Starting phenix.real_space_refine on Wed Mar 4 13:58:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762.map" model { file = "/net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uge_20762/03_2026/6uge_20762_neut.cif" } resolution = 3.6 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 155 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 63 5.16 5 C 8776 2.51 5 N 2430 2.21 5 O 2588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13876 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2235 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2273 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2297 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2318 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2306 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2184 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.75, per 1000 atoms: 0.27 Number of scatterers: 13876 At special positions: 0 Unit cell: (131.76, 139.32, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 15 15.00 Mg 4 11.99 O 2588 8.00 N 2430 7.00 C 8776 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: 1.03 Conformation dependent library (CDL) restraints added in 634.1 milliseconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 7 sheets defined 49.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 198 through 209 removed outlier: 3.521A pdb=" N LYS A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.212A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.855A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.850A pdb=" N LEU A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.547A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.555A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.623A pdb=" N LEU A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 415 removed outlier: 4.014A pdb=" N VAL A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 4.004A pdb=" N ALA A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.786A pdb=" N PHE A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.893A pdb=" N GLY B 162 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 163' Processing helix chain 'B' and resid 171 through 180 removed outlier: 3.598A pdb=" N VAL B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.861A pdb=" N ILE B 195 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.587A pdb=" N LYS B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.822A pdb=" N LEU B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.979A pdb=" N ILE B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 3.536A pdb=" N ARG B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.627A pdb=" N GLU B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.654A pdb=" N ARG B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.544A pdb=" N ARG B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.514A pdb=" N LEU B 389 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.736A pdb=" N GLN B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.859A pdb=" N GLY C 162 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 198 through 209 removed outlier: 3.584A pdb=" N LYS C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.706A pdb=" N LEU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.703A pdb=" N ARG C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 removed outlier: 3.733A pdb=" N ILE C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.670A pdb=" N ARG C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.869A pdb=" N LYS C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 392 removed outlier: 3.645A pdb=" N LEU C 389 " --> pdb=" O ASN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 411 removed outlier: 3.853A pdb=" N SER C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.599A pdb=" N ALA C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 447 removed outlier: 3.873A pdb=" N PHE C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.570A pdb=" N GLY D 162 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 171 through 180 removed outlier: 3.575A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.686A pdb=" N ASP D 194 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 195 " --> pdb=" O LEU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 195' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.755A pdb=" N LEU D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 269 through 285 removed outlier: 3.857A pdb=" N VAL D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.975A pdb=" N LEU D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 321 removed outlier: 4.141A pdb=" N ARG D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.694A pdb=" N GLU D 344 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 345 " --> pdb=" O PRO D 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 341 through 345' Processing helix chain 'D' and resid 367 through 375 removed outlier: 3.506A pdb=" N MET D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.651A pdb=" N LEU D 389 " --> pdb=" O ASN D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.607A pdb=" N VAL D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 439 through 450 removed outlier: 3.778A pdb=" N PHE D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 removed outlier: 3.695A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.751A pdb=" N GLY E 162 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 171 through 180 removed outlier: 3.647A pdb=" N VAL E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.545A pdb=" N LYS E 202 " --> pdb=" O MET E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 4.044A pdb=" N LEU E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.846A pdb=" N ALA E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 285 removed outlier: 4.140A pdb=" N ALA E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 309 through 322 removed outlier: 3.536A pdb=" N VAL E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 removed outlier: 