Starting phenix.real_space_refine on Thu Aug 6 02:43:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0b_66431/08_2026/9x0b_66431.map" } resolution = 3.62 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8316 2.51 5 N 2125 2.21 5 O 2223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12726 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3462 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2903 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'TRP:plan': 1, 'HIS:plan': 3, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3458 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 15, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2903 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'TRP:plan': 1, 'HIS:plan': 3, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Time building chain proxies: 2.60, per 1000 atoms: 0.20 Number of scatterers: 12726 At special positions: 0 Unit cell: (121.706, 100.75, 124.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2223 8.00 N 2125 7.00 C 8316 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: 0.77 Conformation dependent library (CDL) restraints added in 489.2 milliseconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 68.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 129 removed outlier: 3.547A pdb=" N ILE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.583A pdb=" N ASP A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 209 through 239 removed outlier: 3.864A pdb=" N LYS A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER A 235 " --> pdb=" O CYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.832A pdb=" N ALA A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 Processing helix chain 'A' and resid 289 through 320 removed outlier: 3.546A pdb=" N PHE A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.033A pdb=" N ARG A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 371 Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.694A pdb=" N TYR A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.561A pdb=" N GLU A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.883A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 504 through 516 Processing helix chain 'B' and resid 75 through 102 Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 182 through 191 removed outlier: 4.099A pdb=" N MET B 186 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 187 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.538A pdb=" N THR B 216 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 239 removed outlier: 4.389A pdb=" N PHE B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 6.285A pdb=" N PHE B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N MET B 248 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.505A pdb=" N TRP B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 340 removed outlier: 3.587A pdb=" N PHE B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.510A pdb=" N LEU B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.597A pdb=" N ILE B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 392 Processing helix chain 'B' and resid 401 through 411 Processing helix chain 'B' and resid 464 through 471 removed outlier: 4.122A pdb=" N VAL B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 501 through 514 removed outlier: 3.829A pdb=" N ILE B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 533 Processing helix chain 'C' and resid 75 through 92 removed outlier: 3.689A pdb=" N VAL C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 108 through 129 removed outlier: 3.595A pdb=" N ILE C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.583A pdb=" N ASP C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 209 through 239 removed outlier: 3.753A pdb=" N HIS C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C 235 " --> pdb=" O CYS C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.832A pdb=" N ALA C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 276 removed outlier: 3.520A pdb=" N THR C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 320 removed outlier: 3.546A pdb=" N PHE C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.922A pdb=" N ARG C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 371 Processing helix chain 'C' and resid 375 through 387 removed outlier: 3.696A pdb=" N TYR C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.575A pdb=" N GLU C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.884A pdb=" N VAL C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 504 through 516 Processing helix chain 'D' and resid 75 through 102 Proline residue: D 97 - end of helix Processing helix chain 'D' and resid 182 through 191 removed outlier: 4.099A pdb=" N MET D 186 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 187 " --> pdb=" O PHE D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.185A pdb=" N THR D 216 " --> pdb=" O TRP D 212 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 removed outlier: 4.389A pdb=" N PHE D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 6.285A pdb=" N PHE D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET D 248 " --> pdb=" O MET D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 Processing helix chain 'D' and resid 287 through 320 removed outlier: 3.583A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 removed outlier: 3.515A pdb=" N ARG D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.649A pdb=" N ARG D 357 " --> pdb=" O HIS D 353 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.597A pdb=" N ILE D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 383 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 401 through 411 Processing helix chain 'D' and resid 464 through 471 removed outlier: 4.186A pdb=" N VAL D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 501 through 514 removed outlier: 3.829A pdb=" N ILE D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 417 removed outlier: 6.581A pdb=" N GLN A 485 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 433 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 424 removed outlier: 7.039A pdb=" N VAL A 478 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA A 445 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL A 453 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 413 through 414 Processing sheet with id=AA5, first strand: chain 'B' and resid 422 through 424 removed outlier: 6.860A pdb=" N VAL B 478 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 445 removed outlier: 6.184A pdb=" N VAL B 441 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU B 456 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 443 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 452 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain 'C' and resid 413 through 417 removed outlier: 6.580A pdb=" N GLN C 485 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 433 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 422 through 424 removed outlier: 7.039A pdb=" N VAL C 478 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 445 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL C 453 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 413 through 414 Processing sheet with id=AB2, first strand: chain 'D' and resid 422 through 424 removed outlier: 6.859A pdb=" N VAL D 478 " --> pdb=" O VAL D 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 441 through 445 removed outlier: 6.184A pdb=" N VAL D 441 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU D 456 " --> pdb=" O VAL D 441 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 443 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 452 " --> pdb=" O ALA D 445 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2283 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: 1.63 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3995 1.35 - 1.46: 1820 1.46 - 1.58: 7135 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 13050 Sorted by residual: bond pdb=" N VAL D 447 " pdb=" CA VAL D 447 " ideal model delta sigma weight residual 1.458 1.495 -0.037 9.00e-03 1.23e+04 1.71e+01 bond pdb=" N VAL B 447 " pdb=" CA VAL B 447 " ideal model delta sigma weight residual 1.458 1.495 -0.037 9.00e-03 1.23e+04 1.69e+01 bond pdb=" N VAL D 423 " pdb=" CA VAL D 423 " ideal model delta sigma weight residual 1.458 1.492 -0.035 9.00e-03 1.23e+04 1.48e+01 bond pdb=" N VAL B 423 " pdb=" CA VAL B 423 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.44e+01 bond pdb=" N ILE C 371 " pdb=" CA ILE C 371 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.19e+01 ... (remaining 13045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11392 1.34 - 2.68: 5122 2.68 - 4.03: 1075 4.03 - 5.37: 194 5.37 - 6.71: 16 Bond angle restraints: 17799 Sorted by residual: angle pdb=" N LEU A 189 " pdb=" CA LEU A 189 " pdb=" C LEU A 189 " ideal model delta sigma weight residual 113.50 107.37 6.13 1.23e+00 6.61e-01 2.48e+01 angle pdb=" N ASN A 341 " pdb=" CA ASN A 341 " pdb=" C ASN A 341 " ideal model delta sigma weight residual 114.62 109.29 5.33 1.14e+00 7.69e-01 2.19e+01 angle pdb=" N ILE D 299 " pdb=" CA ILE D 299 " pdb=" C ILE D 299 " ideal model delta sigma weight residual 113.22 107.51 5.71 1.23e+00 6.61e-01 2.15e+01 angle pdb=" CA PHE D 102 " pdb=" CB PHE D 102 " pdb=" CG PHE D 102 " ideal model delta sigma weight residual 113.80 118.32 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N ALA C 306 " pdb=" CA ALA C 306 " pdb=" C ALA C 306 " ideal model delta sigma weight residual 113.43 107.77 5.66 1.26e+00 6.30e-01 2.02e+01 ... (remaining 17794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 6738 15.60 - 31.21: 524 31.21 - 46.81: 160 46.81 - 62.42: 130 62.42 - 78.02: 13 Dihedral angle restraints: 7565 sinusoidal: 2775 harmonic: 4790 