248 MET cc_start: 0.7661 (mtp) cc_final: 0.7091 (mtp) REVERT: D 254 MET cc_start: 0.7968 (ppp) cc_final: 0.7668 (ppp) REVERT: D 279 ASN cc_start: 0.8263 (m-40) cc_final: 0.7969 (m-40) REVERT: D 294 PHE cc_start: 0.6855 (t80) cc_final: 0.6564 (t80) REVERT: E 68 MET cc_start: 0.7940 (ppp) cc_final: 0.7683 (ppp) REVERT: E 75 THR cc_start: 0.7526 (m) cc_final: 0.7321 (m) REVERT: E 77 LYS cc_start: 0.7828 (ptpp) cc_final: 0.7554 (ptpp) REVERT: E 97 LEU cc_start: 0.8236 (mt) cc_final: 0.7876 (mt) REVERT: E 158 LEU cc_start: 0.8106 (tp) cc_final: 0.7842 (tp) REVERT: E 180 ARG cc_start: 0.8705 (mpt180) cc_final: 0.8504 (mmt-90) REVERT: E 186 ASN cc_start: 0.8027 (m-40) cc_final: 0.7744 (m-40) REVERT: E 202 GLN cc_start: 0.7759 (pp30) cc_final: 0.7159 (pp30) REVERT: E 219 TYR cc_start: 0.8201 (m-80) cc_final: 0.7661 (m-80) REVERT: E 257 GLN cc_start: 0.7327 (tm-30) cc_final: 0.6814 (tm-30) REVERT: E 288 PHE cc_start: 0.8235 (t80) cc_final: 0.7860 (t80) REVERT: E 290 PHE cc_start: 0.8163 (t80) cc_final: 0.7833 (t80) REVERT: F 25 ASP cc_start: 0.5957 (t0) cc_final: 0.5464 (t0) REVERT: F 48 LEU cc_start: 0.7620 (tp) cc_final: 0.7374 (tp) REVERT: F 123 PHE cc_start: 0.7554 (t80) cc_final: 0.7325 (t80) REVERT: F 124 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8407 (mtmt) REVERT: F 135 ASN cc_start: 0.8552 (p0) cc_final: 0.7898 (p0) REVERT: F 171 ARG cc_start: 0.7405 (tpt90) cc_final: 0.7105 (tpt90) REVERT: F 201 GLN cc_start: 0.8040 (mm110) cc_final: 0.7800 (mm110) REVERT: F 227 ASN cc_start: 0.8223 (m110) cc_final: 0.7879 (m110) REVERT: F 248 MET cc_start: 0.8200 (mmt) cc_final: 0.7760 (mmp) REVERT: F 276 TRP cc_start: 0.8700 (t60) cc_final: 0.8018 (t60) REVERT: F 279 ASN cc_start: 0.8097 (m110) cc_final: 0.7805 (m110) REVERT: F 290 PHE cc_start: 0.7893 (t80) cc_final: 0.7591 (t80) REVERT: G 323 ARG cc_start: 0.7774 (tpm170) cc_final: 0.7571 (tpm170) REVERT: G 387 ASP cc_start: 0.7493 (t70) cc_final: 0.7086 (t70) REVERT: G 427 MET cc_start: 0.7221 (pmm) cc_final: 0.6524 (pmm) REVERT: G 432 ILE cc_start: 0.8312 (tp) cc_final: 0.8057 (tp) REVERT: G 446 LEU cc_start: 0.8625 (mt) cc_final: 0.8366 (mt) REVERT: G 448 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7830 (ttt180) REVERT: G 463 TRP cc_start: 0.7212 (m-90) cc_final: 0.6802 (m-90) REVERT: G 544 ILE cc_start: 0.8332 (mp) cc_final: 0.7610 (mp) REVERT: G 561 ASN cc_start: 0.8326 (t0) cc_final: 0.8123 (t0) REVERT: a 23 GLU cc_start: 0.7684 (tp30) cc_final: 0.7425 (tp30) REVERT: a 70 HIS cc_start: 0.8187 (t-90) cc_final: 0.7976 (t-90) REVERT: a 131 LEU cc_start: 0.7612 (mt) cc_final: 0.7067 (mt) REVERT: a 134 MET cc_start: 0.7304 (ppp) cc_final: 0.6619 (ppp) REVERT: a 181 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7575 (mm-30) REVERT: a 219 MET cc_start: 0.5511 (tmm) cc_final: 0.4844 (tmm) REVERT: N 395 LEU cc_start: 0.8013 (tp) cc_final: 0.7577 (tp) REVERT: N 551 MET cc_start: -0.1944 (ttp) cc_final: -0.2212 (ttp) REVERT: N 586 PHE cc_start: 0.7831 (m-10) cc_final: 0.7595 (m-80) REVERT: N 608 HIS cc_start: 0.8539 (p-80) cc_final: 0.8320 (p90) REVERT: N 677 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7928 (ptpp) REVERT: N 681 TYR cc_start: 0.7342 (t80) cc_final: 0.7122 (t80) REVERT: N 782 GLU cc_start: 0.8887 (tt0) cc_final: 0.8594 (tt0) REVERT: N 860 ARG cc_start: 0.7202 (mmp80) cc_final: 0.6944 (mmp80) REVERT: N 885 LEU cc_start: 0.8402 (tp) cc_final: 0.8076 (tp) REVERT: N 891 THR cc_start: 0.8414 (p) cc_final: 0.8206 (t) REVERT: N 928 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7315 (tp-100) REVERT: N 1038 LEU cc_start: 0.7288 (mm) cc_final: 0.6972 (mm) REVERT: N 1054 TRP cc_start: 0.7400 (t60) cc_final: 0.7053 (t60) REVERT: N 1105 PHE cc_start: 0.7218 (m-80) cc_final: 0.6885 (m-80) REVERT: N 1139 LEU cc_start: 0.8045 (tp) cc_final: 0.7802 (tp) REVERT: N 1142 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6919 (tm-30) REVERT: N 1209 PHE cc_start: 0.7283 (t80) cc_final: 0.6823 (t80) REVERT: N 1225 LEU cc_start: 0.8541 (mm) cc_final: 0.8298 (mm) REVERT: N 1243 PHE cc_start: 0.7796 (t80) cc_final: 0.7292 (t80) REVERT: N 1251 HIS cc_start: 0.6901 (m-70) cc_final: 0.6674 (m-70) outliers start: 7 outliers final: 0 residues processed: 778 average time/residue: 0.1818 time to fit residues: 216.7638 Evaluate side-chains 745 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 217 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 120 optimal weight: 0.3980 chunk 213 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 207 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 235 HIS ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS a 86 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 608 HIS N 790 GLN N 815 GLN N 928 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.172179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137697 restraints weight = 48079.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143052 restraints weight = 29137.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146910 restraints weight = 19868.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149523 restraints weight = 14645.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151773 restraints weight = 11566.362| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26507 Z= 0.121 Angle : 0.576 12.354 36048 Z= 0.296 Chirality : 0.043 0.161 4027 Planarity : 0.004 0.054 4746 Dihedral : 6.529 83.404 3737 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.91 % 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: -0.77 (0.15), residues: 3275 helix: 0.14 (0.14), residues: 1329 sheet: -0.51 (0.28), residues: 365 loop : -1.01 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 271 TYR 0.052 0.001 TYR a 139 PHE 0.032 0.001 PHE E 61 TRP 0.012 0.001 TRP N1054 HIS 0.009 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (26507) covalent geometry : angle 0.57641 / 0.30 (36048) hydrogen bonds : bond 0.03663 / 2.44 ( 1049) hydrogen bonds : angle 5.20651 / 3.69 ( 3033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 785 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7547 (pp30) cc_final: 0.7198 (pp30) REVERT: A 53 THR cc_start: 0.8229 (p) cc_final: 0.7689 (p) REVERT: A 68 MET cc_start: 0.6834 (tpt) cc_final: 0.6504 (tpt) REVERT: A 72 TYR cc_start: 0.6785 (m-80) cc_final: 0.6265 (m-80) REVERT: A 138 LEU cc_start: 0.7710 (tp) cc_final: 0.7349 (tp) REVERT: A 176 HIS cc_start: 0.7917 (t-90) cc_final: 0.7415 (t-90) REVERT: A 215 THR cc_start: 0.8721 (t) cc_final: 0.8427 (t) REVERT: A 244 ILE cc_start: 0.7985 (mt) cc_final: 0.7581 (mt) REVERT: A 248 MET cc_start: 0.7701 (mtm) cc_final: 0.7173 (mtm) REVERT: A 268 MET cc_start: 0.6991 (mmm) cc_final: 0.6519 (mmm) REVERT: A 282 ILE cc_start: 0.8186 (mt) cc_final: 0.7979 (mt) REVERT: B 68 MET cc_start: 0.7217 (ptt) cc_final: 0.6978 (ptt) REVERT: B 130 TRP cc_start: 0.8385 (t60) cc_final: 0.7796 (t60) REVERT: B 155 GLN cc_start: 0.8539 (tp40) cc_final: 0.7804 (tp40) REVERT: B 230 LEU cc_start: 0.8669 (mt) cc_final: 0.8386 (mt) REVERT: B 253 ASP cc_start: 0.7926 (m-30) cc_final: 0.7493 (m-30) REVERT: C 33 TYR cc_start: 0.5766 (m-10) cc_final: 0.5516 (m-10) REVERT: C 40 VAL cc_start: 0.8062 (t) cc_final: 0.7584 (m) REVERT: C 42 GLU cc_start: 0.7406 (pm20) cc_final: 0.6933 (pm20) REVERT: C 47 TYR cc_start: 0.7836 (t80) cc_final: 0.7409 (t80) REVERT: C 49 PHE cc_start: 0.8164 (m-10) cc_final: 0.7530 (m-10) REVERT: C 89 ASN cc_start: 0.8531 (m110) cc_final: 0.8266 (m110) REVERT: C 98 ASP cc_start: 0.7140 (t0) cc_final: 0.6919 (t0) REVERT: C 135 ASN cc_start: 0.8463 (p0) cc_final: 0.7822 (p0) REVERT: C 150 VAL cc_start: 0.8342 (t) cc_final: 0.8068 (t) REVERT: C 227 ASN cc_start: 0.8776 (m110) cc_final: 0.8549 (m110) REVERT: C 240 GLU cc_start: 0.7768 (tp30) cc_final: 0.7434 (tp30) REVERT: C 302 GLU cc_start: 0.7866 (mp0) cc_final: 0.7241 (mp0) REVERT: D 11 LEU cc_start: 0.8198 (mm) cc_final: 0.7954 (mm) REVERT: D 93 VAL cc_start: 0.8435 (t) cc_final: 0.8127 (p) REVERT: D 151 MET cc_start: 0.7251 (tmm) cc_final: 0.6533 (tmm) REVERT: D 168 ASP cc_start: 0.7170 (t0) cc_final: 0.6874 (t0) REVERT: D 207 GLN cc_start: 0.7433 (pt0) cc_final: 0.7141 (pt0) REVERT: D 248 MET cc_start: 0.7560 (mtp) cc_final: 0.7045 (mtp) REVERT: D 254 MET cc_start: 0.7958 (ppp) cc_final: 0.7653 (ppp) REVERT: D 279 ASN cc_start: 0.8192 (m-40) cc_final: 0.7883 (m-40) REVERT: D 294 PHE cc_start: 0.6738 (t80) cc_final: 0.6447 (t80) REVERT: E 68 MET cc_start: 0.7993 (ppp) cc_final: 0.7535 (ppp) REVERT: E 75 THR cc_start: 0.7464 (m) cc_final: 0.7243 (m) REVERT: E 77 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7528 (ptpp) REVERT: E 97 LEU cc_start: 0.8247 (mt) cc_final: 0.7969 (mt) REVERT: E 158 LEU cc_start: 0.8087 (tp) cc_final: 0.7754 (tp) REVERT: E 166 LEU cc_start: 0.8976 (mp) cc_final: 0.8764 (mp) REVERT: E 186 ASN cc_start: 0.7749 (m-40) cc_final: 0.7419 (m-40) REVERT: E 202 GLN cc_start: 0.7799 (pp30) cc_final: 0.7382 (pp30) REVERT: E 219 TYR cc_start: 0.8155 (m-80) cc_final: 0.7608 (m-80) REVERT: E 220 LEU cc_start: 0.7766 (mt) cc_final: 0.7389 (mt) REVERT: E 288 PHE cc_start: 0.8201 (t80) cc_final: 0.7728 (t80) REVERT: E 290 PHE cc_start: 0.8137 (t80) cc_final: 0.7805 (t80) REVERT: F 25 ASP cc_start: 0.5960 (t0) cc_final: 0.5472 (t0) REVERT: F 48 LEU cc_start: 