Starting phenix.real_space_refine on Sat Sep 12 10:11:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xmi_6733/09_2026/5xmi_6733.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 54 5.16 5 C 9362 2.51 5 N 2539 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14969 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "C" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "D" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "E" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "F" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.24 Number of scatterers: 14969 At special positions: 0 Unit cell: (159.398, 164.624, 82.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 15 15.00 O 2999 8.00 N 2539 7.00 C 9362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 656.2 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 48.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.279A pdb=" N LYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 159 removed outlier: 4.048A pdb=" N PHE A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.745A pdb=" N GLU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.433A pdb=" N SER A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.590A pdb=" N ASN A 224 " --> pdb=" O MET A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.622A pdb=" N GLU A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.662A pdb=" N MET A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 419 through 432 removed outlier: 4.102A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.824A pdb=" N LYS B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.918A pdb=" N GLU B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.999A pdb=" N GLU B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 removed outlier: 3.992A pdb=" N ILE B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.688A pdb=" N ARG B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.764A pdb=" N GLU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.762A pdb=" N TYR B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Proline residue: B 350 - end of helix removed outlier: 3.574A pdb=" N SER B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 418 through 431 removed outlier: 3.559A pdb=" N LEU B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.757A pdb=" N LYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 4.163A pdb=" N VAL C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.900A pdb=" N THR C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 removed outlier: 3.810A pdb=" N LYS C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.592A pdb=" N ALA C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 260 removed outlier: 3.713A pdb=" N MET C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 311 Processing helix chain 'C' and resid 321 through 331 removed outlier: 4.248A pdb=" N ARG C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 421 through 432 removed outlier: 3.721A pdb=" N GLN C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.679A pdb=" N LYS D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 155 removed outlier: 4.150A pdb=" N VAL D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.825A pdb=" N GLU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.882A pdb=" N VAL D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 244 through 247 removed outlier: 3.717A pdb=" N GLU D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 244 through 247' Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.540A pdb=" N MET D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 removed outlier: 4.000A pdb=" N ASN D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 300 through 313 removed outlier: 4.318A pdb=" N GLU D 309 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.779A pdb=" N TYR D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.624A pdb=" N ILE D 391 " --> pdb=" O TRP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 413 removed outlier: 3.646A pdb=" N LEU D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 432 removed outlier: 4.176A pdb=" N LEU D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP D 431 " --> pdb=" O GLN D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.578A pdb=" N LYS E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.735A pdb=" N LYS E 160 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.407A pdb=" N ASN E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.650A pdb=" N ALA E 236 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.962A pdb=" N LEU E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 311 removed outlier: 4.052A pdb=" N ASN E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 removed outlier: 3.789A pdb=" N TYR E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N SER E 356 " --> pdb=" O ARG E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.827A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 430 removed outlier: 3.743A pdb=" N LEU E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 178 through 191 removed outlier: 4.398A pdb=" N ASN F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 224 removed outlier: 3.939A pdb=" N VAL F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 removed outlier: 3.787A pdb=" N LEU F 237 " --> pdb=" O VAL F 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 247 through 265 removed outlier: 4.323A pdb=" N ARG F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.634A pdb=" N ARG F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.537A pdb=" N GLY F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 331 removed outlier: 3.630A pdb=" N MET F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 402 through 413 removed outlier: 4.247A pdb=" N PHE F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 432 removed outlier: 4.053A pdb=" N LEU F 422 " --> pdb=" O ASN F 