Sorted by residual: dihedral pdb=" CA TRP B 81 " pdb=" CB TRP B 81 " pdb=" CG TRP B 81 " pdb=" CD1 TRP B 81 " ideal model delta sinusoidal sigma weight residual -90.00 -158.13 68.13 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN A 311 " pdb=" CB ASN A 311 " pdb=" CG ASN A 311 " pdb=" OD1 ASN A 311 " ideal model delta sinusoidal sigma weight residual 120.00 -171.89 -68.11 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN C 311 " pdb=" CB ASN C 311 " pdb=" CG ASN C 311 " pdb=" OD1 ASN C 311 " ideal model delta sinusoidal sigma weight residual 120.00 -173.19 -66.81 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 7562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 706 0.049 - 0.097: 675 0.097 - 0.146: 460 0.146 - 0.195: 165 0.195 - 0.243: 50 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA ILE D 424 " pdb=" N ILE D 424 " pdb=" C ILE D 424 " pdb=" CB ILE D 424 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE B 424 " pdb=" N ILE B 424 " pdb=" C ILE B 424 " pdb=" CB ILE B 424 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL B 462 " pdb=" N VAL B 462 " pdb=" C VAL B 462 " pdb=" CB VAL B 462 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2053 not shown) Planarity restraints: 2231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 339 " 0.274 9.50e-02 1.11e+02 1.23e-01 9.28e+00 pdb=" NE ARG D 339 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 339 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 339 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 339 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 263 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.78e+00 pdb=" NE ARG B 263 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 263 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 263 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 263 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 201 " 0.249 9.50e-02 1.11e+02 1.12e-01 7.66e+00 pdb=" NE ARG A 201 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 201 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 201 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 201 " 0.009 2.00e-02 2.50e+03 ... (remaining 2228 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5187 2.88 - 3.38: 13726 3.38 - 3.89: 22934 3.89 - 4.39: 25839 4.39 - 4.90: 40071 Nonbonded interactions: 107757 Sorted by model distance: nonbonded pdb=" O VAL C 226 " pdb=" OG SER C 271 " model vdw 2.373 3.040 nonbonded pdb=" O VAL A 226 " pdb=" OG SER A 271 " model vdw 2.373 3.040 nonbonded pdb=" OH TYR A 280 " pdb=" OG1 THR D 274 " model vdw 2.382 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" OH TYR C 280 " model vdw 2.395 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" OH TYR D 280 " model vdw 2.409 3.040 ... (remaining 107752 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 70 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 516)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 8.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.300 Find NCS groups from input model: 0.180 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.013 0.040 13050 Z= 0.993 Angle : 1.496 6.710 17799 Z= 1.187 Chirality : 0.092 0.243 2056 Planarity : 0.012 0.123 2231 Dihedral : 15.632 78.019 4469 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 10.85 % Allowed : 10.85 % Favored : 78.30 % 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: -3.37 (0.17), residues: 1606 helix: -1.84 (0.13), residues: 1038 sheet: -2.24 (0.66), residues: 58 loop : -2.75 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 491 TYR 0.014 0.002 TYR C 181 PHE 0.010 0.001 PHE B 247 TRP 0.010 0.002 TRP D 255 HIS 0.008 0.001 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.01314 / 0.99 (13050) covalent geometry : angle 1.49621 / 1.19 (17799) hydrogen bonds : bond 0.20766 / 13.94 ( 794) hydrogen bonds : angle 8.36484 / 6.09 ( 2283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 447 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7398 (mmt-90) cc_final: 0.6950 (ttt90) REVERT: A 190 TRP cc_start: 0.6346 (OUTLIER) cc_final: 0.6034 (t-100) REVERT: A 441 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7217 (m) REVERT: A 471 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 291 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8020 (mtt-85) REVERT: B 299 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 416 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: B 451 ASP cc_start: 0.7206 (m-30) cc_final: 0.6711 (p0) REVERT: C 77 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6878 (ttt90) REVERT: C 190 TRP cc_start: 0.6452 (OUTLIER) cc_final: 0.6212 (t-100) REVERT: C 441 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7261 (m) REVERT: C 471 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.5881 (t80) REVERT: D 299 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7879 (mt) REVERT: D 416 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: D 451 ASP cc_start: 0.7138 (m-30) cc_final: 0.6459 (p0) outliers start: 142 outliers final: 26 residues processed: 518 average time/residue: 0.0962 time to fit residues: 71.3116 Evaluate side-chains 281 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 102 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 239 HIS A 340 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS B 286 ASN B 341 ASN B 349 GLN B 407 GLN B 485 GLN B 515 HIS C 239 HIS C 452 GLN C 474 GLN C 515 HIS D 286 ASN D 341 ASN D 349 GLN D 485 GLN D 515 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.197329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172915 restraints weight = 15059.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175143 restraints weight = 11375.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176781 restraints weight = 8968.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177250 restraints weight = 6839.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177259 restraints weight = 6161.274| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13050 Z= 0.161 Angle : 0.653 10.883 17799 Z= 0.342 Chirality : 0.040 0.260 2056 Planarity : 0.004 0.034 2231 Dihedral : 7.579 59.704 1845 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 7.03 % Allowed : 14.82 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1606 helix: 0.20 (0.15), residues: 1066 sheet: -2.14 (0.55), residues: 78 loop : -2.20 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 206 TYR 0.027 0.002 TYR A 395 PHE 0.027 0.002 PHE D 463 TRP 0.008 0.001 TRP A 156 HIS 0.009 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (13050) covalent geometry : angle 0.65299 / 0.34 (17799) hydrogen bonds : bond 0.05634 / 3.70 ( 794) hydrogen bonds : angle 5.31325 / 3.89 ( 2283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 242 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6416 (ttp80) REVERT: A 219 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7589 (tp) REVERT: A 395 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7328 (p90) REVERT: A 471 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.5362 (t80) REVERT: A 515 HIS cc_start: 0.6664 (m170) cc_final: 0.6358 (t-90) REVERT: B 416 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6960 (m-10) REVERT: B 471 TYR cc_start: 0.6840 (t80) cc_final: 0.6580 (t80) REVERT: B 509 MET cc_start: 0.7348 (tpt) cc_final: 0.6423 (mmt) REVERT: C 77 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6221 (tmt170) REVERT: C 190 TRP cc_start: 0.6525 (OUTLIER) cc_final: 0.6133 (m-10) REVERT: C 219 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7623 (tp) REVERT: C 342 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6738 (pp) REVERT: C 395 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7312 (p90) REVERT: C 471 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.5335 (t80) REVERT: D 291 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (mtt90) REVERT: D 416 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: D 509 MET cc_start: 0.7280 (tpt) cc_final: 0.6555 (mmt) outliers start: 92 outliers final: 43 residues processed: 302 average time/residue: 0.0974 time to fit residues: 42.8504 Evaluate side-chains 253 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN B 301 ASN B 347 GLN B 384 HIS D 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.175818 restraints weight = 15147.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178041 restraints weight = 10605.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179312 restraints weight = 8450.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180652 restraints weight = 7301.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181057 restraints weight = 6599.565| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13050 Z= 0.146 Angle : 0.604 9.660 17799 Z= 0.309 Chirality : 0.039 0.212 2056 Planarity : 0.004 0.045 2231 Dihedral : 6.529 59.990 1812 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.81 % Allowed : 16.65 % Favored : 77.54 % 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: -0.14 (0.21), residues: 1606 helix: 0.83 (0.16), residues: 1040 sheet: -1.63 (0.55), residues: 78 loop : -1.78 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 472 TYR 0.024 0.002 TYR A 395 PHE 0.022 0.002 PHE C 463 TRP 0.011 0.001 TRP A 212 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (13050) covalent geometry : angle 0.60378 / 0.31 (17799) hydrogen bonds : bond 0.04679 / 3.06 ( 794) hydrogen bonds : angle 4.75798 / 3.47 ( 2283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.5931 (tmt170) REVERT: A 219 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 369 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6111 (tp30) REVERT: A 395 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7257 (p90) REVERT: A 432 ASP cc_start: 