0.7584 (tp) cc_final: 0.7309 (tp) REVERT: F 63 TYR cc_start: 0.6434 (m-10) cc_final: 0.6203 (m-10) REVERT: F 98 ASP cc_start: 0.6258 (m-30) cc_final: 0.5627 (m-30) REVERT: F 103 ARG cc_start: 0.7843 (ptt-90) cc_final: 0.7639 (ptt-90) REVERT: F 123 PHE cc_start: 0.7570 (t80) cc_final: 0.7320 (t80) REVERT: F 124 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8420 (mtmt) REVERT: F 135 ASN cc_start: 0.8602 (p0) cc_final: 0.7984 (p0) REVERT: F 151 MET cc_start: 0.7105 (mmp) cc_final: 0.6793 (mmp) REVERT: F 171 ARG cc_start: 0.7408 (tpt90) cc_final: 0.7085 (tpt90) REVERT: F 198 HIS cc_start: 0.7855 (m-70) cc_final: 0.7645 (m90) REVERT: F 201 GLN cc_start: 0.8028 (mm110) cc_final: 0.7739 (mm110) REVERT: F 227 ASN cc_start: 0.8200 (m110) cc_final: 0.7802 (m110) REVERT: F 279 ASN cc_start: 0.8113 (m110) cc_final: 0.7887 (m-40) REVERT: F 290 PHE cc_start: 0.7818 (t80) cc_final: 0.7603 (t80) REVERT: G 387 ASP cc_start: 0.7448 (t70) cc_final: 0.7063 (t70) REVERT: G 427 MET cc_start: 0.7019 (pmm) cc_final: 0.6554 (pmm) REVERT: G 430 ARG cc_start: 0.8158 (ptt90) cc_final: 0.7688 (ptt90) REVERT: G 447 GLU cc_start: 0.7596 (pp20) cc_final: 0.7381 (pp20) REVERT: G 448 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7842 (ttt180) REVERT: G 489 HIS cc_start: 0.5642 (t70) cc_final: 0.3717 (t-170) REVERT: G 526 TRP cc_start: 0.7652 (t60) cc_final: 0.7418 (t60) REVERT: G 544 ILE cc_start: 0.8274 (mp) cc_final: 0.7592 (mp) REVERT: a 23 GLU cc_start: 0.7640 (tp30) cc_final: 0.7397 (tp30) REVERT: a 42 MET cc_start: 0.7634 (mmp) cc_final: 0.7426 (mmp) REVERT: a 70 HIS cc_start: 0.8175 (t-90) cc_final: 0.7954 (t-90) REVERT: a 131 LEU cc_start: 0.7534 (mt) cc_final: 0.7026 (mt) REVERT: a 134 MET cc_start: 0.7184 (ppp) cc_final: 0.6470 (ppp) REVERT: a 181 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7540 (mm-30) REVERT: a 219 MET cc_start: 0.5569 (tmm) cc_final: 0.4730 (tmm) REVERT: N 395 LEU cc_start: 0.7924 (tp) cc_final: 0.7444 (tp) REVERT: N 551 MET cc_start: -0.1822 (ttp) cc_final: -0.2082 (ttp) REVERT: N 782 GLU cc_start: 0.8857 (tt0) cc_final: 0.8571 (tt0) REVERT: N 860 ARG cc_start: 0.7219 (mmp80) cc_final: 0.6905 (mmp80) REVERT: N 881 LYS cc_start: 0.7415 (mtmm) cc_final: 0.7082 (mtmm) REVERT: N 885 LEU cc_start: 0.8365 (tp) cc_final: 0.8032 (tp) REVERT: N 890 TYR cc_start: 0.8763 (t80) cc_final: 0.8477 (t80) REVERT: N 928 GLN cc_start: 0.7716 (tp40) cc_final: 0.7400 (tp40) REVERT: N 1038 LEU cc_start: 0.7174 (mm) cc_final: 0.6803 (mm) REVERT: N 1049 ASP cc_start: 0.8913 (m-30) cc_final: 0.8670 (m-30) REVERT: N 1105 PHE cc_start: 0.7164 (m-80) cc_final: 0.6793 (m-80) REVERT: N 1207 HIS cc_start: 0.7626 (t-90) cc_final: 0.7012 (t-90) REVERT: N 1209 PHE cc_start: 0.7288 (t80) cc_final: 0.6793 (t80) REVERT: N 1225 LEU cc_start: 0.8524 (mm) cc_final: 0.8295 (mm) REVERT: N 1243 PHE cc_start: 0.7824 (t80) cc_final: 0.7273 (t80) REVERT: N 1251 HIS cc_start: 0.6936 (m-70) cc_final: 0.6645 (m-70) outliers start: 4 outliers final: 0 residues processed: 788 average time/residue: 0.1778 time to fit residues: 216.2429 Evaluate side-chains 749 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 749 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 198 optimal weight: 0.0670 chunk 2 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 138 optimal weight: 0.0370 chunk 28 optimal weight: 0.2980 chunk 141 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 207 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 207 GLN E 261 ASN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 815 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139191 restraints weight = 48008.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144640 restraints weight = 29055.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148524 restraints weight = 19685.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151278 restraints weight = 14456.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153301 restraints weight = 11320.824| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26507 Z= 0.107 Angle : 0.555 12.420 36048 Z= 0.283 Chirality : 0.042 0.206 4027 Planarity : 0.004 0.049 4746 Dihedral : 6.091 82.470 3737 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.02 % 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: -0.74 (0.15), residues: 3275 helix: 0.16 (0.14), residues: 1348 sheet: -0.39 (0.29), residues: 343 loop : -1.03 (0.17), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 87 TYR 0.018 0.001 TYR a 139 PHE 0.030 0.001 PHE B 61 TRP 0.020 0.001 TRP N1044 HIS 0.009 0.001 HIS N 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (26507) covalent geometry : angle 0.55453 / 0.28 (36048) hydrogen bonds : bond 0.03307 / 2.22 ( 1049) hydrogen bonds : angle 4.99561 / 3.54 ( 3033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 780 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7566 (pp30) cc_final: 0.7221 (pp30) REVERT: A 53 THR cc_start: 0.8262 (p) cc_final: 0.7727 (p) REVERT: A 68 MET cc_start: 0.6837 (tpt) cc_final: 0.6384 (tpt) REVERT: A 72 TYR cc_start: 0.6786 (m-80) cc_final: 0.6273 (m-80) REVERT: A 215 THR cc_start: 0.8719 (t) cc_final: 0.8438 (t) REVERT: A 244 ILE cc_start: 0.8029 (mt) cc_final: 0.7606 (mt) REVERT: A 248 MET cc_start: 0.7692 (mtm) cc_final: 0.7169 (mtm) REVERT: A 268 MET cc_start: 0.6951 (mmm) cc_final: 0.6485 (mmm) REVERT: A 282 ILE cc_start: 0.8139 (mt) cc_final: 0.7932 (mt) REVERT: B 130 TRP cc_start: 0.8344 (t60) cc_final: 0.7732 (t60) REVERT: B 155 GLN cc_start: 0.8540 (tp40) cc_final: 0.7862 (tp40) REVERT: B 230 LEU cc_start: 0.8619 (mt) cc_final: 0.8363 (mt) REVERT: B 253 ASP cc_start: 0.7898 (m-30) cc_final: 0.7531 (m-30) REVERT: C 42 GLU cc_start: 0.7387 (pm20) cc_final: 0.6933 (pm20) REVERT: C 47 TYR cc_start: 0.7828 (t80) cc_final: 0.7435 (t80) REVERT: C 49 PHE cc_start: 0.8155 (m-10) cc_final: 0.7541 (m-10) REVERT: C 89 ASN cc_start: 0.8483 (m110) cc_final: 0.8210 (m110) REVERT: C 150 VAL cc_start: 0.8338 (t) cc_final: 0.8046 (t) REVERT: C 227 ASN cc_start: 0.8789 (m110) cc_final: 0.8505 (m110) REVERT: C 240 GLU cc_start: 0.7762 (tp30) cc_final: 0.7398 (tp30) REVERT: C 257 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7985 (mm-40) REVERT: C 302 GLU cc_start: 0.7869 (mp0) cc_final: 0.7245 (mp0) REVERT: D 11 LEU cc_start: 0.8128 (mm) cc_final: 0.7875 (mm) REVERT: D 29 MET cc_start: 0.6260 (tpt) cc_final: 0.5993 (tpt) REVERT: D 66 ARG cc_start: 0.6820 (mmt-90) cc_final: 0.6611 (mmt-90) REVERT: D 93 VAL cc_start: 0.8442 (t) cc_final: 0.8093 (p) REVERT: D 94 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7050 (ttm110) REVERT: D 96 ASN cc_start: 0.8432 (m-40) cc_final: 0.8106 (m-40) REVERT: D 151 MET cc_start: 0.7228 (tmm) cc_final: 0.6509 (tmm) REVERT: D 186 ASN cc_start: 0.7750 (p0) cc_final: 0.7375 (p0) REVERT: D 207 GLN cc_start: 0.7458 (pt0) cc_final: 0.7116 (pt0) REVERT: D 237 GLN cc_start: 0.7070 (mt0) cc_final: 0.6842 (mt0) REVERT: D 238 ASN cc_start: 0.8642 (t0) cc_final: 0.8201 (t0) REVERT: D 248 MET cc_start: 0.7555 (mtp) cc_final: 0.7100 (mtp) REVERT: D 254 MET cc_start: 0.7979 (ppp) cc_final: 0.7657 (ppp) REVERT: D 279 ASN cc_start: 0.8144 (m-40) cc_final: 0.7823 (m-40) REVERT: D 294 PHE cc_start: 0.6696 (t80) cc_final: 0.6473 (t80) REVERT: E 57 ILE cc_start: 0.7993 (mm) cc_final: 0.7779 (mm) REVERT: E 68 MET cc_start: 0.7894 (ppp) cc_final: 0.7486 (ppp) REVERT: E 77 LYS cc_start: 0.7891 (ptpp) cc_final: 0.7567 (ptpp) REVERT: E 97 LEU cc_start: 0.8275 (mt) cc_final: 0.7980 (mt) REVERT: E 158 LEU cc_start: 0.8263 (tp) cc_final: 0.7613 (tp) REVERT: E 166 LEU cc_start: 0.8936 (mp) cc_final: 0.8681 (mp) REVERT: E 171 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7998 (ptm160) REVERT: E 186 ASN cc_start: 0.7611 (m-40) cc_final: 0.7286 (m-40) REVERT: E 202 GLN cc_start: 0.7866 (pp30) cc_final: 0.7431 (pp30) REVERT: E 288 PHE cc_start: 0.8184 (t80) cc_final: 0.7754 (t80) REVERT: E 290 PHE cc_start: 0.8084 (t80) cc_final: 0.7806 (t80) REVERT: F 25 ASP cc_start: 0.5958 (t0) cc_final: 0.5405 (t0) REVERT: F 28 MET cc_start: 0.6568 (mmp) cc_final: 0.6169 (mmm) REVERT: F 29 MET cc_start: 0.7780 (mmm) cc_final: 0.7120 (mmm) REVERT: F 48 LEU cc_start: 0.7539 (tp) cc_final: 0.7302 (tp) REVERT: F 63 TYR cc_start: 0.6325 (m-10) cc_final: 0.6106 (m-10) REVERT: F 98 ASP cc_start: 0.6202 (m-30) cc_final: 0.5519 (m-30) REVERT: F 103 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7592 (ptt-90) REVERT: F 123 PHE cc_start: 0.7558 (t80) cc_final: 0.7305 (t80) REVERT: F 124 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8403 (mtmt) REVERT: F 135 ASN cc_start: 0.8623 (p0) cc_final: 0.8006 (p0) REVERT: F 151 MET cc_start: 0.7044 (mmp) cc_final: 0.6744 (mmp) REVERT: F 171 ARG cc_start: 0.7368 (tpt90) cc_final: 0.7058 (tpt90) REVERT: F 201 GLN cc_start: 0.8009 (mm110) cc_final: 0.7706 (mm110) REVERT: F 227 ASN cc_start: 0.8185 (m110) cc_final: 0.7817 (m110) REVERT: F 248 MET cc_start: 0.8325 (mmm) cc_final: 0.8002 (mmt) REVERT: F 256 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7620 (ptp90) REVERT: F 275 THR cc_start: 0.8170 (m) cc_final: 0.7596 (m) REVERT: F 279 ASN cc_start: 0.8117 (m110) cc_final: 0.7836 (m110) REVERT: F 290 PHE cc_start: 0.7857 (t80) cc_final: 0.7607 (t80) REVERT: G 322 THR cc_start: 