Starting phenix.real_space_refine on Sat Mar 7 02:12:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbv_27310/03_2026/8dbv_27310.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23421 2.51 5 N 6300 2.21 5 O 6942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 269 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36862 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "B" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3811 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "X" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1187 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1201 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.23 Number of scatterers: 36862 At special positions: 0 Unit cell: (175.877, 217.958, 133.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 16 15.00 Mg 5 11.99 O 6942 8.00 N 6300 7.00 C 23421 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 23 sheets defined 61.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.740A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.757A pdb=" N HIS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.525A pdb=" N ALA A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 4.151A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.620A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 407 removed outlier: 4.588A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.067A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.360A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.556A pdb=" N MET A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.514A pdb=" N ILE B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 231 through 251 Proline residue: B 239 - end of helix removed outlier: 4.109A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.703A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.748A pdb=" N PHE B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.084A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.681A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.631A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.852A pdb=" N ALA B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 removed outlier: 4.026A pdb=" N SER C 23 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.696A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.610A pdb=" N TYR C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.688A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.545A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.747A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.808A pdb=" N ASP C 336 " --> pdb=" O GLN C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.607A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 463 through 478 removed outlier: 4.067A pdb=" N PHE C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 487 removed outlier: 4.000A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 510 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.677A pdb=" N LEU D 119 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 170 removed outlier: 3.699A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 234 removed outlier: 3.658A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.565A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.632A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 350 through 378 removed outlier: 3.525A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.882A pdb=" N GLU D 408 " --> pdb=" O PHE D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 234 removed outlier: 4.560A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.667A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.701A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.828A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 377 removed outlier: 4.150A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 382 Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.996A pdb=" N SER E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 433 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.658A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.878A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 167 removed outlier: 3.592A pdb=" N ALA F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 214 through 233 removed outlier: 3.502A pdb=" N VAL F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 255 removed outlier: 3.526A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 302 removed outlier: 4.163A pdb=" N ASP F 301 " --> pdb=" O VAL F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.520A pdb=" N THR F 310 " --> pdb=" O PRO F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 315 removed outlier: 4.078A pdb=" N LEU F 315 " --> pdb=" O PHE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.534A pdb=" N ALA F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 3.961A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 383 through 400 Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.707A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 56 Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.727A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 197 through 201 removed outlier: 3.583A pdb=" N HIS G 200 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 197 through 201' Processing helix chain 'G' and resid 210 through 284 removed outlier: 3.561A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU G 276 " --> pdb=" O ILE G 272 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR G 277 " --> pdb=" O THR G 273 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 removed outlier: 4.003A pdb=" N SER H 108 " --> pdb=" O HIS H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 136 Processing helix chain 'W' and resid 3 through 19 Proline residue: W 9 - end of helix removed outlier: 3.546A pdb=" N VAL W 19 " --> pdb=" O PHE W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.675A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.552A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 63 through 