4.157A pdb=" N ARG E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 353' Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'E' and resid 385 through 393 removed outlier: 3.658A pdb=" N LEU E 389 " --> pdb=" O ASN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.978A pdb=" N VAL E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 430 removed outlier: 4.036A pdb=" N ALA E 429 " --> pdb=" O GLU E 425 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 430' Processing helix chain 'E' and resid 439 through 450 removed outlier: 4.028A pdb=" N PHE E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 469 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.651A pdb=" N GLY F 162 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP F 163 " --> pdb=" O SER F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 174 through 180 Processing helix chain 'F' and resid 198 through 215 removed outlier: 5.318A pdb=" N LEU F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Proline residue: F 212 - end of helix Processing helix chain 'F' and resid 220 through 224 removed outlier: 3.685A pdb=" N ARG F 223 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER F 224 " --> pdb=" O GLY F 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 220 through 224' Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.820A pdb=" N SER F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 4.025A pdb=" N VAL F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 4.260A pdb=" N LEU F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.812A pdb=" N LYS F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 375 Processing helix chain 'F' and resid 385 through 392 Processing helix chain 'F' and resid 399 through 416 removed outlier: 4.178A pdb=" N LEU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 432 Processing helix chain 'F' and resid 433 through 436 removed outlier: 3.758A pdb=" N GLU F 436 " --> pdb=" O LEU F 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 433 through 436' Processing helix chain 'F' and resid 439 through 448 Processing helix chain 'F' and resid 455 through 470 removed outlier: 4.484A pdb=" N MET F 459 " --> pdb=" O GLY F 455 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 470 " --> pdb=" O CYS F 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 257 removed outlier: 6.803A pdb=" N PHE A 255 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP A 292 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 257 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 338 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 231 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 357 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 232 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 253 through 254 removed outlier: 6.344A pdb=" N THR B 253 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 290 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU B 336 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 289 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ALA B 338 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE B 291 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 231 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 292 removed outlier: 7.763A pdb=" N SER C 287 " --> pdb=" O PHE C 334 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU C 336 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 289 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ALA C 338 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 291 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ILE C 357 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 230 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 228 through 231 removed outlier: 7.122A pdb=" N SER D 287 " --> pdb=" O PHE D 334 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU D 336 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 289 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA D 338 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE D 291 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D 255 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP D 292 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 257 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.721A pdb=" N PHE E 255 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP E 292 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL E 257 " --> pdb=" O ASP E 292 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA E 338 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE E 291 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 338 through 339 removed outlier: 6.393A pdb=" N LEU F 231 " --> pdb=" O THR F 339 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL F 230 " --> pdb=" O ILE F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 253 through 257 removed outlier: 6.316A pdb=" N THR F 253 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE F 290 " --> pdb=" O THR F 253 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE F 255 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER F 287 " --> pdb=" O PHE F 334 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU F 336 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE F 289 " --> pdb=" O LEU F 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 476 hydrogen bonds defined for protein. 