0.8571 (t) cc_final: 0.8300 (t) REVERT: G 323 ARG cc_start: 0.7731 (tpm170) cc_final: 0.7477 (tpm170) REVERT: G 387 ASP cc_start: 0.7454 (t70) cc_final: 0.7046 (t70) REVERT: G 421 LEU cc_start: 0.8156 (mp) cc_final: 0.7954 (mp) REVERT: G 427 MET cc_start: 0.6959 (pmm) cc_final: 0.6462 (pmm) REVERT: G 430 ARG cc_start: 0.8095 (ptt90) cc_final: 0.7635 (ptt90) REVERT: G 432 ILE cc_start: 0.8347 (tp) cc_final: 0.8116 (tp) REVERT: G 446 LEU cc_start: 0.8602 (mt) cc_final: 0.8364 (mt) REVERT: G 447 GLU cc_start: 0.7602 (pp20) cc_final: 0.7312 (pp20) REVERT: G 463 TRP cc_start: 0.7123 (m-90) cc_final: 0.6605 (m-90) REVERT: G 544 ILE cc_start: 0.8263 (mp) cc_final: 0.7479 (mp) REVERT: a 23 GLU cc_start: 0.7613 (tp30) cc_final: 0.7354 (tp30) REVERT: a 70 HIS cc_start: 0.8175 (t-90) cc_final: 0.7949 (t-90) REVERT: a 131 LEU cc_start: 0.7525 (mt) cc_final: 0.7013 (mt) REVERT: a 134 MET cc_start: 0.7269 (ppp) cc_final: 0.6575 (ppp) REVERT: a 181 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7535 (mm-30) REVERT: a 219 MET cc_start: 0.5569 (tmm) cc_final: 0.4726 (tmm) REVERT: N 395 LEU cc_start: 0.7848 (tp) cc_final: 0.7328 (tp) REVERT: N 551 MET cc_start: -0.1829 (ttp) cc_final: -0.2133 (ttp) REVERT: N 586 PHE cc_start: 0.7569 (m-80) cc_final: 0.7281 (m-80) REVERT: N 681 TYR cc_start: 0.7296 (t80) cc_final: 0.7011 (t80) REVERT: N 782 GLU cc_start: 0.8824 (tt0) cc_final: 0.8526 (tt0) REVERT: N 860 ARG cc_start: 0.7080 (mmp80) cc_final: 0.6791 (mmp80) REVERT: N 880 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8214 (mmtp) REVERT: N 885 LEU cc_start: 0.8326 (tp) cc_final: 0.7997 (tp) REVERT: N 890 TYR cc_start: 0.8741 (t80) cc_final: 0.8394 (t80) REVERT: N 928 GLN cc_start: 0.7671 (tp40) cc_final: 0.7362 (tp40) REVERT: N 948 LYS cc_start: 0.8607 (ptpt) cc_final: 0.8345 (ptpt) REVERT: N 1038 LEU cc_start: 0.7041 (mm) cc_final: 0.6778 (mm) REVERT: N 1049 ASP cc_start: 0.8905 (m-30) cc_final: 0.8658 (m-30) REVERT: N 1105 PHE cc_start: 0.7085 (m-80) cc_final: 0.6701 (m-80) REVERT: N 1209 PHE cc_start: 0.7304 (t80) cc_final: 0.6803 (t80) REVERT: N 1225 LEU cc_start: 0.8513 (mm) cc_final: 0.8285 (mm) REVERT: N 1243 PHE cc_start: 0.7680 (t80) cc_final: 0.6991 (t80) REVERT: N 1251 HIS cc_start: 0.6938 (m-70) cc_final: 0.6677 (m-70) outliers start: 2 outliers final: 0 residues processed: 782 average time/residue: 0.1709 time to fit residues: 205.3936 Evaluate side-chains 745 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 178 optimal weight: 10.0000 chunk 172 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 131 optimal weight: 0.1980 chunk 300 optimal weight: 0.6980 chunk 262 optimal weight: 0.0970 chunk 191 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 89 ASN A 207 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 10 ASN D 10 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS a 86 GLN a 205 GLN ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1088 ASN ** 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 = 0.4212 r_free = 0.4212 target = 0.171483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137559 restraints weight = 48396.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142819 restraints weight = 29351.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146678 restraints weight = 19984.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149366 restraints weight = 14666.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151518 restraints weight = 11487.383| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26507 Z= 0.137 Angle : 0.572 12.712 36048 Z= 0.294 Chirality : 0.043 0.230 4027 Planarity : 0.005 0.060 4746 Dihedral : 6.035 86.340 3737 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.38 % 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: -0.71 (0.15), residues: 3275 helix: 0.21 (0.14), residues: 1338 sheet: -0.48 (0.29), residues: 356 loop : -1.00 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 959 TYR 0.022 0.001 TYR a 139 PHE 0.030 0.001 PHE B 61 TRP 0.016 0.002 TRP F 276 HIS 0.009 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (26507) covalent geometry : angle 0.57184 / 0.29 (36048) hydrogen bonds : bond 0.03400 / 2.26 ( 1049) hydrogen bonds : angle 5.00756 / 3.55 ( 3033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 770 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7592 (pp30) cc_final: 0.7206 (pp30) REVERT: A 53 THR cc_start: 0.8279 (p) cc_final: 0.7743 (p) REVERT: A 68 MET cc_start: 0.6768 (tpt) cc_final: 0.6381 (tpt) REVERT: A 72 TYR cc_start: 0.6669 (m-80) cc_final: 0.6179 (m-80) REVERT: A 138 LEU cc_start: 0.7753 (tp) cc_final: 0.7387 (tp) REVERT: A 154 ILE cc_start: 0.8200 (mp) cc_final: 0.7998 (mp) REVERT: A 176 HIS cc_start: 0.8001 (t-90) cc_final: 0.7500 (t-90) REVERT: A 215 THR cc_start: 0.8757 (t) cc_final: 0.8443 (t) REVERT: A 244 ILE cc_start: 0.8087 (mt) cc_final: 0.7577 (mt) REVERT: A 248 MET cc_start: 0.7672 (mtm) cc_final: 0.7174 (mtm) REVERT: A 268 MET cc_start: 0.7121 (mmm) cc_final: 0.6570 (mmm) REVERT: A 282 ILE cc_start: 0.8170 (mt) cc_final: 0.7933 (mt) REVERT: B 130 TRP cc_start: 0.8377 (t60) cc_final: 0.7819 (t60) REVERT: B 155 GLN cc_start: 0.8569 (tp40) cc_final: 0.8013 (tp40) REVERT: B 230 LEU cc_start: 0.8637 (mt) cc_final: 0.8384 (mt) REVERT: B 253 ASP cc_start: 0.7844 (m-30) cc_final: 0.7521 (m-30) REVERT: C 42 GLU cc_start: 0.7363 (pm20) cc_final: 0.6949 (pm20) REVERT: C 47 TYR cc_start: 0.7844 (t80) cc_final: 0.7476 (t80) REVERT: C 49 PHE cc_start: 0.8161 (m-10) cc_final: 0.7576 (m-10) REVERT: C 89 ASN cc_start: 0.8505 (m110) cc_final: 0.8224 (m110) REVERT: C 103 ARG cc_start: 0.7259 (mtp85) cc_final: 0.6316 (ttm170) REVERT: C 150 VAL cc_start: 0.8320 (t) cc_final: 0.7983 (t) REVERT: C 227 ASN cc_start: 0.8784 (m110) cc_final: 0.8520 (m110) REVERT: C 240 GLU cc_start: 0.7783 (tp30) cc_final: 0.7384 (tp30) REVERT: C 257 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8008 (mm-40) REVERT: C 302 GLU cc_start: 0.7855 (mp0) cc_final: 0.7251 (mp0) REVERT: D 11 LEU cc_start: 0.8180 (mm) cc_final: 0.7920 (mm) REVERT: D 66 ARG cc_start: 0.6876 (mmt-90) cc_final: 0.6593 (mmt-90) REVERT: D 93 VAL cc_start: 0.8452 (t) cc_final: 0.8125 (p) REVERT: D 151 MET cc_start: 0.7340 (tmm) cc_final: 0.6546 (tmm) REVERT: D 186 ASN cc_start: 0.7841 (p0) cc_final: 0.7516 (p0) REVERT: D 207 GLN cc_start: 0.7491 (pt0) cc_final: 0.7201 (pt0) REVERT: D 248 MET cc_start: 0.7565 (mtp) cc_final: 0.7077 (mtp) REVERT: D 254 MET cc_start: 0.7971 (ppp) cc_final: 0.7638 (ppp) REVERT: D 268 MET cc_start: 0.6246 (mtp) cc_final: 0.5855 (mtp) REVERT: D 279 ASN cc_start: 0.8171 (m-40) cc_final: 0.7850 (m-40) REVERT: D 294 PHE cc_start: 0.6824 (t80) cc_final: 0.6506 (t80) REVERT: E 57 ILE cc_start: 0.8017 (mm) cc_final: 0.7810 (mm) REVERT: E 68 MET cc_start: 0.7963 (ppp) cc_final: 0.7550 (ppp) REVERT: E 77 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7619 (ptpp) REVERT: E 97 LEU cc_start: 0.8303 (mt) cc_final: 0.8022 (mt) REVERT: E 166 LEU cc_start: 0.8866 (mp) cc_final: 0.8573 (mp) REVERT: E 186 ASN cc_start: 0.7623 (m-40) cc_final: 0.7325 (m-40) REVERT: E 202 GLN cc_start: 0.7863 (pp30) cc_final: 0.7300 (pp30) REVERT: E 219 TYR cc_start: 0.8192 (m-80) cc_final: 0.7716 (m-80) REVERT: E 288 PHE cc_start: 0.8230 (t80) cc_final: 0.7746 (t80) REVERT: E 290 PHE cc_start: 0.8182 (t80) cc_final: 0.7842 (t80) REVERT: F 25 ASP cc_start: 0.5963 (t0) cc_final: 0.5453 (t0) REVERT: F 63 TYR cc_start: 0.6376 (m-10) cc_final: 0.6165 (m-10) REVERT: F 98 ASP cc_start: 0.6125 (m-30) cc_final: 0.5442 (m-30) REVERT: F 103 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: F 105 ASP cc_start: 0.7593 (t70) cc_final: 0.6996 (t0) REVERT: F 123 PHE cc_start: 0.7570 (t80) cc_final: 0.7325 (t80) REVERT: F 124 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8410 (mtmt) REVERT: F 135 ASN cc_start: 0.8636 (p0) cc_final: 0.8069 (p0) REVERT: F 171 ARG cc_start: 0.7336 (tpt90) cc_final: 0.7055 (tpt90) REVERT: F 201 GLN cc_start: 0.8001 (mm110) cc_final: 0.7740 (mm110) REVERT: F 208 MET cc_start: 0.6603 (tmm) cc_final: 0.6352 (tmm) REVERT: F 227 ASN cc_start: 0.8217 (m110) cc_final: 0.7862 (m110) REVERT: F 275 THR cc_start: 0.8150 (m) cc_final: 0.7663 (m) REVERT: F 279 ASN cc_start: 0.8163 (m110) cc_final: 0.7906 (m110) REVERT: F 290 PHE cc_start: 0.7842 (t80) cc_final: 0.7631 (t80) REVERT: G 323 ARG cc_start: 0.7701 (tpm170) cc_final: 0.7470 (tpm170) REVERT: G 387 ASP cc_start: 0.7572 (t70) cc_final: 0.7121 (t70) REVERT: G 427 MET cc_start: 0.7096 (pmm) cc_final: 0.6505 (pmm) REVERT: G 430 ARG cc_start: 0.8103 (ptt90) cc_final: 0.7647 (ptt90) REVERT: G 432 ILE cc_start: 0.8338 (tp) cc_final: 0.8024 (tp) REVERT: G 446 LEU cc_start: 0.8609 (mt) cc_final: 0.8372 (mt) REVERT: G 447 GLU cc_start: 0.7640 (pp20) cc_final: 0.7364 (pp20) REVERT: G 448 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7824 (tpp80) REVERT: G 489 HIS cc_start: 0.4852 (t70) cc_final: 0.2883 (t-170) REVERT: G 544 ILE cc_start: 0.8303 (mp) cc_final: 0.7583 (mp) REVERT: G 567 LEU cc_start: 0.8766 (tp) cc_final: 0.8549 (tp) REVERT: a 23 GLU cc_start: 0.7675 (tp30) cc_final: 0.7384 (tp30) REVERT: a 70 HIS cc_start: 0.8201 (t-90) cc_final: 0.7969 (t-90) REVERT: a 131 LEU cc_start: 0.7585 (mt) cc_final: 0.7048 (mt) REVERT: a 134 