0.8182 (p0) cc_final: 0.7509 (p0) REVERT: B 81 TRP cc_start: 0.5895 (OUTLIER) cc_final: 0.5681 (t60) REVERT: B 416 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: B 509 MET cc_start: 0.7070 (tpt) cc_final: 0.6300 (mmt) REVERT: C 77 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6068 (tmt170) REVERT: C 219 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7815 (tp) REVERT: C 234 TYR cc_start: 0.8509 (t80) cc_final: 0.8300 (t80) REVERT: C 395 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7266 (p90) REVERT: D 291 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7826 (mtt-85) REVERT: D 331 GLN cc_start: 0.8307 (tp40) cc_final: 0.7914 (tm-30) REVERT: D 407 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7828 (mm110) REVERT: D 416 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: D 471 TYR cc_start: 0.6579 (t80) cc_final: 0.6201 (t80) REVERT: D 509 MET cc_start: 0.7185 (tpt) cc_final: 0.6401 (mmt) REVERT: D 512 LEU cc_start: 0.7440 (tt) cc_final: 0.7218 (tt) REVERT: D 530 GLU cc_start: 0.8328 (tp30) cc_final: 0.8046 (mm-30) outliers start: 76 outliers final: 35 residues processed: 295 average time/residue: 0.0817 time to fit residues: 36.9095 Evaluate side-chains 261 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 81 TRP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN B 301 ASN B 347 GLN C 349 GLN D 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.199684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176059 restraints weight = 15114.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.178324 restraints weight = 10568.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179716 restraints weight = 8365.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180194 restraints weight = 7157.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180199 restraints weight = 6683.790| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13050 Z= 0.162 Angle : 0.612 8.410 17799 Z= 0.309 Chirality : 0.039 0.223 2056 Planarity : 0.004 0.043 2231 Dihedral : 6.318 57.354 1808 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.73 % Allowed : 18.03 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1606 helix: 0.93 (0.16), residues: 1044 sheet: -1.45 (0.53), residues: 78 loop : -1.71 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 488 TYR 0.039 0.002 TYR B 234 PHE 0.020 0.002 PHE A 336 TRP 0.028 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13050) covalent geometry : angle 0.61173 / 0.31 (17799) hydrogen bonds : bond 0.04521 / 2.97 ( 794) hydrogen bonds : angle 4.54872 / 3.31 ( 2283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6188 (tpt170) REVERT: A 219 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 369 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6158 (tp30) REVERT: A 395 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7299 (p90) REVERT: A 432 ASP cc_start: 0.8118 (p0) cc_final: 0.7886 (p0) REVERT: B 291 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: B 416 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: B 509 MET cc_start: 0.7038 (tpt) cc_final: 0.6258 (mmt) REVERT: C 77 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6024 (tmt170) REVERT: C 219 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7878 (tp) REVERT: C 369 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5829 (tp30) REVERT: D 291 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7876 (mtt-85) REVERT: D 331 GLN cc_start: 0.8311 (tp40) cc_final: 0.7960 (tm-30) REVERT: D 416 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: D 471 TYR cc_start: 0.6436 (t80) cc_final: 0.6137 (t80) REVERT: D 509 MET cc_start: 0.7025 (tpt) cc_final: 0.6265 (mmt) REVERT: D 512 LEU cc_start: 0.7443 (tt) cc_final: 0.7187 (tt) REVERT: D 530 GLU cc_start: 0.8297 (tp30) cc_final: 0.8067 (mm-30) outliers start: 75 outliers final: 43 residues processed: 277 average time/residue: 0.0733 time to fit residues: 31.7236 Evaluate side-chains 262 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.198747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175278 restraints weight = 15154.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177330 restraints weight = 10601.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178283 restraints weight = 8416.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179640 restraints weight = 7412.