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.385A pdb=" N THR A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 230 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 195 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP A 232 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 197 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER A 227 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU A 273 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A 275 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 231 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 292 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.541A pdb=" N HIS A 359 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 198 removed outlier: 7.011A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 231 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 169 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR B 276 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 171 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B 294 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 374 removed outlier: 3.637A pdb=" N LYS B 361 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.529A pdb=" N PHE C 195 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 276 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 232 removed outlier: 6.947A pdb=" N SER D 227 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 274 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 172 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'E' and resid 193 through 196 removed outlier: 3.504A pdb=" N LEU E 271 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 274 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 373 through 374 removed outlier: 3.505A pdb=" N ILE E 384 " --> pdb=" O PHE E 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 193 through 194 removed outlier: 6.460A pdb=" N THR F 193 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE F 230 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU F 273 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE F 229 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA F 275 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE F 231 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR F 172 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 361 through 362 removed outlier: 3.505A pdb=" N THR F 374 " --> pdb=" O LYS F 361 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2623 1.31 - 1.43: 3587 1.43 - 1.56: 8879 1.56 - 1.69: 46 1.69 - 1.81: 96 Bond restraints: 15231 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.28e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.28e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 ... (remaining 15226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 20342 3.66 - 7.32: 252 7.32 - 10.99: 26 10.99 - 14.65: 1 14.65 - 18.31: 9 Bond angle restraints: 20630 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 121.92 17.95 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.13 17.74 1.00e+00 1.00e+00 3.15e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 122.30 17.57 1.00e+00 1.00e+00 3.09e+02 ... (remaining 20625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8539 17.76 - 35.52: 612 35.52 - 53.27: 110 53.27 - 71.03: 19 71.03 - 88.79: 5 Dihedral angle restraints: 9285 sinusoidal: 3795 harmonic: 5490 Sorted by residual: dihedral pdb=" CA LYS C 225 " pdb=" C LYS C 225 " pdb=" N PRO C 226 " pdb=" CA PRO C 226 " ideal model delta harmonic sigma weight residual -180.00 -140.79 -39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA THR A 315 " pdb=" C THR A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual -180.00 -141.83 -38.17 0 5.00e+00 4.00e-02 5.83e+01 dihedral pdb=" CA LYS B 225 " pdb=" C LYS B 225 " pdb=" N PRO B 226 " pdb=" CA PRO B 226 " ideal model delta harmonic sigma weight residual 180.00 -142.15 -37.85 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 9282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1752 0.077 - 0.153: 456 0.153 - 0.230: 113 0.230 - 0.307: 18 0.307 - 0.384: 3 Chirality restraints: 2342 Sorted by residual: chirality pdb=" CA PHE A 290 " pdb=" N PHE A 290 " pdb=" C PHE A 290 " pdb=" CB PHE A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLN A 281 " pdb=" N GLN A 281 " pdb=" C GLN A 281 " pdb=" CB GLN A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ARG A 289 " pdb=" N ARG A 289 " pdb=" C ARG A 289 " pdb=" CB ARG A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2339 not shown) Planarity restraints: 2657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 225 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 226 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 151 " 0.065 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO F 152 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO F 152 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 152 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 315 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 316 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " 0.045 5.00e-02 4.00e+02 ... (remaining 2654 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4359 2.85 - 3.37: 14579 3.37 - 3.88: 23288 3.88 - 4.39: 27019 4.39 - 4.90: 43735 Nonbonded interactions: 112980 Sorted by model distance: nonbonded pdb=" O ALA C 303 " pdb=" OG1 THR C 306 " model vdw 2.342 3.040 nonbonded pdb=" O ALA E 303 " pdb=" OG1 THR E 306 " model vdw 2.376 3.040 nonbonded pdb=" O ALA D 303 " pdb=" OG1 THR D 306 " model vdw 2.391 3.040 nonbonded pdb=" O GLN A 425 " pdb=" OG1 THR A 429 " model vdw 2.409 3.040 nonbonded pdb=" OD2 ASP A 201 " pdb=" OG SER F 284 " model vdw 2.432 3.040 ... (remaining 112975 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' selection = (chain 'B' and resid 119 through 437) selection = (chain 'C' and resid 119 through 