65 No H-bonds generated for 'chain 'W' and resid 63 through 65' Processing helix chain 'W' and resid 71 through 82 removed outlier: 4.035A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.609A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 162 through 174 removed outlier: 3.563A pdb=" N ARG W 166 " --> pdb=" O SER W 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 4.110A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.771A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.803A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.834A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.398A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.641A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.653A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.597A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.593A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 78 removed outlier: 3.601A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.388A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU N 31 " --> pdb=" O GLY N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.749A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP N 61 " --> pdb=" O MET N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'O' and resid 5 through 38 removed outlier: 3.919A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 77 removed outlier: 3.756A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.536A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.875A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.911A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.551A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.597A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY Q 58 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.693A pdb=" N VAL Q 68 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.571A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 78 removed outlier: 3.811A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 4.128A pdb=" N VAL R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 8 through 42 removed outlier: 3.623A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 78 removed outlier: 3.621A pdb=" N ALA S 62 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 4.667A pdb=" N ALA S 67 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL S 68 " --> pdb=" O PRO S 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 24 removed outlier: 4.183A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 135 removed outlier: 3.601A pdb=" N LEU X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER X 46 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU X 48 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS X 66 " --> pdb=" O THR X 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA X 128 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU X 133 " --> pdb=" O VAL X 129 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 148 through 153 removed outlier: 3.673A pdb=" N LEU X 152 " --> pdb=" O ILE X 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.743A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 40 removed outlier: 3.704A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN Y 37 " --> pdb=" O ILE Y 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 139 removed outlier: 3.714A pdb=" N GLU Y 48 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Y 59 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN Y 64 " --> pdb=" O SER Y 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN Y 80 " --> pdb=" O ILE Y 76 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 153 Processing helix chain 'a' and resid 7 through 17 Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.541A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.584A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.653A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 168 removed outlier: 3.817A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 181 removed outlier: 3.518A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.882A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER a 199 " --> pdb=" O LEU a 195 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.936A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA a 217 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.923A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.269A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.460A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 67 removed outlier: 5.723A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 70 " --> pdb=" O GLU A 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 75 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 59 through 66 removed outlier: 4.589A pdb=" N TYR C 60 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU C 66 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 70 through 76 current: chain 'D' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 12 through 16 current: chain 'D' and resid 36 through 46 removed outlier: 6.766A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 55 current: chain 'F' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 12 through 16 current: chain 'F' and resid 36 through 45 removed outlier: 6.734A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.526A pdb=" N ALA A 197 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 322 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 7.924A pdb=" N ILE A 330 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.463A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 59 through 66 removed outlier: 5.927A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 75 current: chain 'E' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 12 through 16 current: chain 'E' and resid 36 through 45 removed outlier: 6.800A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 139 through 142 current: chain 'W' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.435A pdb=" N VAL B 108 