MET cc_start: 0.7282 (ppp) cc_final: 0.6587 (ppp) REVERT: a 181 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7531 (mm-30) REVERT: a 219 MET cc_start: 0.5565 (tmm) cc_final: 0.4673 (tmm) REVERT: N 395 LEU cc_start: 0.7959 (tp) cc_final: 0.7666 (tp) REVERT: N 551 MET cc_start: -0.1279 (ttp) cc_final: -0.1587 (ttp) REVERT: N 586 PHE cc_start: 0.7631 (m-80) cc_final: 0.7335 (m-80) REVERT: N 608 HIS cc_start: 0.8343 (p90) cc_final: 0.8119 (p90) REVERT: N 681 TYR cc_start: 0.7363 (t80) cc_final: 0.7047 (t80) REVERT: N 782 GLU cc_start: 0.8841 (tt0) cc_final: 0.8595 (tt0) REVERT: N 860 ARG cc_start: 0.7213 (mmp80) cc_final: 0.6854 (mmp80) REVERT: N 880 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8194 (mmtp) REVERT: N 890 TYR cc_start: 0.8749 (t80) cc_final: 0.8391 (t80) REVERT: N 928 GLN cc_start: 0.7671 (tp40) cc_final: 0.7381 (tp40) REVERT: N 948 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8350 (ptpt) REVERT: N 1038 LEU cc_start: 0.7222 (mm) cc_final: 0.6942 (mm) REVERT: N 1049 ASP cc_start: 0.8891 (m-30) cc_final: 0.8648 (m-30) REVERT: N 1105 PHE cc_start: 0.7052 (m-80) cc_final: 0.6684 (m-80) REVERT: N 1141 GLU cc_start: 0.7467 (pm20) cc_final: 0.7230 (pm20) REVERT: N 1177 TYR cc_start: 0.7818 (m-10) cc_final: 0.7616 (m-10) REVERT: N 1207 HIS cc_start: 0.7594 (t-90) cc_final: 0.6961 (t-90) REVERT: N 1209 PHE cc_start: 0.7312 (t80) cc_final: 0.6827 (t80) REVERT: N 1225 LEU cc_start: 0.8578 (mm) cc_final: 0.8376 (mm) REVERT: N 1243 PHE cc_start: 0.7839 (t80) cc_final: 0.6683 (t80) REVERT: N 1251 HIS cc_start: 0.7145 (m-70) cc_final: 0.6798 (m-70) outliers start: 2 outliers final: 0 residues processed: 771 average time/residue: 0.1789 time to fit residues: 211.0169 Evaluate side-chains 746 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 746 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 183 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 247 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 207 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 205 GLN N 815 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137345 restraints weight = 48477.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142678 restraints weight = 29716.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146526 restraints weight = 20329.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149343 restraints weight = 15079.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151193 restraints weight = 11862.889| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26507 Z= 0.133 Angle : 0.579 13.084 36048 Z= 0.297 Chirality : 0.043 0.203 4027 Planarity : 0.004 0.079 4746 Dihedral : 5.959 84.360 3737 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.42 % 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: -0.73 (0.15), residues: 3275 helix: 0.17 (0.14), residues: 1336 sheet: -0.51 (0.28), residues: 357 loop : -0.98 (0.17), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 393 TYR 0.024 0.001 TYR a 139 PHE 0.043 0.002 PHE D 61 TRP 0.022 0.002 TRP G 526 HIS 0.007 0.001 HIS N 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (26507) covalent geometry : angle 0.57918 / 0.30 (36048) hydrogen bonds : bond 0.03383 / 2.24 ( 1049) hydrogen bonds : angle 4.99332 / 3.55 ( 3033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 776 time to evaluate : 0.995 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 52 GLN cc_start: 0.7602 (pp30) cc_final: 0.7203 (pp30) REVERT: A 53 THR cc_start: 0.8314 (p) cc_final: 0.7790 (p) REVERT: A 68 MET cc_start: 0.6738 (tpt) cc_final: 0.6355 (tpt) REVERT: A 72 TYR cc_start: 0.6681 (m-80) cc_final: 0.6189 (m-80) REVERT: A 88 LEU cc_start: 0.8268 (mp) cc_final: 0.8041 (mp) REVERT: A 138 LEU cc_start: 0.7717 (tp) cc_final: 0.7388 (tp) REVERT: A 154 ILE cc_start: 0.8222 (mp) cc_final: 0.8014 (mp) REVERT: A 176 HIS cc_start: 0.8011 (t-90) cc_final: 0.7502 (t-90) REVERT: A 215 THR cc_start: 0.8738 (t) cc_final: 0.8413 (t) REVERT: A 244 ILE cc_start: 0.8091 (mt) cc_final: 0.7574 (mt) REVERT: A 248 MET cc_start: 0.7673 (mtm) cc_final: 0.7196 (mtm) REVERT: A 268 MET cc_start: 0.7109 (mmm) cc_final: 0.6371 (mmm) REVERT: A 275 THR cc_start: 0.8787 (m) cc_final: 0.8578 (m) REVERT: A 282 ILE cc_start: 0.8184 (mt) cc_final: 0.7957 (mt) REVERT: A 294 PHE cc_start: 0.8152 (t80) cc_final: 0.7667 (t80) REVERT: B 29 MET cc_start: 0.7138 (mmp) cc_final: 0.6760 (mmp) REVERT: B 64 ASN cc_start: 0.8044 (t0) cc_final: 0.7781 (t0) REVERT: B 130 TRP cc_start: 0.8368 (t60) cc_final: 0.7787 (t60) REVERT: B 155 GLN cc_start: 0.8575 (tp40) cc_final: 0.8071 (tp40) REVERT: B 230 LEU cc_start: 0.8635 (mt) cc_final: 0.8396 (mt) REVERT: B 253 ASP cc_start: 0.7993 (m-30) cc_final: 0.7524 (m-30) REVERT: C 42 GLU cc_start: 0.7384 (pm20) cc_final: 0.6967 (pm20) REVERT: C 47 TYR cc_start: 0.7867 (t80) cc_final: 0.7535 (t80) REVERT: C 49 PHE cc_start: 0.8143 (m-10) cc_final: 0.7559 (m-10) REVERT: C 89 ASN cc_start: 0.8504 (m110) cc_final: 0.8217 (m110) REVERT: C 103 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6289 (ttm170) REVERT: C 150 VAL cc_start: 0.8317 (t) cc_final: 0.7859 (p) REVERT: C 240 GLU cc_start: 0.7877 (tp30) cc_final: 0.7433 (tp30) REVERT: C 257 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7859 (mm-40) REVERT: C 302 GLU cc_start: 0.7764 (mp0) cc_final: 0.7167 (mp0) REVERT: D 11 LEU cc_start: 0.8183 (mm) cc_final: 0.7910 (mm) REVERT: D 66 ARG cc_start: 0.6895 (mmt-90) cc_final: 0.6642 (mmt-90) REVERT: D 93 VAL cc_start: 0.8442 (t) cc_final: 0.8115 (p) REVERT: D 151 MET cc_start: 0.7378 (tmm) cc_final: 0.6536 (tmm) REVERT: D 186 ASN cc_start: 0.7814 (p0) cc_final: 0.7526 (p0) REVERT: D 207 GLN cc_start: 0.7512 (pt0) cc_final: 0.7153 (pt0) REVERT: D 248 MET cc_start: 0.7517 (mtp) cc_final: 0.7113 (mtp) REVERT: D 254 MET cc_start: 0.7981 (ppp) cc_final: 0.7633 (ppp) REVERT: D 279 ASN cc_start: 0.8221 (m-40) cc_final: 0.7886 (m-40) REVERT: D 294 PHE cc_start: 0.6831 (t80) cc_final: 0.6579 (t80) REVERT: E 57 ILE cc_start: 0.7996 (mm) cc_final: 0.7761 (mm) REVERT: E 68 MET cc_start: 0.7936 (ppp) cc_final: 0.7554 (ppp) REVERT: E 77 LYS cc_start: 0.7887 (ptpp) cc_final: 0.7569 (ptpp) REVERT: E 97 LEU cc_start: 0.8292 (mt) cc_final: 0.8034 (mt) REVERT: E 166 LEU cc_start: 0.8911 (mp) cc_final: 0.8575 (mp) REVERT: E 186 ASN cc_start: 0.7531 (m-40) cc_final: 0.7148 (m-40) REVERT: E 202 GLN cc_start: 0.7806 (pp30) cc_final: 0.7267 (pp30) REVERT: E 219 TYR cc_start: 0.8205 (m-80) cc_final: 0.7777 (m-80) REVERT: E 288 PHE cc_start: 0.8231 (t80) cc_final: 0.7802 (t80) REVERT: E 290 PHE cc_start: 0.8198 (t80) cc_final: 0.7885 (t80) REVERT: F 25 ASP cc_start: 0.5989 (t0) cc_final: 0.5497 (t0) REVERT: F 28 MET cc_start: 0.6484 (mmp) cc_final: 0.6191 (mmm) REVERT: F 29 MET cc_start: 0.7741 (mmm) cc_final: 0.7010 (mmm) REVERT: F 68 MET cc_start: 0.7056 (tmm) cc_final: 0.6507 (tmm) REVERT: F 98 ASP cc_start: 0.5936 (m-30) cc_final: 0.5183 (m-30) REVERT: F 113 VAL cc_start: 0.8173 (p) cc_final: 0.7920 (t) REVERT: F 123 PHE cc_start: 0.7575 (t80) cc_final: 0.7339 (t80) REVERT: F 124 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8423 (mtmt) REVERT: F 135 ASN cc_start: 0.8652 (p0) cc_final: 0.8086 (p0) REVERT: F 147 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7652 (mtm-85) REVERT: F 151 MET cc_start: 0.7003 (mmp) cc_final: 0.6599 (mmp) REVERT: F 171 ARG cc_start: 0.7407 (tpt90) cc_final: 0.7098 (tpt90) REVERT: F 201 GLN cc_start: 0.8047 (mm110) cc_final: 0.7813 (mm110) REVERT: F 208 MET cc_start: 0.6666 (tmm) cc_final: 0.6426 (tmm) REVERT: F 214 VAL cc_start: 0.8249 (p) cc_final: 0.7382 (p) REVERT: F 227 ASN cc_start: 0.8261 (m110) cc_final: 0.7910 (m110) REVERT: F 256 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7693 (ptp90) REVERT: F 275 THR cc_start: 0.8177 (m) cc_final: 0.7762 (m) REVERT: F 279 ASN cc_start: 0.8207 (m110) cc_final: 0.7967 (m110) REVERT: G 323 ARG cc_start: 0.7785 (tpm170) cc_final: 0.7541 (tpm170) REVERT: G 387 ASP cc_start: 0.7548 (t70) cc_final: 0.7125 (t70) REVERT: G 427 MET cc_start: 0.7110 (pmm) cc_final: 0.6695 (pmm) REVERT: G 430 ARG cc_start: 0.8137 (ptt90) cc_final: 0.7676 (ptt90) REVERT: G 446 LEU cc_start: 0.8630 (mt) cc_final: 0.8419 (mt) REVERT: G 447 GLU cc_start: 0.7671 (pp20) cc_final: 0.7367 (pp20) REVERT: G 544 ILE cc_start: 0.8267 (mp) cc_final: 0.7559 (mp) REVERT: a 23 GLU cc_start: 0.7703 (tp30) cc_final: 0.7395 (tp30) REVERT: a 70 HIS cc_start: 0.8204 (t-90) cc_final: 0.7991 (t-90) REVERT: a 131 LEU cc_start: 0.7627 (mt) cc_final: 0.7105 (mt) REVERT: a 134 MET cc_start: 0.7291 (ppp) cc_final: 0.6598 (ppp) REVERT: a 181 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7545 (mm-30) REVERT: a 219 MET cc_start: 0.5629 (tmm) cc_final: 0.4737 (tmm) REVERT: N 395 LEU cc_start: 0.7918 (tp) cc_final: 0.7372 (tp) REVERT: N 677 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7961 (ptpp) REVERT: N 681 TYR cc_start: 0.7398 (t80) cc_final: 0.7056 (t80) REVERT: N 782 GLU cc_start: 0.8824 (tt0) cc_final: 0.8528 (tt0) REVERT: N 860 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6858 (mmp80) REVERT: N 880 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8273 (mptt) REVERT: N 881 LYS cc_start: 0.7526 (mtmm) cc_final: 0.7141 (mtmm) REVERT: N 885 LEU cc_start: 0.8221 (tp) cc_final: 0.7940 (tp) REVERT: N 890 TYR cc_start: 0.8751 (t80) cc_final: 0.8396 (t80) REVERT: N 928 GLN cc_start: 0.7680 (tp40) cc_final: 0.7348 (tp40) REVERT: N 1038 LEU cc_start: 0.7227 (mm) cc_final: 0.6953 (mm) REVERT: N 1049 ASP cc_start: 0.8899 (m-30) cc_final: 0.8608 (m-30) REVERT: N 1105 PHE cc_start: 0.7088 (m-80) cc_final: 0.6709 (m-80) REVERT: N 1141 GLU cc_start: 0.7525 (pm20) cc_final: 0.7226 (pm20) REVERT: N 1177 TYR cc_start: 0.7848 (m-10) cc_final: 0.7641 (m-10) REVERT: N 1207 HIS cc_start: 0.7607 (t-90) cc_final: 0.6968 (t-90) REVERT: N 1209 PHE cc_start: 0.7307 (t80) cc_final: 0.6828 (t80) REVERT: N 1225 LEU cc_start: 0.8531 (mm) cc_final: 0.8320 (mm) REVERT: N 1243 PHE cc_start: 0.7828 (t80) cc_final: 0.6743 (t80) REVERT: N 1251 HIS cc_start: 0.7142 (m-70) cc_final: 0.6827 (m-70) outliers start: 2 outliers final: 0 residues processed: 778 average time/residue: 0.1961 time to fit residues: 233.5346 Evaluate side-chains 748 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN A 224 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS a 86 GLN a 205 GLN ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.170878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136624 restraints weight = 48120.