437) selection = (chain 'D' and resid 119 through 437) selection = (chain 'E' and resid 119 through 437) selection = (chain 'F' and resid 119 through 437) } 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: 0.540 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 : 0.009 0.086 15231 Z= 0.697 Angle : 1.291 18.308 20630 Z= 0.924 Chirality : 0.075 0.384 2342 Planarity : 0.007 0.112 2657 Dihedral : 13.028 88.791 5733 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 2.47 % Allowed : 8.94 % Favored : 88.59 % Rotamer: Outliers : 1.10 % Allowed : 4.23 % Favored : 94.67 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.06 % 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: -3.05 (0.17), residues: 1902 helix: -1.48 (0.16), residues: 762 sheet: -2.38 (0.33), residues: 169 loop : -2.41 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 304 TYR 0.016 0.002 TYR A 181 PHE 0.019 0.001 PHE B 290 TRP 0.012 0.001 TRP B 280 HIS 0.011 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00925 / 0.70 (15231) covalent geometry : angle 1.29116 / 0.92 (20630) hydrogen bonds : bond 0.17951 / 12.20 ( 565) hydrogen bonds : angle 8.04127 / 5.68 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 614 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6552 (t80) cc_final: 0.6292 (t80) REVERT: A 188 THR cc_start: 0.6964 (m) cc_final: 0.6700 (p) REVERT: A 217 LEU cc_start: 0.5027 (tp) cc_final: 0.4576 (tp) REVERT: A 225 LYS cc_start: 0.5694 (mtmm) cc_final: 0.5481 (pttp) REVERT: A 235 ASP cc_start: 0.5092 (p0) cc_final: 0.4811 (p0) REVERT: A 252 ILE cc_start: 0.5876 (mt) cc_final: 0.5441 (mm) REVERT: A 308 PHE cc_start: 0.8028 (m-80) cc_final: 0.7483 (m-80) REVERT: A 322 GLU cc_start: 0.8628 (tt0) cc_final: 0.8418 (mp0) REVERT: A 323 ASP cc_start: 0.8637 (m-30) cc_final: 0.8415 (t0) REVERT: A 339 ILE cc_start: 0.7514 (mt) cc_final: 0.7188 (mt) REVERT: A 371 ARG cc_start: 0.6004 (ptm-80) cc_final: 0.4568 (mtp180) REVERT: A 386 MET cc_start: 0.5273 (ptp) cc_final: 0.4170 (ppp) REVERT: B 139 GLU cc_start: 0.8604 (mp0) cc_final: 0.8351 (mt-10) REVERT: B 147 GLU cc_start: 0.8298 (tt0) cc_final: 0.7790 (pp20) REVERT: B 160 LYS cc_start: 0.6955 (mtpp) cc_final: 0.6475 (mmtp) REVERT: B 189 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7356 (pm20) REVERT: B 202 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6342 (pt) REVERT: B 211 GLU cc_start: 0.7810 (mp0) cc_final: 0.7503 (mm-30) REVERT: B 252 ILE cc_start: 0.8310 (mt) cc_final: 0.8108 (mp) REVERT: B 272 VAL cc_start: 0.8972 (t) cc_final: 0.8761 (m) REVERT: B 278 ILE cc_start: 0.8640 (mt) cc_final: 0.7931 (mm) REVERT: B 283 ASP cc_start: 0.7242 (t70) cc_final: 0.7031 (t0) REVERT: B 301 LEU cc_start: 0.7564 (tp) cc_final: 0.7318 (pt) REVERT: B 334 TYR cc_start: 0.6282 (m-10) cc_final: 0.5429 (m-10) REVERT: B 397 LYS cc_start: 0.6434 (tptm) cc_final: 0.6081 (ptmt) REVERT: B 427 GLN cc_start: 0.7956 (tt0) cc_final: 0.7529 (tm-30) REVERT: B 435 GLU cc_start: 0.5370 (mm-30) cc_final: 0.5009 (pm20) REVERT: C 126 GLU cc_start: 0.7836 (pt0) cc_final: 0.7553 (tp30) REVERT: C 133 GLU cc_start: 0.7897 (mp0) cc_final: 0.6291 (tp30) REVERT: C 146 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7777 (mmtt) REVERT: C 184 LYS cc_start: 0.6794 (mttm) cc_final: 0.6522 (tttt) REVERT: C 212 LYS cc_start: 0.7089 (tttp) cc_final: 0.6812 (tttp) REVERT: C 292 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7751 (mmm-85) REVERT: C 296 ILE cc_start: 0.8451 (mm) cc_final: 0.7560 (tp) REVERT: C 326 THR cc_start: 0.7178 (m) cc_final: 0.6760 (p) REVERT: C 332 GLU cc_start: 0.6922 (tt0) cc_final: 0.6657 (tm-30) REVERT: C 410 ILE cc_start: 0.6022 (mt) cc_final: 0.5260 (pt) REVERT: C 434 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5394 (tp40) REVERT: D 126 GLU cc_start: 0.7201 (pt0) cc_final: 0.6058 (pm20) REVERT: D 133 GLU cc_start: 0.6568 (pm20) cc_final: 0.5789 (pm20) REVERT: D 160 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6480 (mmmt) REVERT: D 166 THR cc_start: 0.5717 (m) cc_final: 0.5355 (m) REVERT: D 195 PHE cc_start: 0.5237 (m-80) cc_final: 0.4560 (m-80) REVERT: D 245 GLU cc_start: 0.7058 (tp30) cc_final: 0.6604 (tp30) REVERT: D 249 SER cc_start: 0.8868 (t) cc_final: 0.8297 (t) REVERT: D 290 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.5762 (t80) REVERT: D 301 LEU cc_start: 0.8638 (tp) cc_final: 0.8412 (pp) REVERT: D 411 LYS cc_start: 0.7056 (mttt) cc_final: 0.6542 (pttt) REVERT: D 432 PHE cc_start: 0.6949 (m-80) cc_final: 0.6641 (m-80) REVERT: E 129 ASN cc_start: 0.6493 (t0) cc_final: 0.5500 (p0) REVERT: E 164 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7613 (ptpp) REVERT: E 181 TYR cc_start: 0.8130 (t80) cc_final: 0.7643 (t80) REVERT: E 191 ASN cc_start: 0.7916 (t0) cc_final: 0.7692 (t0) REVERT: E 235 ASP cc_start: 0.7059 (p0) cc_final: 0.6403 (p0) REVERT: E 252 ILE cc_start: 0.7204 (mt) cc_final: 0.6652 (mm) REVERT: E 309 GLU cc_start: 0.8280 (pt0) cc_final: 0.7692 (tm-30) REVERT: E 359 HIS cc_start: 0.7713 (m90) cc_final: 0.7380 (m-70) REVERT: E 386 MET cc_start: 0.6200 (ptp) cc_final: 0.5981 (ptm) REVERT: E 389 THR cc_start: 0.7523 (p) cc_final: 0.7296 (p) REVERT: E 404 LYS cc_start: 0.6917 (mtmt) cc_final: 0.6044 (tmmt) REVERT: F 142 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8148 (pptt) REVERT: F 146 LYS cc_start: 0.8535 (mttt) cc_final: 0.8296 (mttt) REVERT: F 172 TYR cc_start: 0.6935 (p90) cc_final: 0.6559 (p90) REVERT: F 184 LYS cc_start: 0.8487 (mttm) cc_final: 0.8276 (mmmt) REVERT: F 194 PHE cc_start: 0.7668 (t80) cc_final: 0.7347 (t80) REVERT: F 195 PHE cc_start: 0.7215 (m-80) cc_final: 0.6458 (m-80) REVERT: F 206 TRP cc_start: 0.6502 (m100) cc_final: 0.5969 (t-100) REVERT: F 207 MET cc_start: 0.1962 (mtm) cc_final: 0.1728 (mtt) REVERT: F 230 PHE cc_start: 0.7954 (t80) cc_final: 0.7741 (t80) REVERT: F 235 ASP cc_start: 0.7744 (p0) cc_final: 0.7167 (p0) REVERT: F 240 THR