1413 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: 1.83 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4570 1.34 - 1.46: 2954 1.46 - 1.58: 6470 1.58 - 1.70: 25 1.70 - 1.82: 109 Bond restraints: 14128 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.72e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.99e+01 ... (remaining 14123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 19083 4.75 - 9.49: 96 9.49 - 14.24: 6 14.24 - 18.99: 2 18.99 - 23.73: 8 Bond angle restraints: 19195 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 116.14 23.73 1.00e+00 1.00e+00 5.63e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 117.35 22.52 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 114.33 22.50 1.00e+00 1.00e+00 5.06e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 118.07 21.80 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 115.80 21.03 1.00e+00 1.00e+00 4.42e+02 ... (remaining 19190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7698 17.95 - 35.90: 726 35.90 - 53.85: 118 53.85 - 71.80: 29 71.80 - 89.75: 10 Dihedral angle restraints: 8581 sinusoidal: 3221 harmonic: 5360 Sorted by residual: dihedral pdb=" CA ILE A 364 " pdb=" C ILE A 364 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " ideal model delta harmonic sigma weight residual -180.00 -148.38 -31.62 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA ALA C 285 " pdb=" C ALA C 285 " pdb=" N PRO C 286 " pdb=" CA PRO C 286 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP C 295 " pdb=" C ASP C 295 " pdb=" N THR C 296 " pdb=" CA THR C 296 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1647 0.055 - 0.110: 494 0.110 - 0.164: 77 0.164 - 0.219: 8 0.219 - 0.274: 3 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE A 195 " pdb=" CA ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CG2 ILE A 195 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU C 262 " pdb=" CB LEU C 262 " pdb=" CD1 LEU C 262 " pdb=" CD2 LEU C 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2226 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 211 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO D 212 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 212 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 212 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.049 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO C 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 285 " 0.048 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO D 286 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " 0.040 5.00e-02 4.00e+02 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 133 2.63 - 3.20: 11348 3.20 - 3.76: 19584 3.76 - 4.33: 25478 4.33 - 4.90: 43183 Nonbonded interactions: 99726 Sorted by model distance: nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 2.060 2.170 nonbonded pdb=" O2G ATP B 501 " pdb="MG MG B 502 " model vdw 2.090 2.170 nonbonded pdb=" O1G ATP E 501 " pdb="MG MG E 502 " model vdw 2.101 2.170 nonbonded pdb=" O3G ATP D 501 " pdb="MG MG D 502 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR E 240 " pdb="MG MG E 502 " model vdw 2.122 2.170 ... (remaining 99721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 189 or (resid 190 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 259 or (resid 260 and (name N or name CA or name C or name O or name CB \ )) or resid 261 through 294 or (resid 295 and (name N or name CA or name C or n \ ame O or name CB )) or resid 296 through 303 or (resid 304 and (name N or name C \ A or name C or name O or name CB )) or resid 305 through 322 or resid 332 throug \ h 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 360 or (resid 361 and (name N or name CA or name C or name O o \ r name CB )) or resid 362 or (resid 363 and (name N or name CA or name C or name \ O or name CB )) or resid 364 through 366 or (resid 367 and (name N or name CA o \ r name C or name O or name CB )) or resid 368 or (resid 369 and (name N or name \ CA or name C or name O or name CB )) or resid 370 through 371 or (resid 372 thro \ ugh 373 and (name N or name CA or name C or name O or name CB )) or resid 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 6 through 377 or (resid 378 and (name N or name CA or name C or name O or name C \ B )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or na \ me CB )) or resid 381 or (resid 382 through 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 or (resid 387 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 399 or (resid 400 \ and (name N or name CA or name C or name O or name CB )) or resid 401 through 40 \ 5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ d 407 through 413 or (resid 414 and (name N or name CA or name C or name O or na \ me CB )) or resid 415 through 417 or (resid 418 through 419 and (name N or name \ CA or name C or name O or name CB )) or resid 420 or (resid 421 through 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 436 or \ (resid 437 through 439 and (name N or name CA or name C or name O or name CB )) \ or resid 440 through 443 or (resid 444 through 446 and (name N or name CA or na \ me C or name O or name CB )) or resid 447 or (resid 448 through 450 and (name N \ or name CA or name C or name O or name CB )) or resid 451 through 457 or (resid \ 458 through 464 and (name N or name CA or name C or name O or name CB )) or resi \ d 465 through 466 or (resid 467 through 468 and (name N or name CA or name C or \ name O or name CB )) or resid 469 through 472)) selection = (chain 'B' and (resid 156 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 182 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 216 or (re \ sid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 243 or (resid 244 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 245 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 278 or (resid 279 and (name N or name C \ A or name C or name O or name CB )) or resid 280 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 320 through 322 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 or (resid 346 through 348 and (name N or name CA or name C or n \ ame O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 360 or (res \ id 361 and (name N or name CA or name C or name O or name CB )) or resid 362 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 through 387 or \ (resid 388 through 394 and (name N or name CA or name C or name O or name CB )) \ or resid 395 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 405 or (resid 406 and (name N or name CA or \ name C or name O or name CB )) or resid 407 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 