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141856 restraints weight = 29391.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145746 restraints weight = 20075.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148349 restraints weight = 14824.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150571 restraints weight = 11676.510| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26507 Z= 0.136 Angle : 0.583 12.851 36048 Z= 0.299 Chirality : 0.043 0.179 4027 Planarity : 0.004 0.049 4746 Dihedral : 5.907 85.105 3737 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.31 % 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: -0.73 (0.15), residues: 3275 helix: 0.16 (0.14), residues: 1331 sheet: -0.46 (0.29), residues: 354 loop : -0.98 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 959 TYR 0.023 0.001 TYR a 139 PHE 0.030 0.002 PHE B 61 TRP 0.015 0.002 TRP G 526 HIS 0.009 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (26507) covalent geometry : angle 0.58327 / 0.30 (36048) hydrogen bonds : bond 0.03365 / 2.23 ( 1049) hydrogen bonds : angle 5.02706 / 3.58 ( 3033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 1.019 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 52 GLN cc_start: 0.7609 (pp30) cc_final: 0.7213 (pp30) REVERT: A 53 THR cc_start: 0.8323 (p) cc_final: 0.7833 (p) REVERT: A 72 TYR cc_start: 0.6722 (m-80) cc_final: 0.6190 (m-80) REVERT: A 81 ILE cc_start: 0.8128 (mm) cc_final: 0.7917 (mm) REVERT: A 88 LEU cc_start: 0.8339 (mp) cc_final: 0.8060 (mp) REVERT: A 138 LEU cc_start: 0.7785 (tp) cc_final: 0.7472 (tp) REVERT: A 176 HIS cc_start: 0.7998 (t-90) cc_final: 0.7507 (t-90) REVERT: A 215 THR cc_start: 0.8779 (t) cc_final: 0.8401 (t) REVERT: A 244 ILE cc_start: 0.8085 (mt) cc_final: 0.7562 (mt) REVERT: A 248 MET cc_start: 0.7650 (mtm) cc_final: 0.7157 (mtm) REVERT: A 268 MET cc_start: 0.7185 (mmm) cc_final: 0.6417 (mmm) REVERT: A 275 THR cc_start: 0.8770 (m) cc_final: 0.8556 (m) REVERT: A 282 ILE cc_start: 0.8184 (mt) cc_final: 0.7931 (mt) REVERT: A 294 PHE cc_start: 0.8158 (t80) cc_final: 0.7648 (t80) REVERT: B 29 MET cc_start: 0.7119 (mmp) cc_final: 0.6721 (mmp) REVERT: B 64 ASN cc_start: 0.8009 (t0) cc_final: 0.7782 (t0) REVERT: B 130 TRP cc_start: 0.8383 (t60) cc_final: 0.7777 (t60) REVERT: B 155 GLN cc_start: 0.8547 (tp40) cc_final: 0.8107 (tp40) REVERT: B 230 LEU cc_start: 0.8649 (mt) cc_final: 0.8398 (mt) REVERT: B 253 ASP cc_start: 0.7841 (m-30) cc_final: 0.7496 (m-30) REVERT: C 42 GLU cc_start: 0.7388 (pm20) cc_final: 0.6975 (pm20) REVERT: C 47 TYR cc_start: 0.7872 (t80) cc_final: 0.7546 (t80) REVERT: C 49 PHE cc_start: 0.8147 (m-10) cc_final: 0.7572 (m-10) REVERT: C 89 ASN cc_start: 0.8509 (m110) cc_final: 0.8215 (m110) REVERT: C 103 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6109 (ttm170) REVERT: C 150 VAL cc_start: 0.8287 (t) cc_final: 0.7859 (p) REVERT: C 240 GLU cc_start: 0.7817 (tp30) cc_final: 0.7381 (tp30) REVERT: C 257 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 302 GLU cc_start: 0.7859 (mp0) cc_final: 0.7282 (mp0) REVERT: D 11 LEU cc_start: 0.8187 (mm) cc_final: 0.7901 (mm) REVERT: D 66 ARG cc_start: 0.6924 (mmt-90) cc_final: 0.6706 (mmt180) REVERT: D 93 VAL cc_start: 0.8442 (t) cc_final: 0.8135 (p) REVERT: D 96 ASN cc_start: 0.8492 (m-40) cc_final: 0.8290 (m-40) REVERT: D 151 MET cc_start: 0.7407 (tmm) cc_final: 0.6505 (tmm) REVERT: D 186 ASN cc_start: 0.7843 (p0) cc_final: 0.7500 (p0) REVERT: D 207 GLN cc_start: 0.7489 (pt0) cc_final: 0.7121 (pt0) REVERT: D 248 MET cc_start: 0.7491 (mtp) cc_final: 0.7087 (mtp) REVERT: D 254 MET cc_start: 0.7988 (ppp) cc_final: 0.7626 (ppp) REVERT: D 279 ASN cc_start: 0.8060 (m-40) cc_final: 0.7755 (m-40) REVERT: D 294 PHE cc_start: 0.6936 (t80) cc_final: 0.6485 (t80) REVERT: E 77 LYS cc_start: 0.7903 (ptpp) cc_final: 0.7532 (ptpp) REVERT: E 97 LEU cc_start: 0.8296 (mt) cc_final: 0.8043 (mt) REVERT: E 166 LEU cc_start: 0.8929 (mp) cc_final: 0.8576 (mp) REVERT: E 186 ASN cc_start: 0.7475 (m-40) cc_final: 0.7105 (m-40) REVERT: E 202 GLN cc_start: 0.7951 (pp30) cc_final: 0.7594 (tm-30) REVERT: E 219 TYR cc_start: 0.8264 (m-80) cc_final: 0.7785 (m-80) REVERT: E 288 PHE cc_start: 0.8243 (t80) cc_final: 0.7749 (t80) REVERT: E 290 PHE cc_start: 0.8230 (t80) cc_final: 0.7905 (t80) REVERT: F 25 ASP cc_start: 0.6164 (t0) cc_final: 0.5754 (t0) REVERT: F 63 TYR cc_start: 0.6374 (m-10) cc_final: 0.6149 (m-10) REVERT: F 98 ASP cc_start: 0.5998 (m-30) cc_final: 0.5197 (m-30) REVERT: F 105 ASP cc_start: 0.7639 (t70) cc_final: 0.6989 (t0) REVERT: F 123 PHE cc_start: 0.7568 (t80) cc_final: 0.7324 (t80) REVERT: F 124 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8415 (mtmt) REVERT: F 135 ASN cc_start: 0.8645 (p0) cc_final: 0.8083 (p0) REVERT: F 171 ARG cc_start: 0.7368 (tpt90) cc_final: 0.7090 (tpt90) REVERT: F 201 GLN cc_start: 0.8048 (mm110) cc_final: 0.7784 (mm110) REVERT: F 208 MET cc_start: 0.6672 (tmm) cc_final: 0.6401 (tmm) REVERT: F 227 ASN cc_start: 0.8285 (m110) cc_final: 0.7934 (m110) REVERT: F 248 MET cc_start: 0.8237 (mmt) cc_final: 0.7984 (mmt) REVERT: F 275 THR cc_start: 0.8177 (m) cc_final: 0.7751 (m) REVERT: F 279 ASN cc_start: 0.8202 (m110) cc_final: 0.7951 (m110) REVERT: G 387 ASP cc_start: 0.7643 (t70) cc_final: 0.7238 (t70) REVERT: G 427 MET cc_start: 0.7130 (pmm) cc_final: 0.6642 (pmm) REVERT: G 430 ARG cc_start: 0.8127 (ptt90) cc_final: 0.7668 (ptt90) REVERT: G 446 LEU cc_start: 0.8614 (mt) cc_final: 0.8367 (mt) REVERT: G 447 GLU cc_start: 0.7642 (pp20) cc_final: 0.7317 (pp20) REVERT: G 544 ILE cc_start: 0.8279 (mp) cc_final: 0.7550 (mp) REVERT: G 567 LEU cc_start: 0.8778 (tp) cc_final: 0.8288 (tp) REVERT: a 23 GLU cc_start: 0.7677 (tp30) cc_final: 0.7372 (tp30) REVERT: a 70 HIS cc_start: 0.8214 (t-90) cc_final: 0.7993 (t-90) REVERT: a 131 LEU cc_start: 0.7641 (mt) cc_final: 0.7103 (mt) REVERT: a 134 MET cc_start: 0.7291 (ppp) cc_final: 0.6617 (ppp) REVERT: a 181 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7492 (mm-30) REVERT: a 219 MET cc_start: 0.5597 (tmm) cc_final: 0.4689 (tmm) REVERT: N 395 LEU cc_start: 0.7892 (tp) cc_final: 0.7446 (tp) REVERT: N 617 GLU cc_start: 0.7343 (pm20) cc_final: 0.6974 (pm20) REVERT: N 681 TYR cc_start: 0.7425 (t80) cc_final: 0.7134 (t80) REVERT: N 782 GLU cc_start: 0.8832 (tt0) cc_final: 0.8521 (tt0) REVERT: N 860 ARG cc_start: 0.7239 (mmp80) cc_final: 0.6876 (mmp80) REVERT: N 880 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8331 (mttm) REVERT: N 885 LEU cc_start: 0.8256 (tp) cc_final: 0.7981 (tp) REVERT: N 890 TYR cc_start: 0.8748 (t80) cc_final: 0.8387 (t80) REVERT: N 928 GLN cc_start: 0.7648 (tp40) cc_final: 0.7378 (tp40) REVERT: N 1038 LEU cc_start: 0.7236 (mm) cc_final: 0.6959 (mm) REVERT: N 1049 ASP cc_start: 0.8892 (m-30) cc_final: 0.8622 (m-30) REVERT: N 1105 PHE cc_start: 0.7008 (m-80) cc_final: 0.6582 (m-80) REVERT: N 1141 GLU cc_start: 0.7564 (pm20) cc_final: 0.7195 (pm20) REVERT: N 1156 TRP cc_start: 0.8279 (t60) cc_final: 0.8069 (t60) REVERT: N 1207 HIS cc_start: 0.7624 (t-90) cc_final: 0.6969 (t-90) REVERT: N 1209 PHE cc_start: 0.7331 (t80) cc_final: 0.6844 (t80) REVERT: N 1225 LEU cc_start: 0.8565 (mm) cc_final: 0.8355 (mm) REVERT: N 1243 PHE cc_start: 0.7801 (t80) cc_final: 0.6691 (t80) REVERT: N 1251 HIS cc_start: 0.7122 (m-70) cc_final: 0.6865 (m-70) outliers start: 1 outliers final: 0 residues processed: 769 average time/residue: 0.1933 time to fit residues: 228.1561 Evaluate side-chains 741 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 9 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 263 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 192 optimal weight: 0.3980 chunk 247 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 207 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS a 86 GLN a 205 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.171761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137313 restraints weight = 48472.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142715 restraints weight = 29409.