cc_start: 0.4054 (OUTLIER) cc_final: 0.3661 (t) REVERT: F 265 ASN cc_start: 0.7623 (m-40) cc_final: 0.7222 (t0) REVERT: F 323 ASP cc_start: 0.7173 (m-30) cc_final: 0.6722 (t0) REVERT: F 327 LEU cc_start: 0.7266 (mt) cc_final: 0.6601 (mt) REVERT: F 344 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6563 (tptt) REVERT: F 345 ASP cc_start: 0.8277 (t70) cc_final: 0.7983 (t70) REVERT: F 388 TRP cc_start: 0.6875 (p-90) cc_final: 0.6460 (p-90) REVERT: F 397 LYS cc_start: 0.7280 (tptm) cc_final: 0.6679 (ttpt) outliers start: 18 outliers final: 4 residues processed: 623 average time/residue: 0.1401 time to fit residues: 124.1361 Evaluate side-chains 345 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 338 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain F residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS A 268 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN B 261 ASN C 425 GLN D 216 GLN D 233 GLN D 265 ASN D 277 ASN D 437 ASN E 216 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 355 GLN ** F 425 GLN ** 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 = 0.4417 r_free = 0.4417 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.142517 restraints weight = 36515.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.142546 restraints weight = 36800.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.144140 restraints weight = 30028.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.144125 restraints weight = 20011.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.144601 restraints weight = 20073.021| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15231 Z= 0.168 Angle : 0.758 10.192 20630 Z= 0.387 Chirality : 0.044 0.257 2342 Planarity : 0.006 0.117 2657 Dihedral : 8.024 88.783 2059 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.52 % Favored : 91.85 % Rotamer: Outliers : 4.84 % Allowed : 13.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.06 % 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: -1.59 (0.19), residues: 1902 helix: -0.13 (0.18), residues: 794 sheet: -1.52 (0.36), residues: 188 loop : -1.77 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 287 TYR 0.017 0.002 TYR C 334 PHE 0.021 0.002 PHE C 432 TRP 0.010 0.002 TRP E 280 HIS 0.019 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (15231) covalent geometry : angle 0.75794 / 0.39 (20630) hydrogen bonds : bond 0.04200 / 2.76 ( 565) hydrogen bonds : angle 5.09969 / 3.57 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 343 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.7036 (m-80) cc_final: 0.6569 (p90) REVERT: A 171 LEU cc_start: 0.7429 (mt) cc_final: 0.7192 (mt) REVERT: A 252 ILE cc_start: 0.6050 (mt) cc_final: 0.5830 (mm) REVERT: A 386 MET cc_start: 0.3369 (ptp) cc_final: 0.2955 (ppp) REVERT: A 430 ARG cc_start: 0.6465 (mtm180) cc_final: 0.4172 (tpm170) REVERT: B 202 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6011 (pt) REVERT: C 240 THR cc_start: 0.4856 (OUTLIER) cc_final: 0.4540 (p) REVERT: C 271 LEU cc_start: 0.7478 (tp) cc_final: 0.6918 (mm) REVERT: D 126 GLU cc_start: 0.6734 (pt0) cc_final: 0.6440 (pm20) REVERT: D 195 PHE cc_start: 0.4146 (m-80) cc_final: 0.3229 (m-80) REVERT: D 232 ASP cc_start: 0.6937 (t0) cc_final: 0.6573 (m-30) REVERT: E 207 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4611 (mtp) REVERT: E 404 LYS cc_start: 0.7365 (mtmt) cc_final: 0.7114 (tmmt) REVERT: F 207 MET cc_start: 0.3906 (mtm) cc_final: 0.3145 (mtt) REVERT: F 290 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.5186 (m-80) outliers start: 79 outliers final: 41 residues processed: 392 average time/residue: 0.1338 time to fit residues: 76.0934 Evaluate side-chains 291 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 38 optimal weight: 0.0040 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 311 ASN D 425 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN F 355 GLN ** F 425 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.155454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.136299 restraints weight = 37218.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.135521 restraints weight = 43010.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.136649 restraints weight = 37738.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.136860 restraints weight = 26834.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137096 restraints weight = 24581.086| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15231 Z= 0.189 Angle : 0.746 12.775 20630 Z= 0.386 Chirality : 0.045 0.192 2342 Planarity : 0.007 0.118 2657 Dihedral : 7.623 79.069 2056 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.20 % Favored : 91.17 % Rotamer: Outliers : 5.45 % Allowed : 15.81 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.11 % 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: -1.45 (0.19), residues: 1902 helix: -0.16 (0.18), residues: 794 sheet: -1.25 (0.37), residues: 191 loop : -1.60 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 430 TYR 0.035 0.003 TYR A 181 PHE 0.031 0.002 PHE C 432 TRP 0.020 0.002 TRP A 132 HIS 0.006 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (15231) covalent geometry : angle 0.74647 / 0.39 (20630) hydrogen bonds : bond 0.03982 / 2.65 ( 565) hydrogen bonds : angle 4.96034 / 3.45 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 278 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 SER cc_start: 0.5079 (OUTLIER) cc_final: 0.4798 (t) REVERT: A 202 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.3669 (pp) REVERT: A 232 ASP cc_start: 0.7593 (p0) cc_final: 0.7219 (p0) REVERT: A 403 ILE cc_start: 0.5380 (mm) cc_final: 0.5066 (mm) REVERT: B 202 LEU cc_start: 0.6820 (mt) cc_final: 0.5746 (pt) REVERT: B 222 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7251 (mpt180) REVERT: B 260 MET cc_start: 0.7465 (ppp) cc_final: 0.7021 (ppp) REVERT: B 289 ARG cc_start: 