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.180035 restraints weight = 6696.160| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13050 Z= 0.157 Angle : 0.608 11.787 17799 Z= 0.304 Chirality : 0.039 0.189 2056 Planarity : 0.004 0.044 2231 Dihedral : 6.257 56.199 1808 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.19 % Allowed : 20.09 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1606 helix: 0.83 (0.15), residues: 1078 sheet: -1.09 (0.55), residues: 78 loop : -1.90 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 426 TYR 0.032 0.002 TYR B 234 PHE 0.018 0.002 PHE D 463 TRP 0.014 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (13050) covalent geometry : angle 0.60809 / 0.30 (17799) hydrogen bonds : bond 0.04347 / 2.85 ( 794) hydrogen bonds : angle 4.40797 / 3.21 ( 2283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.5807 (tmt170) REVERT: A 219 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 369 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5917 (tp30) REVERT: A 395 TYR cc_start: 0.7808 (p90) cc_final: 0.7255 (p90) REVERT: A 432 ASP cc_start: 0.8055 (p0) cc_final: 0.7843 (p0) REVERT: B 291 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7914 (mtt-85) REVERT: B 416 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: B 509 MET cc_start: 0.7037 (tpt) cc_final: 0.6171 (mmt) REVERT: C 77 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5929 (tmt170) REVERT: D 291 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: D 331 GLN cc_start: 0.8320 (tp40) cc_final: 0.7785 (tm-30) REVERT: D 416 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7048 (m-10) REVERT: D 509 MET cc_start: 0.7080 (tpt) cc_final: 0.6272 (mmt) REVERT: D 530 GLU cc_start: 0.8229 (tp30) cc_final: 0.7963 (mm-30) outliers start: 68 outliers final: 45 residues processed: 277 average time/residue: 0.0760 time to fit residues: 33.0769 Evaluate side-chains 262 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS D 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.198491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.174538 restraints weight = 15063.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.176732 restraints weight = 10617.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177687 restraints weight = 8464.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.179056 restraints weight = 7489.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179320 restraints weight = 6780.642| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13050 Z= 0.154 Angle : 0.607 13.802 17799 Z= 0.301 Chirality : 0.039 0.150 2056 Planarity : 0.004 0.048 2231 Dihedral : 6.202 56.190 1808 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.88 % Allowed : 21.47 % Favored : 72.65 % 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: 0.08 (0.21), residues: 1606 helix: 0.98 (0.16), residues: 1074 sheet: -0.88 (0.55), residues: 78 loop : -1.98 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.030 0.002 TYR B 234 PHE 0.030 0.002 PHE A 336 TRP 0.014 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (13050) covalent geometry : angle 0.60683 / 0.30 (17799) hydrogen bonds : bond 0.04230 / 2.77 ( 794) hydrogen bonds : angle 4.30218 / 3.13 ( 2283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.5857 (tmt170) REVERT: A 369 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5820 (tp30) REVERT: A 432 ASP cc_start: 0.8030 (p0) cc_final: 0.7807 (p0) REVERT: B 291 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7912 (mtt-85) REVERT: B 416 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: B 509 MET cc_start: 0.7122 (tpt) cc_final: 0.6229 (mmt) REVERT: C 77 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5851 (tmt170) REVERT: C 219 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7966 (tt) REVERT: D 291 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: D 331 GLN cc_start: 0.8359 (tp40) cc_final: 0.7946 (tm-30) REVERT: D 416 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7056 (m-10) REVERT: D 509 MET cc_start: 0.7178 (tpt) cc_final: 0.6303 (mmt) outliers start: 77 outliers final: 53 residues processed: 275 average time/residue: 0.0709 time to fit residues: 30.5199 Evaluate side-chains 257 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.200217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179416 restraints weight = 15075.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178787 restraints weight = 12635.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181423 restraints weight = 11919.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181344 restraints weight = 8329.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181891 restraints weight = 7301.385| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13050 Z= 0.141 Angle : 0.602 14.358 17799 Z= 0.297 Chirality : 0.039 0.154 2056 Planarity : 0.004 0.052 2231 Dihedral : 6.111 56.352 1808 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.42 % Allowed : 22.54 % Favored : 72.04 % 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: 0.29 (0.21), residues: 1606 helix: 1.10 (0.16), residues: 1076 sheet: -0.55 (0.59), residues: 66 loop : -1.84 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.040 0.001 TYR B 234 PHE 0.020 0.001 PHE C 247 TRP 0.015 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13050) covalent geometry : angle 0.60160 / 0.30 (17799) hydrogen bonds : bond 0.04039 / 2.63 ( 