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146551 restraints weight = 19967.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.149244 restraints weight = 14726.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151255 restraints weight = 11614.776| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26507 Z= 0.119 Angle : 0.582 12.974 36048 Z= 0.298 Chirality : 0.043 0.171 4027 Planarity : 0.004 0.050 4746 Dihedral : 5.764 82.941 3737 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 1.51 % Favored : 98.45 % 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: -0.74 (0.15), residues: 3275 helix: 0.13 (0.14), residues: 1335 sheet: -0.41 (0.29), residues: 351 loop : -0.97 (0.17), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 959 TYR 0.024 0.001 TYR a 139 PHE 0.028 0.002 PHE D 61 TRP 0.015 0.001 TRP N 477 HIS 0.008 0.001 HIS N 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (26507) covalent geometry : angle 0.58213 / 0.30 (36048) hydrogen bonds : bond 0.03228 / 2.12 ( 1049) hydrogen bonds : angle 5.01240 / 3.56 ( 3033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 773 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7630 (pp30) cc_final: 0.7249 (pp30) REVERT: A 53 THR cc_start: 0.8283 (p) cc_final: 0.7836 (p) REVERT: A 68 MET cc_start: 0.6834 (tpt) cc_final: 0.6442 (tpt) REVERT: A 72 TYR cc_start: 0.6718 (m-80) cc_final: 0.6229 (m-80) REVERT: A 83 GLN cc_start: 0.8398 (mp10) cc_final: 0.7815 (mp10) REVERT: A 88 LEU cc_start: 0.8208 (mp) cc_final: 0.7935 (mp) REVERT: A 133 GLN cc_start: 0.8363 (mt0) cc_final: 0.8158 (mt0) REVERT: A 138 LEU cc_start: 0.7779 (tp) cc_final: 0.7544 (tp) REVERT: A 176 HIS cc_start: 0.7981 (t-90) cc_final: 0.7459 (t-90) REVERT: A 207 GLN cc_start: 0.7945 (pt0) cc_final: 0.7700 (pt0) REVERT: A 215 THR cc_start: 0.8741 (t) cc_final: 0.8411 (t) REVERT: A 244 ILE cc_start: 0.8062 (mt) cc_final: 0.7529 (mt) REVERT: A 248 MET cc_start: 0.7653 (mtm) cc_final: 0.7133 (mtm) REVERT: A 268 MET cc_start: 0.7182 (mmm) cc_final: 0.6415 (mmm) REVERT: A 275 THR cc_start: 0.8750 (m) cc_final: 0.8533 (m) REVERT: A 282 ILE cc_start: 0.8165 (mt) cc_final: 0.7919 (mt) REVERT: A 294 PHE cc_start: 0.8158 (t80) cc_final: 0.7669 (t80) REVERT: B 29 MET cc_start: 0.7121 (mmp) cc_final: 0.6718 (mmp) REVERT: B 130 TRP cc_start: 0.8347 (t60) cc_final: 0.7737 (t60) REVERT: B 155 GLN cc_start: 0.8520 (tp40) cc_final: 0.8087 (tp40) REVERT: B 230 LEU cc_start: 0.8637 (mt) cc_final: 0.8394 (mt) REVERT: B 253 ASP cc_start: 0.7822 (m-30) cc_final: 0.7456 (m-30) REVERT: B 296 ASN cc_start: 0.8604 (m-40) cc_final: 0.8372 (m-40) REVERT: B 303 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7921 (mmm160) REVERT: C 42 GLU cc_start: 0.7398 (pm20) cc_final: 0.6998 (pm20) REVERT: C 47 TYR cc_start: 0.7855 (t80) cc_final: 0.7522 (t80) REVERT: C 49 PHE cc_start: 0.8134 (m-10) cc_final: 0.7552 (m-10) REVERT: C 89 ASN cc_start: 0.8468 (m110) cc_final: 0.8197 (m110) REVERT: C 150 VAL cc_start: 0.8251 (t) cc_final: 0.8041 (p) REVERT: C 240 GLU cc_start: 0.7841 (tp30) cc_final: 0.7400 (tp30) REVERT: C 257 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7798 (mm-40) REVERT: C 302 GLU cc_start: 0.7863 (mp0) cc_final: 0.7268 (mp0) REVERT: D 11 LEU cc_start: 0.8154 (mm) cc_final: 0.7923 (mm) REVERT: D 66 ARG cc_start: 0.6922 (mmt-90) cc_final: 0.6697 (mmt180) REVERT: D 93 VAL cc_start: 0.8453 (t) cc_final: 0.8128 (p) REVERT: D 151 MET cc_start: 0.7388 (tmm) cc_final: 0.6340 (tmm) REVERT: D 186 ASN cc_start: 0.7812 (p0) cc_final: 0.7514 (p0) REVERT: D 207 GLN cc_start: 0.7495 (pt0) cc_final: 0.7094 (pt0) REVERT: D 248 MET cc_start: 0.7463 (mtp) cc_final: 0.7049 (mtp) REVERT: D 254 MET cc_start: 0.7999 (ppp) cc_final: 0.7697 (ppp) REVERT: D 279 ASN cc_start: 0.8043 (m-40) cc_final: 0.7704 (m-40) REVERT: D 294 PHE cc_start: 0.6959 (t80) cc_final: 0.6357 (t80) REVERT: E 68 MET cc_start: 0.7979 (ppp) cc_final: 0.7670 (ppp) REVERT: E 77 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7560 (ptpp) REVERT: E 97 LEU cc_start: 0.8281 (mt) cc_final: 0.8019 (mt) REVERT: E 158 LEU cc_start: 0.8021 (tp) cc_final: 0.7764 (tp) REVERT: E 166 LEU cc_start: 0.8929 (mp) cc_final: 0.8576 (mp) REVERT: E 186 ASN cc_start: 0.7390 (m-40) cc_final: 0.6997 (m-40) REVERT: E 202 GLN cc_start: 0.7912 (pp30) cc_final: 0.7411 (pp30) REVERT: E 219 TYR cc_start: 0.8155 (m-80) cc_final: 0.7758 (m-80) REVERT: E 220 LEU cc_start: 0.7805 (mt) cc_final: 0.7470 (mt) REVERT: E 288 PHE cc_start: 0.8226 (t80) cc_final: 0.7882 (t80) REVERT: E 290 PHE cc_start: 0.8163 (t80) cc_final: 0.7837 (t80) REVERT: F 25 ASP cc_start: 0.6276 (t0) cc_final: 0.5855 (t0) REVERT: F 63 TYR cc_start: 0.6332 (m-10) cc_final: 0.6118 (m-10) REVERT: F 68 MET cc_start: 0.7088 (tmm) cc_final: 0.6773 (tmm) REVERT: F 98 ASP cc_start: 0.6068 (m-30) cc_final: 0.5277 (m-30) REVERT: F 105 ASP cc_start: 0.7610 (t70) cc_final: 0.6979 (t0) REVERT: F 123 PHE cc_start: 0.7580 (t80) cc_final: 0.7316 (t80) REVERT: F 124 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8408 (mtmt) REVERT: F 135 ASN cc_start: 0.8634 (p0) cc_final: 0.8089 (p0) REVERT: F 151 MET cc_start: 0.6863 (mmp) cc_final: 0.6509 (mmp) REVERT: F 171 ARG cc_start: 0.7356 (tpt90) cc_final: 0.7118 (tpt90) REVERT: F 201 GLN cc_start: 0.8062 (mm110) cc_final: 0.7822 (mm110) REVERT: F 208 MET cc_start: 0.6615 (tmm) cc_final: 0.6371 (tmm) REVERT: F 227 ASN cc_start: 0.8293 (m110) cc_final: 0.7939 (m110) REVERT: F 279 ASN cc_start: 0.8214 (m110) cc_final: 0.7970 (m110) REVERT: G 323 ARG cc_start: 0.7731 (tpm170) cc_final: 0.7476 (tpm170) REVERT: G 387 ASP cc_start: 0.7583 (t70) cc_final: 0.7145 (t70) REVERT: G 430 ARG cc_start: 0.8117 (ptt90) cc_final: 0.7651 (ptt90) REVERT: G 446 LEU cc_start: 0.8616 (mt) cc_final: 0.8349 (mt) REVERT: G 544 ILE cc_start: 0.8275 (mp) cc_final: 0.7525 (mp) REVERT: G 567 LEU cc_start: 0.8755 (tp) cc_final: 0.8546 (tp) REVERT: a 23 GLU cc_start: 0.7671 (tp30) cc_final: 0.7358 (tp30) REVERT: a 70 HIS cc_start: 0.8174 (t-90) cc_final: 0.7954 (t-90) REVERT: a 90 ASN cc_start: 0.8305 (t0) cc_final: 0.7890 (t0) REVERT: a 131 LEU cc_start: 0.7626 (mt) cc_final: 0.7071 (mt) REVERT: a 134 MET cc_start: 0.7275 (ppp) cc_final: 0.6597 (ppp) REVERT: a 181 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7497 (mm-30) REVERT: a 219 MET cc_start: 0.5580 (tmm) cc_final: 0.4672 (tmm) REVERT: N 395 LEU cc_start: 0.7865 (tp) cc_final: 0.7644 (tp) REVERT: N 472 GLU cc_start: 0.8715 (mp0) cc_final: 0.8423 (mp0) REVERT: N 617 GLU cc_start: 0.7278 (pm20) cc_final: 0.6975 (pm20) REVERT: N 681 TYR cc_start: 0.7422 (t80) cc_final: 0.7124 (t80) REVERT: N 782 GLU cc_start: 0.8817 (tt0) cc_final: 0.8518 (tt0) REVERT: N 860 ARG cc_start: 0.7216 (mmp80) cc_final: 0.6856 (mmp80) REVERT: N 880 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8345 (mttm) REVERT: N 885 LEU cc_start: 0.8270 (tp) cc_final: 0.7986 (tp) REVERT: N 890 TYR cc_start: 0.8668 (t80) cc_final: 0.8348 (t80) REVERT: N 928 GLN cc_start: 0.7652 (tp40) cc_final: 0.7368 (tp40) REVERT: N 1038 LEU cc_start: 0.7139 (mm) cc_final: 0.6859 (mm) REVERT: N 1049 ASP cc_start: 0.8872 (m-30) cc_final: 0.8612 (m-30) REVERT: N 1054 TRP cc_start: 0.7394 (t60) cc_final: 0.7047 (t60) REVERT: N 1105 PHE cc_start: 0.6938 (m-80) cc_final: 0.6539 (m-80) REVERT: N 1141 GLU cc_start: 0.7504 (pm20) cc_final: 0.7194 (pm20) REVERT: N 1156 TRP cc_start: 0.8193 (t60) cc_final: 0.7979 (t60) REVERT: N 1209 PHE cc_start: 0.7341 (t80) cc_final: 0.6896 (t80) REVERT: N 1225 LEU cc_start: 0.8551 (mm) cc_final: 0.8351 (mm) REVERT: N 1243 PHE cc_start: 0.7820 (t80) cc_final: 0.6615 (t80) REVERT: N 1251 HIS cc_start: 0.7135 (m-70) cc_final: 0.6782 (m-70) outliers start: 1 outliers final: 0 residues processed: 774 average time/residue: 0.1945 time to fit residues: 230.9413 Evaluate side-chains 753 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 753 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 296 ASN D 10 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS a 86 GLN a 205 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136188 restraints weight = 48281.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141485 restraints weight = 29372.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145348 restraints weight = 19911.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148001 restraints weight = 14672.