417 or (res \ id 418 through 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 422 and (name N or name CA or name C or name O or \ name CB )) or resid 423 through 435 or (resid 436 through 439 and (name N or na \ me CA or name C or name O or name CB )) or resid 440 through 443 or (resid 444 t \ hrough 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ or (resid 448 through 450 and (name N or name CA or name C or name O or name CB \ )) or resid 451 through 452 or (resid 453 through 454 and (name N or name CA or \ name C or name O or name CB )) or resid 455 through 457 or (resid 458 through 4 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 465 through \ 466 or (resid 467 through 468 and (name N or name CA or name C or name O or nam \ e CB )) or resid 469 through 471 or (resid 472 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'C' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 222 or (resid 223 and (name N or name CA or name C or name O or na \ me CB )) or resid 224 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 258 or (resid 259 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 268 or (resid 269 and (name N or name CA or \ name C or name O or name CB )) or resid 270 or (resid 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 278 or (resid 279 and ( \ name N or name CA or name C or name O or name CB )) or resid 280 through 294 or \ (resid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 or (resid 306 and (name N or name CA or name C or name O or nam \ e CB )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C \ or name O or name CB )) or resid 310 through 314 or (resid 315 through 316 and ( \ name N or name CA or name C or name O or name CB )) or resid 317 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 322 or (resid 332 and (name N or name CA or name C or name O or name CB \ )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 354 or (resid 355 throu \ gh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or n \ ame O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and ( \ name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 382 or (resid 383 through 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 387 or (resid 388 through 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 420 or (resid 421 through 422 and (name N or name CA or nam \ e C or name O or name CB )) or resid 423 through 435 or (resid 436 through 439 a \ nd (name N or name CA or name C or name O or name CB )) or resid 440 through 443 \ or (resid 444 through 446 and (name N or name CA or name C or name O or name CB \ )) or resid 447 or (resid 448 through 450 and (name N or name CA or name C or n \ ame O or name CB )) or resid 451 through 452 or (resid 453 through 454 and (name \ N or name CA or name C or name O or name CB )) or resid 455 through 456 or (res \ id 457 through 464 and (name N or name CA or name C or name O or name CB )) or r \ esid 465 through 467 or (resid 468 and (name N or name CA or name C or name O or \ name CB )) or resid 469 through 472)) selection = (chain 'D' and (resid 156 through 175 or (resid 176 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 189 or (resid 190 \ through 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 or (resid 193 through 194 and (name N or name CA or name C or name O or name C \ B )) or resid 195 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 245 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 258 or (resid 259 throu \ gh 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thr \ ough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 294 or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 or (resid 3 \ 08 through 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 314 or (resid 315 through 316 and (name N or name CA or name C or n \ ame O or name CB )) or resid 317 through 318 or (resid 319 and (name N or name C \ A or name C or name O or name CB )) or resid 320 through 322 or (resid 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 or (resid 3 \ 82 through 385 and (name N or name CA or name C or name O or name CB )) or resid \ 386 or (resid 387 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 through 422 and (name N or name CA or name C or n \ ame O or name CB )) or resid 423 through 436 or (resid 437 through 439 and (name \ N or name CA or name C or name O or name CB )) or resid 440 through 447 or (res \ id 448 through 450 and (name N or name CA or name C or name O or name CB )) or r \ esid 451 through 457 or (resid 458 through 464 and (name N or name CA or name C \ or name O or name CB )) or resid 465 through 467 or (resid 468 and (name N or na \ me CA or name C or name O or name CB )) or resid 469 through 472)) selection = (chain 'E' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 226 or (resid 227 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB or name CG )) or resid 245 through 248 or (resid 249 and (name N or name C \ A or name C or name O or name CB )) or resid 250 or (resid 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 t \ hrough 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 or (resid 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 294 or (resid 295 and (name N or na \ me CA or name C or name O or name CB )) or resid 296 through 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 through 314 \ or (resid 315 through 316 and (name N or name CA or name C or name O or name CB \ )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 322 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 346 or \ (resid 347 through 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 354 or (resid 355 through 356 and (name N or name CA or nam \ e C or name O or name CB )) or resid 357 through 360 or (resid 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366 or (resid 3 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 368 or (res \ id 369 and (name N or name CA or name C or name O or name CB )) or resid 370 thr \ ough 371 or (resid 372 through 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 and (name N or name CA or name C or name \ O or name CB )) or resid 376 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 383 or (resid 384 through 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 388 or (resid 389 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 436 or (resid 437 through 439 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 449 or (resid 450 and (name \ N or name CA or name C or name O or name CB )) or resid 451 through 452 or (res \ id 453 through 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 457 or (resid 458 through 464 and (name N or name CA or name C \ or name O or name CB )) or resid 465 through 467 or (resid 468 and (name N or na \ me CA or name C or name O or name CB )) or resid 469 through 472)) selection = (chain 'F' and (resid 156 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 192 or (resid 193 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 through 226 or (re \ sid 227 through 228 and (name N or name CA or name C or name O or name CB )) or \ resid 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 314 or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 322 or resid 332 through 345 or (r \ esid 346 through 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 354 or (resid 355 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 417 or (resid 418 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 or (resid 421 through 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 443 or (resid 444 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 or (resid 448 through 450 and (na \ me N or name CA or name C or name O or name CB )) or resid 451 through 452 or (r \ esid 453 through 454 and (name N or name CA or name C or name O or name CB )) or \ resid 455 through 472)) } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 14128 Z= 0.398 Angle : 1.069 23.732 19195 Z= 0.729 Chirality : 0.052 0.274 2229 Planarity : 0.007 0.078 2444 Dihedral : 14.609 89.749 5095 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.23 % Allowed : 7.83 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.80 (0.14), residues: 1826 helix: -3.38 (0.11), residues: 787 sheet: -2.70 (0.33), residues: 189 loop : -3.02 (0.16), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 350 TYR 0.023 0.002 TYR C 284 PHE 0.024 0.002 PHE C 317 TRP 0.013 0.002 TRP B 226 HIS 0.006 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00760 (14128) covalent geometry : angle 1.06948 (19195) hydrogen bonds : bond 0.15606 ( 476) hydrogen bonds : angle 6.09703 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: 0.1878 (mtm) cc_final: 0.1533 (tmm) REVERT: A 190 MET cc_start: 0.3896 (mtm) cc_final: 0.3523 (mtm) REVERT: B 173 TYR cc_start: 0.7667 (p90) cc_final: 0.7447 (p90) REVERT: B 416 TYR cc_start: 0.8155 (m-80) cc_final: 0.7814 (m-80) REVERT: B 459 MET cc_start: 0.7018 (ttp) cc_final: 0.6774 (ttp) REVERT: C 220 GLN cc_start: 0.8630 (mt0) cc_final: 0.8252 (mt0) REVERT: E 440 ASN cc_start: 0.8275 (t0) cc_final: 0.8035 (t0) REVERT: F 176 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6733 (tm-30) outliers start: 3 outliers final: 1 residues processed: 165 average time/residue: 0.1056 time to fit residues: 26.6409 Evaluate side-chains 126 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS C 220 GLN C 320 GLN E 320 GLN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097978 restraints weight = 25576.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093552 restraints weight = 18458.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095650 restraints weight = 13825.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095767 restraints weight = 9791.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095940 restraints weight = 9182.297| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14128 Z= 0.107 Angle : 0.508 7.874 19195 Z= 0.268 Chirality : 0.039 0.136 2229 Planarity : 0.005 0.056 2444 Dihedral : 9.323 89.152 2157 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.43 % Allowed : 10.91 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.17), residues: 1826 helix: -1.49 (0.16), residues: 793 sheet: -2.06 (0.36), residues: 175 loop : -2.42 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 367 TYR 0.008 0.001 TYR B 173 PHE 0.011 0.001 PHE C 317 TRP 0.010 0.001 TRP F 465 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00246 (14128) covalent geometry : angle 0.50806 (19195) hydrogen bonds : bond 0.03490 ( 476) hydrogen bonds : angle 4.10870 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: -0.0389 (mtm) cc_final: -0.1224 (tmm) REVERT: B 249 GLU cc_start: 0.8935 (pp20) cc_final: 0.8644 (pp20) REVERT: B 375 MET cc_start: 0.8068 (mtp) cc_final: 0.7813 (tpp) REVERT: C 346 ASP cc_start: 0.8528 (t0) cc_final: 0.8319 (t0) REVERT: E 440 ASN cc_start: 0.8116 (t0) cc_final: 0.7893 (t0) REVERT: F 176 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 396 PHE cc_start: 0.8142 (m-80) cc_final: 0.7713 (m-80) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 0.0939 time to fit residues: 25.5755 Evaluate side-chains 143 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 340 ASN E 307 HIS E 320 GLN E 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093132 restraints weight = 26129.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088999 restraints weight = 20730.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090194 restraints weight = 16388.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090406 restraints weight = 12369.