794) hydrogen bonds : angle 4.18560 / 3.04 ( 2283) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5715 (tmt170) REVERT: A 219 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 369 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5773 (tp30) REVERT: B 291 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7912 (mtt-85) REVERT: B 416 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: B 509 MET cc_start: 0.7202 (tpt) cc_final: 0.6170 (mmt) REVERT: C 77 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.5793 (tmt170) REVERT: C 191 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.5951 (mtm-85) REVERT: C 219 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7655 (tt) REVERT: C 248 MET cc_start: 0.8386 (mmm) cc_final: 0.8032 (mmm) REVERT: D 291 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7946 (mtt-85) REVERT: D 305 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8248 (mt) REVERT: D 331 GLN cc_start: 0.8426 (tp40) cc_final: 0.8014 (tm-30) REVERT: D 416 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: D 509 MET cc_start: 0.7208 (tpt) cc_final: 0.6299 (mmt) outliers start: 71 outliers final: 47 residues processed: 275 average time/residue: 0.0794 time to fit residues: 33.7823 Evaluate side-chains 259 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.198356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176629 restraints weight = 14986.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176479 restraints weight = 12559.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177886 restraints weight = 11139.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178011 restraints weight = 9292.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178742 restraints weight = 8190.391| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13050 Z= 0.157 Angle : 0.631 14.783 17799 Z= 0.309 Chirality : 0.039 0.164 2056 Planarity : 0.004 0.054 2231 Dihedral : 5.988 56.878 1806 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.12 % Allowed : 22.99 % Favored : 71.89 % 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: 0.53 (0.21), residues: 1606 helix: 1.26 (0.16), residues: 1060 sheet: -0.58 (0.54), residues: 78 loop : -1.56 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.045 0.001 TYR D 234 PHE 0.023 0.002 PHE C 247 TRP 0.015 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (13050) covalent geometry : angle 0.63118 / 0.31 (17799) hydrogen bonds : bond 0.04107 / 2.68 ( 794) hydrogen bonds : angle 4.18580 / 3.04 ( 2283) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.5657 (tmt170) REVERT: A 219 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7655 (tt) REVERT: A 369 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 291 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7981 (mmt180) REVERT: B 416 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7202 (m-10) REVERT: B 509 MET cc_start: 0.7306 (tpt) cc_final: 0.6451 (mmt) REVERT: C 77 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.5683 (tmt170) REVERT: C 219 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7676 (tt) REVERT: C 248 MET cc_start: 0.8362 (mmm) cc_final: 0.8052 (mmm) REVERT: D 291 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7894 (mtt-85) REVERT: D 305 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8243 (mt) REVERT: D 331 GLN cc_start: 0.8437 (tp40) cc_final: 0.8101 (tm-30) REVERT: D 416 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: D 509 MET cc_start: 0.7266 (tpt) cc_final: 0.6255 (mmt) outliers start: 67 outliers final: 55 residues processed: 256 average time/residue: 0.0872 time to fit residues: 34.3088 Evaluate side-chains 260 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 521 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.199253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178178 restraints weight = 15106.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178384 restraints weight = 12222.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180408 restraints weight = 12047.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180717 restraints weight = 8260.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181175 restraints weight = 7242.282| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13050 Z= 0.136 Angle : 0.614 14.981 17799 Z= 0.298 Chirality : 0.038 0.176 2056 Planarity : 0.004 0.052 2231 Dihedral : 5.882 57.292 1806 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.04 % Allowed : 23.07 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1606 helix: 1.39 (0.16), residues: 1062 sheet: -0.33 (0.60), residues: 66 loop : -1.45 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.038 0.001 TYR D 234 PHE 0.022 0.001 PHE C 247 TRP 0.019 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13050) covalent geometry : angle 0.61374 / 0.30 (17799) hydrogen bonds : bond 0.03903 / 2.55 ( 794) hydrogen bonds : angle 