0.4958 (mmm160) cc_final: 0.3622 (mmp80) REVERT: B 290 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6613 (t80) REVERT: C 223 GLU cc_start: 0.5055 (OUTLIER) cc_final: 0.3556 (pp20) REVERT: C 240 THR cc_start: 0.4927 (OUTLIER) cc_final: 0.4440 (p) REVERT: C 278 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6681 (pt) REVERT: C 280 TRP cc_start: 0.7604 (p-90) cc_final: 0.7332 (p90) REVERT: D 195 PHE cc_start: 0.3911 (m-80) cc_final: 0.3155 (m-80) REVERT: D 232 ASP cc_start: 0.7296 (t0) cc_final: 0.6849 (m-30) REVERT: D 288 ARG cc_start: 0.7058 (mpt180) cc_final: 0.6647 (mpt180) REVERT: D 307 MET cc_start: 0.6588 (ttm) cc_final: 0.6354 (tpp) REVERT: E 215 LYS cc_start: 0.8141 (tppt) cc_final: 0.7517 (mmtm) REVERT: F 207 MET cc_start: 0.3946 (mtm) cc_final: 0.3366 (mtt) REVERT: F 260 MET cc_start: 0.3882 (ptt) cc_final: 0.3463 (tmm) REVERT: F 307 MET cc_start: 0.7669 (tpp) cc_final: 0.7341 (tpp) outliers start: 89 outliers final: 51 residues processed: 343 average time/residue: 0.1232 time to fit residues: 62.9105 Evaluate side-chains 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 175 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.147674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.125171 restraints weight = 38915.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.124382 restraints weight = 33997.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.124410 restraints weight = 26251.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.124658 restraints weight = 26004.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.124874 restraints weight = 23102.096| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15231 Z= 0.275 Angle : 0.843 9.681 20630 Z= 0.437 Chirality : 0.048 0.318 2342 Planarity : 0.007 0.120 2657 Dihedral : 7.774 75.655 2051 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.10 % Favored : 90.27 % Rotamer: Outliers : 5.58 % Allowed : 18.20 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.11 % 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: -1.80 (0.19), residues: 1902 helix: -0.58 (0.17), residues: 798 sheet: -1.52 (0.37), residues: 196 loop : -1.62 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 222 TYR 0.021 0.003 TYR A 172 PHE 0.036 0.003 PHE C 432 TRP 0.017 0.002 TRP A 132 HIS 0.006 0.002 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (15231) covalent geometry : angle 0.84336 / 0.44 (20630) hydrogen bonds : bond 0.04445 / 2.93 ( 565) hydrogen bonds : angle 5.30830 / 3.72 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 242 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 SER cc_start: 0.5376 (OUTLIER) cc_final: 0.5076 (t) REVERT: A 202 LEU cc_start: 0.5079 (OUTLIER) cc_final: 0.4402 (pp) REVERT: A 386 MET cc_start: 0.4086 (ptp) cc_final: 0.3884 (ptp) REVERT: B 245 GLU cc_start: 0.6171 (tp30) cc_final: 0.5484 (tt0) REVERT: B 260 MET cc_start: 0.8002 (ppp) cc_final: 0.7690 (ppp) REVERT: B 278 ILE cc_start: 0.8522 (mp) cc_final: 0.8251 (mm) REVERT: B 290 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7460 (t80) REVERT: B 308 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: B 334 TYR cc_start: 0.5268 (m-10) cc_final: 0.5026 (m-10) REVERT: C 139 GLU cc_start: 0.6582 (tp30) cc_final: 0.5806 (tp30) REVERT: C 290 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 385 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: C 418 ASN cc_start: 0.7871 (t0) cc_final: 0.7658 (t0) REVERT: D 195 PHE cc_start: 0.4398 (m-80) cc_final: 0.3590 (m-80) REVERT: F 207 MET cc_start: 0.3639 (mtm) cc_final: 0.2936 (mtm) REVERT: F 247 GLU cc_start: 0.5232 (mp0) cc_final: 0.3856 (tm-30) REVERT: F 339 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (mm) outliers start: 91 outliers final: 59 residues processed: 308 average time/residue: 0.1097 time to fit residues: 51.8058 Evaluate side-chains 266 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN C 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.149652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.127553 restraints weight = 38860.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.127108 restraints weight = 44284.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128453 restraints weight = 32852.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129142 restraints weight = 24640.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.129321 restraints weight = 22612.919| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15231 Z= 0.171 Angle : 0.724 11.748 20630 Z= 0.371 Chirality : 0.045 0.239 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.567 87.822 2051 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.62 % Favored : 90.85 % Rotamer: Outliers : 5.33 % Allowed : 20.10 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.11 % 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: -1.35 (0.19), residues: 1902 helix: -0.14 (0.18), residues: 791 sheet: -1.41 (0.37), residues: 196 loop : -1.41 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 222 TYR 0.015 0.002 TYR B 181 PHE 0.032 0.002 PHE E 290 TRP 0.027 0.002 TRP E 280 HIS 0.016 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15231) covalent geometry : angle 0.72380 / 0.37 (20630) hydrogen bonds : bond 0.03644 / 2.41 ( 565) hydrogen bonds : angle 4.90835 / 3.43 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 SER cc_start: 0.5817 (OUTLIER) cc_final: 0.5544 (t) REVERT: A 202 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4409 (pp) REVERT: A 232 ASP cc_start: 0.7917 (p0) cc_final: 0.7609 (p0) REVERT: B 202 LEU cc_start: 0.6765 (mt) cc_final: 0.5641 (pt) REVERT: B 260 MET cc_start: 0.7908 (ppp) cc_final: 0.7593 (ppp) REVERT: B 290 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7548 (t80) REVERT: B 308 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: B 334 TYR cc_start: 0.5701 (m-10) cc_final: 0.5441 (m-10) REVERT: C 139 GLU