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090747 restraints weight = 10486.009| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14128 Z= 0.237 Angle : 0.604 9.467 19195 Z= 0.314 Chirality : 0.042 0.169 2229 Planarity : 0.004 0.050 2444 Dihedral : 9.357 84.062 2156 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.11 % Allowed : 14.00 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 1826 helix: -0.69 (0.18), residues: 791 sheet: -1.91 (0.36), residues: 182 loop : -2.22 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.010 0.001 TYR C 173 PHE 0.016 0.001 PHE C 317 TRP 0.010 0.001 TRP B 226 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00574 (14128) covalent geometry : angle 0.60391 (19195) hydrogen bonds : bond 0.04465 ( 476) hydrogen bonds : angle 4.16722 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.498 Fit side-chains REVERT: A 182 MET cc_start: -0.0497 (mtm) cc_final: -0.1335 (tmm) REVERT: B 249 GLU cc_start: 0.9046 (pp20) cc_final: 0.8749 (pp20) REVERT: C 220 GLN cc_start: 0.8356 (mt0) cc_final: 0.8152 (mp10) REVERT: C 427 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6907 (m) REVERT: E 440 ASN cc_start: 0.8190 (t0) cc_final: 0.7968 (t0) REVERT: F 176 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8342 (tm-30) REVERT: F 396 PHE cc_start: 0.8156 (m-80) cc_final: 0.7607 (m-80) REVERT: G 11 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7836 (mt-10) outliers start: 28 outliers final: 17 residues processed: 150 average time/residue: 0.0923 time to fit residues: 22.1007 Evaluate side-chains 144 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN E 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098839 restraints weight = 25833.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094651 restraints weight = 18482.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096376 restraints weight = 14478.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096529 restraints weight = 10413.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096749 restraints weight = 9111.882| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14128 Z= 0.091 Angle : 0.476 9.732 19195 Z= 0.246 Chirality : 0.039 0.137 2229 Planarity : 0.004 0.048 2444 Dihedral : 8.473 86.169 2156 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.43 % Allowed : 15.50 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.19), residues: 1826 helix: -0.12 (0.19), residues: 788 sheet: -1.58 (0.37), residues: 177 loop : -1.93 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 415 TYR 0.009 0.001 TYR F 416 PHE 0.012 0.001 PHE B 353 TRP 0.007 0.001 TRP F 465 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00210 (14128) covalent geometry : angle 0.47595 (19195) hydrogen bonds : bond 0.02863 ( 476) hydrogen bonds : angle 3.62073 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.510 Fit side-chains REVERT: A 182 MET cc_start: -0.0305 (mtm) cc_final: -0.1310 (tmm) REVERT: A 190 MET cc_start: 0.3394 (mtm) cc_final: 0.3117 (mtm) REVERT: C 346 ASP cc_start: 0.8419 (t0) cc_final: 0.8145 (t0) REVERT: C 427 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6983 (m) REVERT: F 176 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8203 (tm-30) REVERT: F 396 PHE cc_start: 0.8131 (m-80) cc_final: 0.7545 (m-80) REVERT: F 448 GLN cc_start: 0.8485 (mt0) cc_final: 0.8020 (mm-40) REVERT: G 3 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6449 (pm20) REVERT: G 11 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7868 (mt-10) outliers start: 19 outliers final: 10 residues processed: 158 average time/residue: 0.0871 time to fit residues: 22.6006 Evaluate side-chains 139 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 76 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 179 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.093877 restraints weight = 26119.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090568 restraints weight = 18318.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092679 restraints weight = 14250.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092421 restraints weight = 10265.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092620 restraints weight = 9364.411| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14128 Z= 0.177 Angle : 0.535 9.822 19195 Z= 0.276 Chirality : 0.041 0.150 2229 Planarity : 0.004 0.046 2444 Dihedral : 8.529 84.566 2156 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.26 % Allowed : 15.43 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.19), residues: 1826 helix: 0.06 (0.19), residues: 786 sheet: -1.41 (0.37), residues: 183 loop : -1.85 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 179 TYR 0.026 0.001 TYR B 173 PHE 0.012 0.001 PHE C 317 TRP 0.007 0.001 TRP B 226 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00430 (14128) covalent geometry : angle 0.53538 (19195) hydrogen bonds : bond 0.03750 ( 476) hydrogen bonds : angle 3.75581 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.479 Fit side-chains REVERT: A 190 MET cc_start: 0.3686 (mtm) cc_final: 0.3459 (mtm) REVERT: B 249 GLU cc_start: 0.8986 (pp20) cc_final: 0.8696 (pp20) REVERT: B 261 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 336 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8508 (mt) REVERT: C 346 ASP cc_start: 0.8453 (t0) cc_final: 0.8154 (t0) REVERT: C 427 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6894 (m) REVERT: F 176 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8313 (tm-30) REVERT: F 396 PHE cc_start: 0.8168 (m-80) cc_final: 0.7535 (m-80) REVERT: F 448 GLN cc_start: 0.8413 (mt0) cc_final: 0.8014 (mm-40) REVERT: G 3 GLU cc_start: 0.7747 (tm-30) cc_final: 0.6565 (pm20) REVERT: G 11 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7833 (mt-10) outliers start: 30 outliers final: 21 residues processed: 155 average time/residue: 0.0878 time to fit residues: 21.8835 Evaluate side-chains 157 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103093 restraints weight = 25723.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101914 restraints weight = 16845.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102460 restraints weight = 15657.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102729 restraints weight = 11111.