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150045 restraints weight = 11525.578| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26507 Z= 0.141 Angle : 0.596 12.909 36048 Z= 0.306 Chirality : 0.044 0.191 4027 Planarity : 0.004 0.048 4746 Dihedral : 5.801 86.643 3737 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.12 % 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: -0.74 (0.15), residues: 3275 helix: 0.13 (0.14), residues: 1334 sheet: -0.38 (0.29), residues: 346 loop : -0.99 (0.17), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 959 TYR 0.023 0.001 TYR a 139 PHE 0.027 0.002 PHE D 61 TRP 0.015 0.002 TRP B 276 HIS 0.008 0.001 HIS N 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (26507) covalent geometry : angle 0.59646 / 0.31 (36048) hydrogen bonds : bond 0.03369 / 2.22 ( 1049) hydrogen bonds : angle 5.06258 / 3.60 ( 3033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 765 time to evaluate : 0.987 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 52 GLN cc_start: 0.7610 (pp30) cc_final: 0.7243 (pp30) REVERT: A 53 THR cc_start: 0.8298 (p) cc_final: 0.7781 (p) REVERT: A 68 MET cc_start: 0.6742 (tpt) cc_final: 0.6438 (tpt) REVERT: A 72 TYR cc_start: 0.6709 (m-80) cc_final: 0.6220 (m-80) REVERT: A 83 GLN cc_start: 0.8478 (mp10) cc_final: 0.7851 (mp10) REVERT: A 133 GLN cc_start: 0.8335 (mt0) cc_final: 0.8093 (mt0) REVERT: A 138 LEU cc_start: 0.7817 (tp) cc_final: 0.7526 (tp) REVERT: A 176 HIS cc_start: 0.7979 (t-90) cc_final: 0.7478 (t-90) REVERT: A 215 THR cc_start: 0.8750 (t) cc_final: 0.8416 (t) REVERT: A 244 ILE cc_start: 0.8118 (mt) cc_final: 0.7558 (mt) REVERT: A 248 MET cc_start: 0.7629 (mtm) cc_final: 0.7138 (mtm) REVERT: A 268 MET cc_start: 0.7228 (mmm) cc_final: 0.6452 (mmm) REVERT: A 275 THR cc_start: 0.8733 (m) cc_final: 0.8507 (m) REVERT: A 282 ILE cc_start: 0.8124 (mt) cc_final: 0.7844 (mt) REVERT: A 294 PHE cc_start: 0.8168 (t80) cc_final: 0.7629 (t80) REVERT: B 29 MET cc_start: 0.7108 (mmp) cc_final: 0.6731 (mmp) REVERT: B 130 TRP cc_start: 0.8363 (t60) cc_final: 0.7796 (t60) REVERT: B 155 GLN cc_start: 0.8451 (tp40) cc_final: 0.7773 (tp40) REVERT: B 167 LEU cc_start: 0.7093 (tp) cc_final: 0.6800 (tp) REVERT: B 230 LEU cc_start: 0.8648 (mt) cc_final: 0.8400 (mt) REVERT: B 248 MET cc_start: 0.7760 (mmt) cc_final: 0.7560 (tpt) REVERT: B 253 ASP cc_start: 0.7914 (m-30) cc_final: 0.7451 (m-30) REVERT: B 266 THR cc_start: 0.7716 (p) cc_final: 0.7504 (p) REVERT: B 291 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7209 (mtp-110) REVERT: B 296 ASN cc_start: 0.8581 (m-40) cc_final: 0.8339 (m-40) REVERT: B 303 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7840 (mmm160) REVERT: C 42 GLU cc_start: 0.7407 (pm20) cc_final: 0.7015 (pm20) REVERT: C 47 TYR cc_start: 0.7840 (t80) cc_final: 0.7544 (t80) REVERT: C 49 PHE cc_start: 0.8151 (m-10) cc_final: 0.7713 (m-10) REVERT: C 89 ASN cc_start: 0.8481 (m110) cc_final: 0.8218 (m110) REVERT: C 150 VAL cc_start: 0.8303 (t) cc_final: 0.8028 (p) REVERT: C 227 ASN cc_start: 0.8827 (m110) cc_final: 0.8578 (m110) REVERT: C 240 GLU cc_start: 0.7841 (tp30) cc_final: 0.7397 (tp30) REVERT: C 257 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7854 (mm-40) REVERT: C 302 GLU cc_start: 0.7902 (mp0) cc_final: 0.7309 (mp0) REVERT: D 11 LEU cc_start: 0.8174 (mm) cc_final: 0.7940 (mm) REVERT: D 66 ARG cc_start: 0.6947 (mmt-90) cc_final: 0.6738 (mmt180) REVERT: D 93 VAL cc_start: 0.8456 (t) cc_final: 0.8137 (p) REVERT: D 96 ASN cc_start: 0.8513 (m-40) cc_final: 0.8313 (m-40) REVERT: D 151 MET cc_start: 0.7433 (tmm) cc_final: 0.6347 (tmm) REVERT: D 186 ASN cc_start: 0.7879 (p0) cc_final: 0.7537 (p0) REVERT: D 207 GLN cc_start: 0.7510 (pt0) cc_final: 0.7036 (pt0) REVERT: D 211 TRP cc_start: 0.8162 (m100) cc_final: 0.5962 (m100) REVERT: D 248 MET cc_start: 0.7489 (mtp) cc_final: 0.7076 (mtp) REVERT: D 254 MET cc_start: 0.7980 (ppp) cc_final: 0.7666 (ppp) REVERT: D 279 ASN cc_start: 0.8043 (m-40) cc_final: 0.7717 (m-40) REVERT: D 294 PHE cc_start: 0.6995 (t80) cc_final: 0.6364 (t80) REVERT: E 77 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7526 (ptpp) REVERT: E 97 LEU cc_start: 0.8284 (mt) cc_final: 0.8033 (mt) REVERT: E 158 LEU cc_start: 0.7999 (tp) cc_final: 0.7773 (tp) REVERT: E 166 LEU cc_start: 0.8971 (mp) cc_final: 0.8601 (mp) REVERT: E 180 ARG cc_start: 0.8590 (mpt180) cc_final: 0.7711 (mmp80) REVERT: E 186 ASN cc_start: 0.7396 (m-40) cc_final: 0.7053 (m-40) REVERT: E 202 GLN cc_start: 0.7858 (pp30) cc_final: 0.7334 (pp30) REVERT: E 219 TYR cc_start: 0.8140 (m-80) cc_final: 0.7832 (m-80) REVERT: E 220 LEU cc_start: 0.7832 (mt) cc_final: 0.7505 (mt) REVERT: E 288 PHE cc_start: 0.8311 (t80) cc_final: 0.8016 (t80) REVERT: E 290 PHE cc_start: 0.8224 (t80) cc_final: 0.7898 (t80) REVERT: E 294 PHE cc_start: 0.7193 (t80) cc_final: 0.6777 (t80) REVERT: F 25 ASP cc_start: 0.6402 (t0) cc_final: 0.5849 (t0) REVERT: F 63 TYR cc_start: 0.6385 (m-10) cc_final: 0.6166 (m-10) REVERT: F 64 ASN cc_start: 0.7998 (t0) cc_final: 0.7797 (t0) REVERT: F 68 MET cc_start: 0.7071 (tmm) cc_final: 0.6718 (tmm) REVERT: F 98 ASP cc_start: 0.6076 (m-30) cc_final: 0.5320 (m-30) REVERT: F 105 ASP cc_start: 0.7627 (t70) cc_final: 0.6975 (t0) REVERT: F 123 PHE cc_start: 0.7565 (t80) cc_final: 0.7316 (t80) REVERT: F 124 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8425 (mtmt) REVERT: F 135 ASN cc_start: 0.8643 (p0) cc_final: 0.8091 (p0) REVERT: F 151 MET cc_start: 0.6852 (mmp) cc_final: 0.6491 (mmp) REVERT: F 171 ARG cc_start: 0.7363 (tpt90) cc_final: 0.7104 (tpt90) REVERT: F 201 GLN cc_start: 0.8065 (mm110) cc_final: 0.7838 (mm110) REVERT: F 208 MET cc_start: 0.6719 (tmm) cc_final: 0.6183 (tmm) REVERT: F 227 ASN cc_start: 0.8282 (m110) cc_final: 0.7933 (m110) REVERT: F 279 ASN cc_start: 0.8212 (m110) cc_final: 0.7979 (m110) REVERT: G 323 ARG cc_start: 0.7705 (tpm170) cc_final: 0.7476 (tpm170) REVERT: G 387 ASP cc_start: 0.7701 (t70) cc_final: 0.7275 (t70) REVERT: G 427 MET cc_start: 0.6883 (pmm) cc_final: 0.6212 (pmm) REVERT: G 430 ARG cc_start: 0.8159 (ptt90) cc_final: 0.7700 (ptt90) REVERT: G 432 ILE cc_start: 0.8260 (tp) cc_final: 0.7885 (tp) REVERT: G 446 LEU cc_start: 0.8619 (mt) cc_final: 0.8348 (mt) REVERT: G 448 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7524 (tpp80) REVERT: G 544 ILE cc_start: 0.8270 (mp) cc_final: 0.7467 (mp) REVERT: G 567 LEU cc_start: 0.8746 (tp) cc_final: 0.8524 (tp) REVERT: a 23 GLU cc_start: 0.7661 (tp30) cc_final: 0.7359 (tp30) REVERT: a 70 HIS cc_start: 0.8180 (t-90) cc_final: 0.7970 (t-90) REVERT: a 90 ASN cc_start: 0.8338 (t0) cc_final: 0.7926 (t0) REVERT: a 108 PHE cc_start: 0.6963 (t80) cc_final: 0.6720 (t80) REVERT: a 131 LEU cc_start: 0.7646 (mt) cc_final: 0.7102 (mt) REVERT: a 134 MET cc_start: 0.7305 (ppp) cc_final: 0.6610 (ppp) REVERT: a 181 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7490 (mm-30) REVERT: a 219 MET cc_start: 0.5581 (tmm) cc_final: 0.4676 (tmm) REVERT: N 385 LEU cc_start: 0.6377 (mm) cc_final: 0.6144 (pt) REVERT: N 395 LEU cc_start: 0.7924 (tp) cc_final: 0.7491 (tp) REVERT: N 472 GLU cc_start: 0.8758 (mp0) cc_final: 0.8466 (mp0) REVERT: N 608 HIS cc_start: 0.8459 (p90) cc_final: 0.8163 (p90) REVERT: N 617 GLU cc_start: 0.7307 (pm20) cc_final: 0.6975 (pm20) REVERT: N 681 TYR cc_start: 0.7466 (t80) cc_final: 0.7160 (t80) REVERT: N 782 GLU cc_start: 0.8826 (tt0) cc_final: 0.8528 (tt0) REVERT: N 860 ARG cc_start: 0.7286 (mmp80) cc_final: 0.6842 (mmp80) REVERT: N 880 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8225 (mmtp) REVERT: N 881 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7114 (mtmm) REVERT: N 885 LEU cc_start: 0.8306 (tp) cc_final: 0.8025 (tp) REVERT: N 890 TYR cc_start: 0.8695 (t80) cc_final: 0.8387 (t80) REVERT: N 928 GLN cc_start: 0.7653 (tp40) cc_final: 0.7361 (tp40) REVERT: N 1038 LEU cc_start: 0.7233 (mm) cc_final: 0.6946 (mm) REVERT: N 1054 TRP cc_start: 0.7403 (t60) cc_final: 0.7053 (t60) REVERT: N 1105 PHE cc_start: 0.7015 (m-80) cc_final: 0.6563 (m-80) REVERT: N 1141 GLU cc_start: 0.7521 (pm20) cc_final: 0.7283 (pm20) REVERT: N 1156 TRP cc_start: 0.8268 (t60) cc_final: 0.8038 (t60) REVERT: N 1177 TYR cc_start: 0.7791 (m-10) cc_final: 0.7590 (m-10) REVERT: N 1209 PHE cc_start: 0.7360 (t80) cc_final: 0.6924 (t80) REVERT: N 1251 HIS cc_start: 0.7119 (m-70) cc_final: 0.6772 (m-70) outliers start: 1 outliers final: 1 residues processed: 766 average time/residue: 0.1876 time to fit residues: 221.0242 Evaluate side-chains 750 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 749 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 164 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN D 10 ASN D 73 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1083 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134755 restraints weight = 48095.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140074 restraints weight = 29279.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143896 restraints weight = 19841.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146562 restraints weight = 14604.