cc_start: 0.6915 (tp30) cc_final: 0.6355 (tp30) REVERT: C 143 GLU cc_start: 0.5956 (mm-30) cc_final: 0.4491 (mm-30) REVERT: C 240 THR cc_start: 0.4975 (OUTLIER) cc_final: 0.4545 (p) REVERT: C 278 ILE cc_start: 0.7918 (mm) cc_final: 0.7192 (pt) REVERT: C 280 TRP cc_start: 0.7851 (p-90) cc_final: 0.7332 (p90) REVERT: C 290 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7488 (t80) REVERT: C 385 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: D 195 PHE cc_start: 0.4693 (m-80) cc_final: 0.3938 (m-80) REVERT: D 232 ASP cc_start: 0.7021 (t0) cc_final: 0.6745 (m-30) REVERT: E 215 LYS cc_start: 0.8563 (tppt) cc_final: 0.8162 (mmtm) REVERT: F 207 MET cc_start: 0.4182 (mtm) cc_final: 0.3575 (mtm) REVERT: F 247 GLU cc_start: 0.4331 (mp0) cc_final: 0.3666 (tm-30) REVERT: F 260 MET cc_start: 0.3798 (ptt) cc_final: 0.3389 (tmm) REVERT: F 307 MET cc_start: 0.7970 (tpp) cc_final: 0.7550 (tpp) REVERT: F 323 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.5343 (t0) REVERT: F 349 GLN cc_start: 0.8431 (mm110) cc_final: 0.8111 (tp40) outliers start: 87 outliers final: 56 residues processed: 300 average time/residue: 0.1064 time to fit residues: 49.1982 Evaluate side-chains 272 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 323 ASP Chi-restraints excluded: chain F residue 339 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.151492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.130831 restraints weight = 38336.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.130478 restraints weight = 39209.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.130698 restraints weight = 31750.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131200 restraints weight = 28565.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.131295 restraints weight = 26750.610| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15231 Z= 0.132 Angle : 0.677 11.476 20630 Z= 0.344 Chirality : 0.043 0.211 2342 Planarity : 0.006 0.119 2657 Dihedral : 7.232 87.830 2051 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.15 % Favored : 91.38 % Rotamer: Outliers : 4.41 % Allowed : 22.18 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.11 % 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: -1.11 (0.20), residues: 1902 helix: 0.03 (0.18), residues: 794 sheet: -1.24 (0.37), residues: 197 loop : -1.26 (0.22), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 289 TYR 0.023 0.002 TYR A 172 PHE 0.028 0.002 PHE C 432 TRP 0.027 0.001 TRP E 280 HIS 0.015 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15231) covalent geometry : angle 0.67671 / 0.34 (20630) hydrogen bonds : bond 0.03256 / 2.16 ( 565) hydrogen bonds : angle 4.67813 / 3.27 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 SER cc_start: 0.5904 (OUTLIER) cc_final: 0.5687 (t) REVERT: A 202 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.4418 (pp) REVERT: A 232 ASP cc_start: 0.7789 (p0) cc_final: 0.7361 (p0) REVERT: A 260 MET cc_start: 0.3873 (ttp) cc_final: 0.3527 (ttp) REVERT: A 331 THR cc_start: 0.5963 (OUTLIER) cc_final: 0.5752 (p) REVERT: B 202 LEU cc_start: 0.6456 (mt) cc_final: 0.5723 (pt) REVERT: B 290 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 308 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: C 240 THR cc_start: 0.4849 (OUTLIER) cc_final: 0.4365 (p) REVERT: C 278 ILE cc_start: 0.7771 (mm) cc_final: 0.7197 (pt) REVERT: C 280 TRP cc_start: 0.7705 (p-90) cc_final: 0.7345 (p90) REVERT: C 290 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 385 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: D 195 PHE cc_start: 0.4121 (m-80) cc_final: 0.3676 (m-80) REVERT: D 232 ASP cc_start: 0.6973 (t0) cc_final: 0.6759 (m-30) REVERT: E 207 MET cc_start: 0.5426 (mtp) cc_final: 0.5218 (mtm) REVERT: E 215 LYS cc_start: 0.8320 (tppt) cc_final: 0.8049 (tptt) REVERT: E 386 MET cc_start: 0.3520 (ppp) cc_final: 0.3283 (ppp) REVERT: F 207 MET cc_start: 0.4195 (mtm) cc_final: 0.3443 (mtm) REVERT: F 247 GLU cc_start: 0.4177 (mp0) cc_final: 0.3609 (tm-30) REVERT: F 260 MET cc_start: 0.4069 (ptt) cc_final: 0.3498 (tmm) REVERT: F 307 MET cc_start: 0.7798 (tpp) cc_final: 0.7383 (tpp) REVERT: F 349 GLN cc_start: 0.8258 (mm110) cc_final: 0.7874 (tp40) outliers start: 72 outliers final: 43 residues processed: 305 average time/residue: 0.1102 time to fit residues: 51.1431 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 143 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 117 optimal weight: 0.0470 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 185 optimal weight: 5.9990 overall best weight: 3.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS C 437 ASN D 162 ASN D 427 GLN E 157 HIS E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.124597 restraints weight = 38727.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124384 restraints weight = 40190.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.125411 restraints weight = 30557.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.125957 restraints weight = 23781.