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103224 restraints weight = 9839.729| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14128 Z= 0.104 Angle : 0.474 9.976 19195 Z= 0.244 Chirality : 0.039 0.142 2229 Planarity : 0.003 0.046 2444 Dihedral : 8.079 86.764 2156 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.03 % Allowed : 16.48 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1826 helix: 0.31 (0.19), residues: 788 sheet: -1.23 (0.37), residues: 184 loop : -1.71 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 367 TYR 0.010 0.001 TYR F 416 PHE 0.009 0.001 PHE B 353 TRP 0.006 0.001 TRP C 266 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00248 (14128) covalent geometry : angle 0.47424 (19195) hydrogen bonds : bond 0.02962 ( 476) hydrogen bonds : angle 3.51220 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.573 Fit side-chains REVERT: A 182 MET cc_start: 0.0241 (mtt) cc_final: 0.0031 (tmm) REVERT: B 249 GLU cc_start: 0.8866 (pp20) cc_final: 0.8597 (pp20) REVERT: B 261 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8213 (t0) REVERT: B 336 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 346 ASP cc_start: 0.8398 (t0) cc_final: 0.8080 (t0) REVERT: C 427 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6918 (m) REVERT: F 176 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8315 (tm-30) REVERT: F 396 PHE cc_start: 0.8163 (m-80) cc_final: 0.7646 (m-80) REVERT: F 448 GLN cc_start: 0.8454 (mt0) cc_final: 0.8142 (mp10) REVERT: G 11 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.0918 time to fit residues: 23.6004 Evaluate side-chains 154 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN D 158 GLN D 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092106 restraints weight = 25961.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088881 restraints weight = 18462.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090674 restraints weight = 14581.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090661 restraints weight = 10592.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090828 restraints weight = 9635.567| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14128 Z= 0.233 Angle : 0.590 9.725 19195 Z= 0.304 Chirality : 0.043 0.147 2229 Planarity : 0.004 0.046 2444 Dihedral : 8.650 84.798 2156 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.41 % Allowed : 16.85 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1826 helix: 0.21 (0.19), residues: 789 sheet: -1.17 (0.38), residues: 184 loop : -1.76 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.026 0.001 TYR B 173 PHE 0.015 0.002 PHE D 334 TRP 0.010 0.001 TRP B 226 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00568 (14128) covalent geometry : angle 0.59042 (19195) hydrogen bonds : bond 0.04266 ( 476) hydrogen bonds : angle 3.95391 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.513 Fit side-chains REVERT: A 392 ARG cc_start: 0.3452 (tpm170) cc_final: 0.2384 (mtm110) REVERT: B 249 GLU cc_start: 0.9008 (pp20) cc_final: 0.8672 (pp20) REVERT: B 336 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8529 (mt) REVERT: C 346 ASP cc_start: 0.8496 (t0) cc_final: 0.8223 (t0) REVERT: C 427 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6874 (m) REVERT: F 176 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8392 (tm-30) REVERT: F 396 PHE cc_start: 0.8226 (m-80) cc_final: 0.7550 (m-80) REVERT: F 448 GLN cc_start: 0.8353 (mt0) cc_final: 0.8094 (mp10) REVERT: G 11 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7872 (mt-10) outliers start: 32 outliers final: 25 residues processed: 159 average time/residue: 0.0914 time to fit residues: 23.2253 Evaluate side-chains 158 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN D 158 GLN D 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101590 restraints weight = 25925.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101246 restraints weight = 16915.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101628 restraints weight = 14148.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101792 restraints weight = 10550.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102073 restraints weight = 9280.419| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14128 Z= 0.118 Angle : 0.502 9.992 19195 Z= 0.256 Chirality : 0.040 0.145 2229 Planarity : 0.004 0.045 2444 Dihedral : 8.203 87.661 2156 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.26 % Allowed : 17.61 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1826 helix: 0.44 (0.19), residues: 792 sheet: -1.13 (0.38), residues: 182 loop : -1.59 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 367 TYR 0.012 0.001 TYR F 416 PHE 0.008 0.001 PHE C 317 TRP 0.009 0.001 TRP C 266 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00283 (14128) covalent geometry : angle 0.50218 (19195) hydrogen bonds : bond 0.03165 ( 476) hydrogen bonds : angle 3.60706 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.391 Fit side-chains REVERT: A 392 ARG cc_start: 0.3952 (tpm170) cc_final: 0.2537 (mtm110) REVERT: B 249 GLU cc_start: 0.8908 (pp20) cc_final: 0.8623 (pp20) REVERT: B 261 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8540 (t0) REVERT: B 317 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8821 (t80) REVERT: B 336 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 346 ASP cc_start: 0.8480 (t0) cc_final: 0.8194 (t0) REVERT: D 448 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (tp40) REVERT: F 176 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8414 (tm-30) REVERT: F 396 PHE cc_start: 0.8184 (m-80) cc_final: 0.7591 (m-80) REVERT: F 448 GLN cc_start: 0.8562 (mt0) cc_final: 0.8241 (mp10) REVERT: G 3 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6499 (pm20) REVERT: G 9 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8139 (mt-10) REVERT: G 11 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7884 (mt-10) outliers start: 30 outliers final: 22 residues processed: 160 average time/residue: 0.0845 time to fit residues: 22.1641 Evaluate side-chains 159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 181 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 126 optimal weight: 0.0060 chunk 103 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.154233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115095 restraints weight = 25889.