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.477A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.512A pdb=" N GLY C 322 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.422A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.302A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.373A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.216A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N TYR D 297 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.708A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.002A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.465A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC1, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.183A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 132 through 135 removed outlier: 7.157A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 207 current: chain 'H' and resid 13 through 25 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 32 through 34 current: chain 'H' and resid 58 through 69 Processing sheet with id=AC4, first strand: chain 'W' and resid 105 through 106 Processing sheet with id=AC5, first strand: chain 'a' and resid 21 through 22 2152 hydrogen bonds defined for protein. 6285 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: 7.49 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8280 1.32 - 1.45: 6986 1.45 - 1.57: 21769 1.57 - 1.69: 28 1.69 - 1.81: 356 Bond restraints: 37419 Sorted by residual: bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" C4 ATP C 600 " pdb=" N9 ATP C 600 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.75e+01 ... (remaining 37414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 50284 4.65 - 9.30: 348 9.30 - 13.95: 8 13.95 - 18.60: 4 18.60 - 23.24: 4 Bond angle restraints: 50648 Sorted by residual: angle pdb=" PA ATP F 502 " pdb=" O3A ATP F 502 " pdb=" PB ATP F 502 " ideal model delta sigma weight residual 136.83 113.59 23.24 1.00e+00 1.00e+00 5.40e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.91 22.96 1.00e+00 1.00e+00 5.27e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 117.28 22.59 1.00e+00 1.00e+00 5.10e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.85 22.02 1.00e+00 1.00e+00 4.85e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.39 18.44 1.00e+00 1.00e+00 3.40e+02 ... (remaining 50643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.25: 21915 29.25 - 58.50: 739 58.50 - 87.76: 87 87.76 - 117.01: 5 117.01 - 146.26: 2 Dihedral angle restraints: 22748 sinusoidal: 9006 harmonic: 13742 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.26 -146.26 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 62.78 -122.78 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" C ASP X 147 " pdb=" N ASP X 147 " pdb=" CA ASP X 147 " pdb=" CB ASP X 147 " ideal model delta harmonic sigma weight residual -122.60 -137.02 14.42 0 2.50e+00 1.60e-01 3.33e+01 ... (remaining 22745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5545 0.119 - 0.237: 341 0.237 - 0.356: 14 0.356 - 0.474: 1 0.474 - 0.593: 1 Chirality restraints: 5902 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" CA ASP X 147 " pdb=" N ASP X 147 " pdb=" C ASP X 147 " pdb=" CB ASP X 147 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB ILE H 131 " pdb=" CA ILE H 131 " pdb=" CG1 ILE H 131 " pdb=" CG2 ILE H 131 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 5899 not shown) Planarity restraints: 6530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " -0.162 9.50e-02 1.11e+02 9.29e-02 4.55e+01 pdb=" NE ARG B 59 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.111 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " 0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 376 " -0.162 9.50e-02 1.11e+02 8.89e-02 3.64e+01 pdb=" NE ARG A 376 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 376 " -0.098 2.00e-02 2.50e+03 pdb=" NH1 ARG A 376 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG A 376 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 41 " -0.144 9.50e-02 1.11e+02 8.14e-02 3.31e+01 pdb=" NE ARG N 41 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG N 41 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG N 41 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG N 41 " 0.027 2.00e-02 2.50e+03 ... (remaining 6527 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 38 2.38 - 3.01: 21157 3.01 - 3.64: 55426 3.64 - 4.27: 84050 4.27 - 4.90: 142221 Nonbonded interactions: 302892 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.749 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.774 2.170 nonbonded pdb="MG MG F 501 " pdb=" O1G ATP F 502 " model vdw 1.783 2.170 nonbonded pdb=" O3B ATP B 600 " pdb="MG MG B 601 " model vdw 1.841 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.850 2.170 ... (remaining 302887 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 7 through 511 or resid 600 through 601)) selection = chain 'B' selection = (chain 'C' and resid 7 through 601) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 1 through 153) } 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 33.440 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.010 0.103 37419 Z= 0.491 Angle : 1.229 23.244 50648 Z= 0.773 Chirality : 0.063 0.593 5902 Planarity : 0.010 0.146 6530 Dihedral : 14.766 146.259 13958 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.86 % Allowed : 7.69 % Favored : 90.