4.07447 / 2.96 ( 2283) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5638 (tmt170) REVERT: A 219 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 369 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: B 291 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7924 (mmt180) REVERT: B 416 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: B 509 MET cc_start: 0.7317 (tpt) cc_final: 0.6260 (mmt) REVERT: C 77 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.5581 (tmt170) REVERT: C 219 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7651 (tt) REVERT: C 248 MET cc_start: 0.8348 (mmm) cc_final: 0.8042 (mmm) REVERT: D 291 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7835 (mtt-85) REVERT: D 305 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8263 (mt) REVERT: D 331 GLN cc_start: 0.8409 (tp40) cc_final: 0.8154 (tm-30) REVERT: D 416 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6983 (m-10) REVERT: D 509 MET cc_start: 0.7243 (tpt) cc_final: 0.6205 (mmt) outliers start: 66 outliers final: 49 residues processed: 252 average time/residue: 0.0804 time to fit residues: 31.3096 Evaluate side-chains 250 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 62 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS B 340 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178778 restraints weight = 15102.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178728 restraints weight = 12639.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.179692 restraints weight = 12934.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180544 restraints weight = 10194.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180943 restraints weight = 8923.708| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13050 Z= 0.132 Angle : 0.617 15.281 17799 Z= 0.299 Chirality : 0.038 0.181 2056 Planarity : 0.004 0.052 2231 Dihedral : 5.759 57.518 1802 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.66 % Allowed : 24.14 % Favored : 71.20 % 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: 0.87 (0.21), residues: 1606 helix: 1.48 (0.16), residues: 1064 sheet: -0.13 (0.61), residues: 66 loop : -1.39 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 488 TYR 0.034 0.001 TYR D 234 PHE 0.022 0.001 PHE C 247 TRP 0.020 0.001 TRP D 212 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13050) covalent geometry : angle 0.61687 / 0.30 (17799) hydrogen bonds : bond 0.03828 / 2.50 ( 794) hydrogen bonds : angle 4.03308 / 2.93 ( 2283) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.5590 (tmt170) REVERT: A 219 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 369 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: B 291 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7859 (mmt180) REVERT: B 416 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: B 509 MET cc_start: 0.7265 (tpt) cc_final: 0.6218 (mmt) REVERT: C 77 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5513 (tmt170) REVERT: C 219 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (tt) REVERT: C 248 MET cc_start: 0.8289 (mmm) cc_final: 0.7999 (mmm) REVERT: D 291 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7770 (mtt-85) REVERT: D 331 GLN cc_start: 0.8373 (tp40) cc_final: 0.8100 (tm-30) REVERT: D 416 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: D 509 MET cc_start: 0.7233 (tpt) cc_final: 0.6217 (mmt) outliers start: 61 outliers final: 47 residues processed: 244 average time/residue: 0.0824 time to fit residues: 30.7581 Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.200288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.174597 restraints weight = 15000.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.177314 restraints weight = 9863.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178763 restraints weight = 7542.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180235 restraints weight = 6434.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180651 restraints weight = 5767.893| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13050 Z= 0.130 Angle : 0.616 15.285 17799 Z= 0.297 Chirality : 0.038 0.182 2056 Planarity : 0.004 0.051 2231 Dihedral : 5.730 58.002 1802 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.58 % Allowed : 24.60 % Favored : 70.82 % 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: 0.97 (0.21), residues: 1606 helix: 1.56 (0.16), residues: 1064 sheet: 0.01 (0.61), residues: 66 loop : -1.37 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 214 TYR 0.032 0.001 TYR D 234 PHE 0.022 0.001 PHE C 247 TRP 0.020 0.001 TRP D 212 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13050) covalent geometry : angle 0.61575 / 0.30 (17799) hydrogen bonds : bond 0.03767 / 2.46 ( 794) hydrogen bonds : angle 3.97734 / 2.89 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.44 seconds wall clock time: 32 minutes 33.88 seconds (1953.88 seconds total)