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.126044 restraints weight = 22277.833| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15231 Z= 0.206 Angle : 0.765 10.579 20630 Z= 0.394 Chirality : 0.045 0.184 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.401 89.679 2051 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.25 % Favored : 90.27 % Rotamer: Outliers : 4.96 % Allowed : 22.37 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.06 % 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: -1.28 (0.19), residues: 1902 helix: -0.05 (0.18), residues: 786 sheet: -1.41 (0.36), residues: 200 loop : -1.38 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 289 TYR 0.031 0.002 TYR E 181 PHE 0.034 0.002 PHE C 432 TRP 0.025 0.002 TRP E 280 HIS 0.015 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (15231) covalent geometry : angle 0.76543 / 0.39 (20630) hydrogen bonds : bond 0.03768 / 2.51 ( 565) hydrogen bonds : angle 4.91663 / 3.44 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 224 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 200 SER cc_start: 0.5958 (OUTLIER) cc_final: 0.5750 (t) REVERT: A 202 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4789 (pp) REVERT: A 232 ASP cc_start: 0.7998 (p0) cc_final: 0.7529 (p0) REVERT: A 385 GLU cc_start: 0.4013 (pm20) cc_final: 0.3699 (pm20) REVERT: A 427 GLN cc_start: 0.6545 (mp10) cc_final: 0.5465 (pp30) REVERT: B 202 LEU cc_start: 0.6742 (mt) cc_final: 0.5778 (pt) REVERT: B 250 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7168 (tpt90) REVERT: B 290 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 308 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: C 290 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7417 (t80) REVERT: C 385 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: D 143 GLU cc_start: 0.7666 (pp20) cc_final: 0.7088 (pp20) REVERT: D 195 PHE cc_start: 0.4028 (m-80) cc_final: 0.3376 (m-80) REVERT: F 207 MET cc_start: 0.3988 (mtm) cc_final: 0.3657 (mtm) REVERT: F 247 GLU cc_start: 0.4534 (mp0) cc_final: 0.3789 (tm-30) REVERT: F 307 MET cc_start: 0.8022 (tpp) cc_final: 0.7552 (tpp) REVERT: F 349 GLN cc_start: 0.8566 (mm110) cc_final: 0.8203 (tp40) outliers start: 81 outliers final: 55 residues processed: 287 average time/residue: 0.1048 time to fit residues: 47.0497 Evaluate side-chains 268 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 348 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.126500 restraints weight = 38317.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126964 restraints weight = 38345.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.127319 restraints weight = 27755.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.127853 restraints weight = 24998.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.127893 restraints weight = 23757.516| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15231 Z= 0.145 Angle : 0.708 10.492 20630 Z= 0.362 Chirality : 0.044 0.212 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.227 88.097 2051 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.57 % Favored : 91.01 % Rotamer: Outliers : 3.86 % Allowed : 23.65 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.06 % 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: -1.12 (0.20), residues: 1902 helix: 0.02 (0.18), residues: 794 sheet: -1.36 (0.36), residues: 200 loop : -1.23 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 289 TYR 0.043 0.002 TYR E 181 PHE 0.030 0.002 PHE E 290 TRP 0.030 0.002 TRP E 280 HIS 0.015 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15231) covalent geometry : angle 0.70850 / 0.36 (20630) hydrogen bonds : bond 0.03317 / 2.19 ( 565) hydrogen bonds : angle 4.73175 / 3.31 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7845 (p0) cc_final: 0.7507 (p0) REVERT: A 260 MET cc_start: 0.3616 (ttp) cc_final: 0.3313 (tmm) REVERT: A 410 ILE cc_start: 0.8076 (mm) cc_final: 0.7870 (pt) REVERT: B 202 LEU cc_start: 0.6687 (mt) cc_final: 0.5813 (pt) REVERT: B 290 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7493 (t80) REVERT: B 308 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7049 (m-10) REVERT: C 240 THR cc_start: 0.4821 (OUTLIER) cc_final: 0.4319 (p) REVERT: C 290 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 385 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: D 143 GLU cc_start: 0.7567 (pp20) cc_final: 0.7096 (pp20) REVERT: D 195 PHE cc_start: 0.3796 (m-80) cc_final: 0.3377 (m-80) REVERT: D 204 SER cc_start: 0.8384 (p) cc_final: 0.8150 (m) REVERT: D 288 ARG cc_start: 0.7031 (mpt180) cc_final: 0.5512 (tpp80) REVERT: E 207 MET cc_start: 0.5422 (mtp) cc_final: 0.5167 (mtm) REVERT: F 207 MET cc_start: 0.3928 (mtm) cc_final: 0.3515 (mtm) REVERT: F 247 GLU cc_start: 0.4262 (mp0) cc_final: 0.3726 (tm-30) REVERT: F 307 MET cc_start: 0.7996 (tpp) cc_final: 0.7540 (tpp) REVERT: F 349 GLN cc_start: 0.8437 (mm110) cc_final: 0.8140 (tp40) outliers start: 63 outliers final: 48 residues processed: 274 average time/residue: 0.1111 time to fit residues: 47.1063 Evaluate side-chains 267 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 348 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 127 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.147986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.125696 restraints weight = 38234.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.126132 restraints weight = 41893.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126248 restraints weight = 31036.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.126784 restraints weight = 27172.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126907 restraints weight = 24619.232| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.8512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15231 Z= 0.170 Angle : 0.753 10.730 20630 Z= 0.386 Chirality : 0.044 0.225 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.241 85.391 2051 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.57 % Favored : 90.01 % Rotamer: Outliers : 4.29 % Allowed : 23.84 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.11 % 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: -1.12 (0.20), residues: 1902 helix: 0.06 (0.19), residues: 789 sheet: -1.36 (0.36), residues: 198 loop : -1.26 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 289 TYR 0.037 0.002 TYR E 181 PHE 0.033 0.002 PHE E 290 TRP 0.046 0.002 TRP F 132 HIS 0.014 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (15231) covalent geometry : angle 0.75303 / 0.39 (20630) hydrogen bonds : bond 0.03408 / 2.27 ( 565) hydrogen bonds : angle 4.80536 / 3.35 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7940 (p0) cc_final: 0.7521 (p0) REVERT: A 410 ILE cc_start: 0.8025 (mm) cc_final: 0.7707 (pt) REVERT: A 427 GLN cc_start: 0.6269 (mp10) cc_final: 0.5289 (pp30) REVERT: B 202 LEU cc_start: 0.6815 (mt) cc_final: 0.5866 (pt) REVERT: B 290 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 308 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: C 240 THR cc_start: 0.4594 (OUTLIER) cc_final: 0.4081 (p) REVERT: C 290 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7192 (t80) REVERT: C 385 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: D 145 LEU cc_start: 0.8905 (mp) cc_final: 0.8488 (mp) REVERT: D 195 PHE cc_start: 0.3910 (m-80) cc_final: 0.3513 (m-80) REVERT: E 245 GLU cc_start: 0.7249 (pm20) cc_final: 0.6908 (pm20) REVERT: F 207 MET cc_start: 0.3763 (mtm) cc_final: 0.3497 (mtm) REVERT: F 247 GLU cc_start: 0.4548 (mp0) cc_final: 0.3686 (tm-30) REVERT: F 307 MET cc_start: 0.7893 (tpp) cc_final: 0.7191 (tpp) REVERT: F 349 GLN cc_start: 0.8448 (mm110) cc_final: 0.8150 (tp40) REVERT: F 425 GLN cc_start: 0.7926 (mm110) cc_final: 0.7374 (mm110) outliers start: 70 outliers final: 53 residues processed: 278 average time/residue: 0.1115 time to fit residues: 48.1964 Evaluate side-chains 273 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN C 434 GLN E 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.128138 restraints weight = 38490.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.128040 restraints weight = 38451.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.128208 restraints weight = 30048.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128658 restraints weight = 27679.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128709 restraints weight = 26968.201| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15231 Z= 0.140 Angle : 0.728 13.824 20630 Z= 0.370 Chirality : 0.044 0.223 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.113 88.581 2051 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.20 % Favored : 91.38 % Rotamer: Outliers : 3.49 % Allowed : 24.82 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.06 % 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: -1.07 (0.20), residues: 1902 helix: 0.03 (0.18), residues: 799 sheet: -1.27 (0.36), residues: 193 loop : -1.19 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 289 TYR 0.034 0.002 TYR E 181 PHE 0.031 0.002 PHE E 290 TRP 0.033 0.002 TRP F 132 HIS 0.015 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15231) covalent geometry : angle 0.72832 / 0.37 (20630) hydrogen bonds : bond 0.03214 / 2.13 ( 565) hydrogen bonds : angle 4.76149 / 3.33 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7831 (p0) cc_final: 0.7416 (p0) REVERT: A 260 MET cc_start: 0.3786 (ttp) cc_final: 0.3251 (tmm) REVERT: A 410 ILE cc_start: 0.8195 (mm) cc_final: 0.7863 (pt) REVERT: A 427 GLN cc_start: 0.6419 (mp10) cc_final: 0.5368 (pp30) REVERT: B 202 LEU cc_start: 0.6973 (mt) cc_final: 0.6096 (pt) REVERT: B 207 MET cc_start: 0.2689 (mtm) cc_final: 0.2430 (mtp) REVERT: B 290 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7633 (t80) REVERT: B 308 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7170 (m-10) REVERT: B 351 ILE cc_start: 0.6327 (mm) cc_final: 0.6025 (mp) REVERT: C 240 THR cc_start: 0.4851 (OUTLIER) cc_final: 0.4352 (p) REVERT: C 290 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7037 (t80) REVERT: C 385 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: D 195 PHE cc_start: 0.3895 (m-80) cc_final: 0.3558 (m-80) REVERT: D 288 ARG cc_start: 0.6961 (mpt180) cc_final: 0.5275 (tpp80) REVERT: E 207 MET cc_start: 0.5411 (mtp) cc_final: 0.5160 (mtm) REVERT: E 245 GLU cc_start: 0.6617 (pm20) cc_final: 0.6324 (pm20) REVERT: F 207 MET cc_start: 0.3694 (mtm) cc_final: 0.3420 (mtm) REVERT: F 247 GLU cc_start: 0.4410 (mp0) cc_final: 0.3602 (tm-30) REVERT: F 307 MET cc_start: 0.8032 (tpp) cc_final: 0.7448 (tpp) REVERT: F 311 ASN cc_start: 0.8227 (m110) cc_final: 0.7879 (m110) REVERT: F 339 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8869 (tp) REVERT: F 349 GLN cc_start: 0.8346 (mm110) cc_final: 0.8067 (tp40) outliers start: 57 outliers final: 43 residues processed: 272 average time/residue: 0.1096 time to fit residues: 46.1596 Evaluate side-chains 267 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 349 GLN Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 173 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 149 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.149692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128637 restraints weight = 38387.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.128437 restraints weight = 36700.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.128218 restraints weight = 30861.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.128877 restraints weight = 28313.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129002 restraints weight = 24339.757| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 15231 Z= 0.228 Angle : 0.903 59.197 20630 Z= 0.501 Chirality : 0.045 0.435 2342 Planarity : 0.006 0.120 2657 Dihedral : 7.015 88.567 2050 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.41 % Favored : 91.22 % Rotamer: Outliers : 3.25 % Allowed : 25.61 % Favored : 71.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.06 % 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: -1.06 (0.20), residues: 1902 helix: 0.03 (0.18), residues: 799 sheet: -1.26 (0.36), residues: 193 loop : -1.19 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 287 TYR 0.028 0.002 TYR E 181 PHE 0.028 0.002 PHE E 290 TRP 0.046 0.002 TRP F 132 HIS 0.014 0.002 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (15231) covalent geometry : angle 0.90253 / 0.50 (20630) hydrogen bonds : bond 0.03246 / 2.14 ( 565) hydrogen bonds : angle 4.76555 / 3.32 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.22 seconds wall clock time: 42 minutes 47.30 seconds (2567.30 seconds total)