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.148652 restraints weight = 11451.781| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26507 Z= 0.188 Angle : 0.635 13.554 36048 Z= 0.329 Chirality : 0.045 0.232 4027 Planarity : 0.005 0.052 4746 Dihedral : 6.072 85.210 3737 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.27 % Favored : 91.69 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.56 % 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: -0.86 (0.15), residues: 3275 helix: 0.05 (0.14), residues: 1333 sheet: -0.58 (0.28), residues: 361 loop : -1.04 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 959 TYR 0.022 0.002 TYR a 139 PHE 0.029 0.002 PHE F 294 TRP 0.018 0.002 TRP B 276 HIS 0.007 0.001 HIS N1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (26507) covalent geometry : angle 0.63542 / 0.33 (36048) hydrogen bonds : bond 0.03647 / 2.42 ( 1049) hydrogen bonds : angle 5.19228 / 3.69 ( 3033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 778 time to evaluate : 0.818 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 52 GLN cc_start: 0.7621 (pp30) cc_final: 0.7233 (pp30) REVERT: A 53 THR cc_start: 0.8365 (p) cc_final: 0.7856 (p) REVERT: A 68 MET cc_start: 0.6785 (tpt) cc_final: 0.6450 (tpt) REVERT: A 72 TYR cc_start: 0.6736 (m-80) cc_final: 0.6230 (m-80) REVERT: A 133 GLN cc_start: 0.8339 (mt0) cc_final: 0.8114 (mt0) REVERT: A 138 LEU cc_start: 0.7807 (tp) cc_final: 0.7493 (tp) REVERT: A 154 ILE cc_start: 0.8227 (mp) cc_final: 0.8025 (mp) REVERT: A 169 GLN cc_start: 0.8173 (mp10) cc_final: 0.7940 (mp10) REVERT: A 176 HIS cc_start: 0.7992 (t-90) cc_final: 0.7510 (t-90) REVERT: A 215 THR cc_start: 0.8731 (t) cc_final: 0.8404 (t) REVERT: A 244 ILE cc_start: 0.8129 (mt) cc_final: 0.7555 (mt) REVERT: A 248 MET cc_start: 0.7640 (mtm) cc_final: 0.7107 (mtm) REVERT: A 268 MET cc_start: 0.7275 (mmm) cc_final: 0.6467 (mmm) REVERT: A 275 THR cc_start: 0.8760 (m) cc_final: 0.8545 (m) REVERT: A 294 PHE cc_start: 0.8153 (t80) cc_final: 0.7531 (t80) REVERT: B 29 MET cc_start: 0.7131 (mmp) cc_final: 0.6737 (mmp) REVERT: B 130 TRP cc_start: 0.8380 (t60) cc_final: 0.7790 (t60) REVERT: B 155 GLN cc_start: 0.8506 (tp40) cc_final: 0.7897 (tp40) REVERT: B 230 LEU cc_start: 0.8711 (mt) cc_final: 0.8456 (mt) REVERT: B 253 ASP cc_start: 0.7911 (m-30) cc_final: 0.7531 (m-30) REVERT: B 266 THR cc_start: 0.7747 (p) cc_final: 0.7539 (p) REVERT: B 291 ARG cc_start: 0.7647 (mtp-110) cc_final: 0.7177 (mtp-110) REVERT: C 29 MET cc_start: 0.6290 (ptm) cc_final: 0.5722 (ptm) REVERT: C 42 GLU cc_start: 0.7438 (pm20) cc_final: 0.7037 (pm20) REVERT: C 47 TYR cc_start: 0.7860 (t80) cc_final: 0.7595 (t80) REVERT: C 49 PHE cc_start: 0.8149 (m-10) cc_final: 0.7712 (m-10) REVERT: C 89 ASN cc_start: 0.8518 (m110) cc_final: 0.8222 (m110) REVERT: C 95 VAL cc_start: 0.8485 (t) cc_final: 0.8114 (p) REVERT: C 138 LEU cc_start: 0.8049 (mt) cc_final: 0.7842 (mt) REVERT: C 150 VAL cc_start: 0.8332 (t) cc_final: 0.8079 (p) REVERT: C 227 ASN cc_start: 0.8832 (m110) cc_final: 0.8546 (m110) REVERT: C 240 GLU cc_start: 0.7855 (tp30) cc_final: 0.7437 (tp30) REVERT: C 257 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8003 (mm-40) REVERT: C 302 GLU cc_start: 0.7946 (mp0) cc_final: 0.7355 (mp0) REVERT: D 11 LEU cc_start: 0.8196 (mm) cc_final: 0.7969 (mm) REVERT: D 42 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6786 (mm-30) REVERT: D 93 VAL cc_start: 0.8428 (t) cc_final: 0.8137 (p) REVERT: D 142 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7536 (mt-10) REVERT: D 149 ASP cc_start: 0.8428 (m-30) cc_final: 0.7976 (m-30) REVERT: D 151 MET cc_start: 0.7505 (tmm) cc_final: 0.6386 (tmm) REVERT: D 186 ASN cc_start: 0.7873 (p0) cc_final: 0.7667 (p0) REVERT: D 207 GLN cc_start: 0.7512 (pt0) cc_final: 0.7121 (pt0) REVERT: D 211 TRP cc_start: 0.8161 (m100) cc_final: 0.6710 (m100) REVERT: D 246 ASN cc_start: 0.8540 (m-40) cc_final: 0.8264 (m-40) REVERT: D 248 MET cc_start: 0.7510 (mtp) cc_final: 0.7062 (mtp) REVERT: D 254 MET cc_start: 0.8029 (ppp) cc_final: 0.7720 (ppp) REVERT: D 279 ASN cc_start: 0.8148 (m-40) cc_final: 0.7825 (m-40) REVERT: D 294 PHE cc_start: 0.6990 (t80) cc_final: 0.6406 (t80) REVERT: D 300 GLU cc_start: 0.7591 (mp0) cc_final: 0.7266 (mp0) REVERT: D 302 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7606 (mt-10) REVERT: E 68 MET cc_start: 0.8108 (ppp) cc_final: 0.7801 (ppp) REVERT: E 77 LYS cc_start: 0.7857 (ptpp) cc_final: 0.7531 (ptpp) REVERT: E 97 LEU cc_start: 0.8293 (mt) cc_final: 0.8025 (mt) REVERT: E 158 LEU cc_start: 0.7956 (tp) cc_final: 0.7694 (tp) REVERT: E 166 LEU cc_start: 0.8990 (mp) cc_final: 0.8578 (mp) REVERT: E 186 ASN cc_start: 0.7369 (m-40) cc_final: 0.6969 (m-40) REVERT: E 202 GLN cc_start: 0.8009 (pp30) cc_final: 0.7771 (tm-30) REVERT: E 219 TYR cc_start: 0.8190 (m-80) cc_final: 0.7865 (m-80) REVERT: E 220 LEU cc_start: 0.7900 (mt) cc_final: 0.7585 (mt) REVERT: E 288 PHE cc_start: 0.8319 (t80) cc_final: 0.7896 (t80) REVERT: F 25 ASP cc_start: 0.6629 (t0) cc_final: 0.6084 (t0) REVERT: F 68 MET cc_start: 0.7107 (tmm) cc_final: 0.6879 (tmm) REVERT: F 98 ASP cc_start: 0.6035 (m-30) cc_final: 0.5280 (m-30) REVERT: F 123 PHE cc_start: 0.7585 (t80) cc_final: 0.7344 (t80) REVERT: F 124 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8410 (mtmt) REVERT: F 135 ASN cc_start: 0.8645 (p0) cc_final: 0.8073 (p0) REVERT: F 144 ASP cc_start: 0.8495 (p0) cc_final: 0.8238 (p0) REVERT: F 171 ARG cc_start: 0.7419 (tpt90) cc_final: 0.7151 (tpt90) REVERT: F 201 GLN cc_start: 0.8080 (mm110) cc_final: 0.7861 (mm110) REVERT: F 208 MET cc_start: 0.6876 (tmm) cc_final: 0.6409 (tmm) REVERT: F 227 ASN cc_start: 0.8321 (m110) cc_final: 0.7985 (m110) REVERT: F 279 ASN cc_start: 0.8276 (m110) cc_final: 0.8048 (m110) REVERT: G 323 ARG cc_start: 0.7757 (tpm170) cc_final: 0.7516 (tpm170) REVERT: G 387 ASP cc_start: 0.7745 (t70) cc_final: 0.7327 (t70) REVERT: G 407 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7242 (mm-30) REVERT: G 427 MET cc_start: 0.6956 (pmm) cc_final: 0.6325 (pmm) REVERT: G 430 ARG cc_start: 0.8206 (ptt90) cc_final: 0.7780 (ptt90) REVERT: G 432 ILE cc_start: 0.8279 (tp) cc_final: 0.7942 (tp) REVERT: G 446 LEU cc_start: 0.8635 (mt) cc_final: 0.8369 (mt) REVERT: G 448 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7387 (tpp80) REVERT: G 526 TRP cc_start: 0.7702 (t60) cc_final: 0.7460 (t60) REVERT: G 544 ILE cc_start: 0.8302 (mp) cc_final: 0.7512 (mp) REVERT: G 562 TYR cc_start: 0.6740 (t80) cc_final: 0.6029 (t80) REVERT: G 573 GLU cc_start: 0.7947 (tp30) cc_final: 0.7569 (tt0) REVERT: a 23 GLU cc_start: 0.7731 (tp30) cc_final: 0.7393 (tp30) REVERT: a 70 HIS cc_start: 0.8219 (t-90) cc_final: 0.8017 (t-90) REVERT: a 90 ASN cc_start: 0.8358 (t0) cc_final: 0.7932 (t0) REVERT: a 108 PHE cc_start: 0.6996 (t80) cc_final: 0.6740 (t80) REVERT: a 131 LEU cc_start: 0.7717 (mt) cc_final: 0.7178 (mt) REVERT: a 134 MET cc_start: 0.7320 (ppp) cc_final: 0.6596 (ppp) REVERT: a 181 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7545 (mm-30) REVERT: a 219 MET cc_start: 0.5541 (tmm) cc_final: 0.4650 (tmm) REVERT: N 395 LEU cc_start: 0.7876 (tp) cc_final: 0.7612 (tp) REVERT: N 617 GLU cc_start: 0.7252 (pm20) cc_final: 0.6897 (pm20) REVERT: N 681 TYR cc_start: 0.7539 (t80) cc_final: 0.7218 (t80) REVERT: N 782 GLU cc_start: 0.8857 (tt0) cc_final: 0.8586 (tt0) REVERT: N 860 ARG cc_start: 0.7361 (mmp80) cc_final: 0.6972 (mmp80) REVERT: N 880 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8255 (mmtp) REVERT: N 885 LEU cc_start: 0.8401 (tp) cc_final: 0.8110 (tp) REVERT: N 890 TYR cc_start: 0.8689 (t80) cc_final: 0.8389 (t80) REVERT: N 928 GLN cc_start: 0.7669 (tp40) cc_final: 0.7365 (tp40) REVERT: N 948 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8390 (ptpt) REVERT: N 1038 LEU cc_start: 0.7363 (mm) cc_final: 0.7092 (mm) REVERT: N 1054 TRP cc_start: 0.7437 (t60) cc_final: 0.7152 (t60) REVERT: N 1086 VAL cc_start: 0.7625 (t) cc_final: 0.7411 (p) REVERT: N 1105 PHE cc_start: 0.7012 (m-80) cc_final: 0.6627 (m-80) REVERT: N 1141 GLU cc_start: 0.7589 (pm20) cc_final: 0.7320 (pm20) REVERT: N 1156 TRP cc_start: 0.8388 (t60) cc_final: 0.8164 (t60) REVERT: N 1161 MET cc_start: 0.8534 (mmm) cc_final: 0.8249 (mmm) REVERT: N 1209 PHE cc_start: 0.7400 (t80) cc_final: 0.6926 (t80) REVERT: N 1225 LEU cc_start: 0.8580 (mm) cc_final: 0.8377 (mm) REVERT: N 1243 PHE cc_start: 0.7855 (t80) cc_final: 0.6584 (t80) REVERT: N 1251 HIS cc_start: 0.7164 (m-70) cc_final: 0.6742 (m-70) outliers start: 1 outliers final: 0 residues processed: 779 average time/residue: 0.1733 time to fit residues: 207.5634 Evaluate side-chains 760 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 272 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 558 ASN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 GLN ** N 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 689 GLN ** N 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1083 GLN ** N1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131088 restraints weight = 48104.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136253 restraints weight = 29532.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139975 restraints weight = 20185.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142649 restraints weight = 14924.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144498 restraints weight = 11738.839| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26507 Z= 0.279 Angle : 0.723 13.861 36048 Z= 0.382 Chirality : 0.048 0.248 4027 Planarity : 0.006 0.068 4746 Dihedral : 6.675 84.353 3737 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.37 % Favored : 90.60 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.45 % 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: -1.25 (0.15), residues: 3275 helix: -0.30 (0.14), residues: 1334 sheet: -0.89 (0.27), residues: 376 loop : -1.20 (0.17), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 959 TYR 0.026 0.002 TYR C 219 PHE 0.043 0.002 PHE E 283 TRP 0.025 0.003 TRP B 276 HIS 0.010 0.002 HIS N1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.28 (26507) covalent geometry : angle 0.72345 / 0.38 (36048) hydrogen bonds : bond 0.04480 / 2.98 ( 1049) hydrogen bonds : angle 5.64018 / 4.04 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5368.44 seconds wall clock time: 93 minutes 8.34 seconds (5588.34 seconds total)