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112753 restraints weight = 17052.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113821 restraints weight = 16788.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113869 restraints weight = 11232.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114374 restraints weight = 10149.760| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14128 Z= 0.091 Angle : 0.474 10.096 19195 Z= 0.242 Chirality : 0.039 0.141 2229 Planarity : 0.003 0.047 2444 Dihedral : 7.857 88.434 2156 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.11 % Allowed : 17.83 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.20), residues: 1826 helix: 0.62 (0.20), residues: 796 sheet: -0.96 (0.38), residues: 190 loop : -1.46 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 352 TYR 0.013 0.001 TYR F 416 PHE 0.008 0.001 PHE D 334 TRP 0.011 0.001 TRP C 266 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00213 (14128) covalent geometry : angle 0.47441 (19195) hydrogen bonds : bond 0.02730 ( 476) hydrogen bonds : angle 3.41464 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 392 ARG cc_start: 0.3911 (tpm170) cc_final: 0.2667 (mtm110) REVERT: B 249 GLU cc_start: 0.8837 (pp20) cc_final: 0.8567 (pp20) REVERT: B 261 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8521 (t0) REVERT: B 336 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8628 (mt) REVERT: C 346 ASP cc_start: 0.8373 (t0) cc_final: 0.8067 (t0) REVERT: C 427 THR cc_start: 0.7092 (OUTLIER) cc_final: 0.6848 (m) REVERT: D 375 MET cc_start: 0.9066 (mtp) cc_final: 0.8851 (ttm) REVERT: D 430 MET cc_start: 0.8988 (tpp) cc_final: 0.8699 (mmm) REVERT: F 176 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8358 (tm-30) REVERT: F 396 PHE cc_start: 0.8103 (m-80) cc_final: 0.7593 (m-80) REVERT: F 448 GLN cc_start: 0.8549 (mt0) cc_final: 0.8261 (mp10) REVERT: G 3 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6604 (pm20) outliers start: 28 outliers final: 18 residues processed: 165 average time/residue: 0.0860 time to fit residues: 23.1880 Evaluate side-chains 154 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 ASN C 320 GLN D 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116095 restraints weight = 25773.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114266 restraints weight = 16610.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115335 restraints weight = 15641.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115388 restraints weight = 10854.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115801 restraints weight = 9801.370| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14128 Z= 0.088 Angle : 0.475 10.137 19195 Z= 0.240 Chirality : 0.039 0.138 2229 Planarity : 0.003 0.046 2444 Dihedral : 7.643 89.027 2156 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.96 % Allowed : 18.21 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1826 helix: 0.77 (0.20), residues: 797 sheet: -0.76 (0.38), residues: 190 loop : -1.36 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 352 TYR 0.013 0.001 TYR F 416 PHE 0.008 0.001 PHE D 334 TRP 0.011 0.001 TRP C 266 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00205 (14128) covalent geometry : angle 0.47504 (19195) hydrogen bonds : bond 0.02579 ( 476) hydrogen bonds : angle 3.32963 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 392 ARG cc_start: 0.3958 (tpm170) cc_final: 0.2726 (mtm110) REVERT: B 249 GLU cc_start: 0.8821 (pp20) cc_final: 0.8555 (pp20) REVERT: B 261 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8535 (t0) REVERT: C 346 ASP cc_start: 0.8390 (t0) cc_final: 0.8036 (t0) REVERT: C 427 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6805 (m) REVERT: D 375 MET cc_start: 0.9040 (mtp) cc_final: 0.8813 (ttm) REVERT: D 430 MET cc_start: 0.8955 (tpp) cc_final: 0.8667 (mmm) REVERT: D 448 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: F 176 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 396 PHE cc_start: 0.8097 (m-80) cc_final: 0.7692 (m-80) REVERT: F 448 GLN cc_start: 0.8545 (mt0) cc_final: 0.8077 (mm-40) REVERT: G 3 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6579 (pm20) REVERT: G 11 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7878 (mt-10) outliers start: 26 outliers final: 15 residues processed: 159 average time/residue: 0.0844 time to fit residues: 21.9285 Evaluate side-chains 153 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 466 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 108 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115823 restraints weight = 25852.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113923 restraints weight = 16943.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114753 restraints weight = 16242.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115117 restraints weight = 11279.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115357 restraints weight = 10099.132| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14128 Z= 0.096 Angle : 0.477 10.102 19195 Z= 0.241 Chirality : 0.039 0.138 2229 Planarity : 0.003 0.047 2444 Dihedral : 7.587 89.308 2156 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.58 % Allowed : 18.74 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1826 helix: 0.89 (0.20), residues: 797 sheet: -0.63 (0.39), residues: 190 loop : -1.33 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 352 TYR 0.013 0.001 TYR F 416 PHE 0.008 0.001 PHE D 334 TRP 0.012 0.001 TRP C 266 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00230 (14128) covalent geometry : angle 0.47650 (19195) hydrogen bonds : bond 0.02652 ( 476) hydrogen bonds : angle 3.30720 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.85 seconds wall clock time: 34 minutes 42.45 seconds (2082.45 seconds total)