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.11), residues: 4793 helix: -0.81 (0.09), residues: 2609 sheet: -0.55 (0.22), residues: 524 loop : -1.07 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.113 0.012 ARG B 59 TYR 0.052 0.007 TYR G 205 PHE 0.061 0.004 PHE O 54 TRP 0.048 0.006 TRP a 186 HIS 0.014 0.003 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.01004 (37419) covalent geometry : angle 1.22898 (50648) hydrogen bonds : bond 0.15937 ( 2152) hydrogen bonds : angle 6.55842 ( 6285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 479 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8054 (p90) REVERT: H 34 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6170 (mp) REVERT: H 58 HIS cc_start: 0.8476 (m-70) cc_final: 0.8268 (m-70) REVERT: H 63 TYR cc_start: 0.5814 (t80) cc_final: 0.4764 (t80) REVERT: H 75 ASN cc_start: 0.8414 (m110) cc_final: 0.8126 (t0) REVERT: H 100 LYS cc_start: 0.7275 (mttm) cc_final: 0.7066 (mttt) REVERT: H 109 HIS cc_start: 0.8049 (t70) cc_final: 0.7819 (m90) REVERT: W 28 GLN cc_start: 0.7202 (tt0) cc_final: 0.6664 (tm-30) REVERT: I 60 VAL cc_start: 0.2491 (t) cc_final: 0.1974 (t) REVERT: J 17 MET cc_start: 0.5579 (mtp) cc_final: 0.3965 (tpp) REVERT: J 61 ASP cc_start: 0.7202 (m-30) cc_final: 0.6798 (p0) REVERT: M 6 MET cc_start: 0.3807 (mtp) cc_final: 0.3369 (ptt) REVERT: M 17 MET cc_start: 0.6507 (mtm) cc_final: 0.5192 (tpt) REVERT: M 22 ILE cc_start: 0.6456 (mt) cc_final: 0.6140 (mt) REVERT: M 42 GLN cc_start: 0.7743 (pt0) cc_final: 0.7508 (pp30) REVERT: N 11 MET cc_start: 0.5942 (tpp) cc_final: 0.5417 (tmm) REVERT: O 17 MET cc_start: 0.7500 (ttm) cc_final: 0.7258 (mtm) REVERT: O 37 GLU cc_start: 0.8083 (tt0) cc_final: 0.7839 (tp30) REVERT: O 68 VAL cc_start: 0.6678 (t) cc_final: 0.6454 (m) REVERT: P 16 MET cc_start: 0.6548 (mtt) cc_final: 0.6032 (tpp) REVERT: Q 17 MET cc_start: 0.2662 (mtm) cc_final: 0.1313 (tpt) REVERT: Q 28 ILE cc_start: 0.7427 (mt) cc_final: 0.7126 (tp) REVERT: R 28 ILE cc_start: 0.7900 (mt) cc_final: 0.7277 (tt) REVERT: R 53 PHE cc_start: 0.7638 (t80) cc_final: 0.7337 (t80) REVERT: S 16 MET cc_start: 0.7113 (mtp) cc_final: 0.6830 (ttm) REVERT: S 51 THR cc_start: 0.8602 (p) cc_final: 0.7433 (p) REVERT: S 57 MET cc_start: 0.7148 (tmt) cc_final: 0.6731 (ptt) REVERT: S 75 MET cc_start: 0.1527 (ttt) cc_final: 0.1198 (mtt) REVERT: X 63 ASP cc_start: 0.3825 (t0) cc_final: 0.2970 (m-30) REVERT: X 66 LYS cc_start: 0.7433 (mmmt) cc_final: 0.7039 (mmtm) REVERT: X 124 VAL cc_start: 0.7808 (p) cc_final: 0.7601 (p) REVERT: Y 1 MET cc_start: 0.1469 (ptt) cc_final: 0.0940 (tpp) REVERT: Y 96 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8241 (tm-30) REVERT: a 46 MET cc_start: 0.3603 (mmm) cc_final: 0.2997 (mtt) REVERT: a 139 LEU cc_start: 0.1488 (OUTLIER) cc_final: 0.1273 (tp) outliers start: 71 outliers final: 13 residues processed: 543 average time/residue: 0.2602 time to fit residues: 221.7275 Evaluate side-chains 295 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 344 ASN A 443 GLN A 484 GLN A 511 GLN B 58 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 4 ASN C 147 GLN C 186 GLN C 333 GLN C 443 GLN E 324 GLN F 19 GLN F 437 HIS G 54 HIS G 91 ASN G 252 ASN G 265 ASN G 269 GLN H 75 ASN W 67 GLN W 73 GLN W 82 ASN R 5 ASN S 5 ASN S 52 GLN X 37 GLN a 132 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.070187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046643 restraints weight = 205626.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047287 restraints weight = 110720.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047526 restraints weight = 73878.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047642 restraints weight = 55103.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.047711 restraints weight = 53598.288| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37419 Z= 0.218 Angle : 0.712 11.369 50648 Z= 0.369 Chirality : 0.045 0.240 5902 Planarity : 0.005 0.047 6530 Dihedral : 7.799 139.709 5376 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.65 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 10.70 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.36 (0.12), residues: 4793 helix: 1.00 (0.10), residues: 2603 sheet: -0.15 (0.22), residues: 526 loop : -0.75 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 220 TYR 0.023 0.002 TYR N 10 PHE 0.051 0.002 PHE S 54 TRP 0.020 0.002 TRP a 186 HIS 0.009 0.001 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00468 (37419) covalent geometry : angle 0.71240 (50648) hydrogen bonds : bond 0.05962 ( 2152) hydrogen bonds : angle 4.88934 ( 6285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: B 456 LEU cc_start: 0.9370 (mt) cc_final: 0.9100 (pt) REVERT: D 379 MET cc_start: 0.8276 (tpp) cc_final: 0.7834 (tmm) REVERT: E 88 MET cc_start: 0.8760 (mpp) cc_final: 0.8544 (mpp) REVERT: E 193 MET cc_start: 0.8733 (mtm) cc_final: 0.8313 (mpp) REVERT: F 193 MET cc_start: 0.9070 (mmm) cc_final: 0.8645 (mmm) REVERT: F 431 MET cc_start: 0.8686 (mtp) cc_final: 0.8462 (mtp) REVERT: H 52 ILE cc_start: 0.6456 (mm) cc_final: 0.6199 (mm) REVERT: H 58 HIS cc_start: 0.8319 (m-70) cc_final: 0.7971 (m-70) REVERT: H 75 ASN cc_start: 0.8577 (m-40) cc_final: 0.8303 (t0) REVERT: H 81 ASP cc_start: 0.7941 (m-30) cc_final: 0.7148 (t70) REVERT: H 99 ARG cc_start: 0.8769 (ttp-110) cc_final: 0.8481 (mmp-170) REVERT: H 100 LYS cc_start: 0.7145 (mttm) cc_final: 0.6916 (mttt) REVERT: H 109 HIS cc_start: 0.8297 (t70) cc_final: 0.8061 (m90) REVERT: W 16 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8176 (p0) REVERT: W 73 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: I 19 LEU cc_start: 0.8109 (mt) cc_final: 0.7689 (tp) REVERT: J 17 MET cc_start: 0.5788 (mtp) cc_final: 0.4187 (tpp) REVERT: J 61 ASP cc_start: 0.7047 (m-30) cc_final: 0.6523 (p0) REVERT: L 65 MET cc_start: 0.3340 (mmm) cc_final: 0.2544 (ppp) REVERT: M 6 MET cc_start: 0.4229 (mtp) cc_final: 0.3849 (ptt) REVERT: M 17 MET cc_start: 0.6959 (mtm) cc_final: 0.5286 (tpp) REVERT: M 42 GLN cc_start: 0.8146 (pt0) cc_final: 0.7539 (pp30) REVERT: N 11 MET cc_start: 0.5779 (tpp) cc_final: 0.5492 (tmm) REVERT: N 17 MET cc_start: 0.5781 (tpt) cc_final: 0.5542 (tpt) REVERT: O 53 PHE cc_start: 0.7947 (t80) cc_final: 0.7627 (t80) REVERT: P 61 ASP cc_start: 0.0762 (OUTLIER) cc_final: 0.0308 (t0) REVERT: S 16 MET cc_start: 0.6969 (mtp) cc_final: 0.6729 (ttm) REVERT: S 57 MET cc_start: 0.7137 (tmt) cc_final: 0.6852 (tpt) REVERT: X 48 GLU cc_start: 0.4069 (OUTLIER) cc_final: 0.3585 (tt0) REVERT: X 63 ASP cc_start: 0.4241 (t0) cc_final: 0.3519 (m-30) REVERT: Y 96 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8258 (tm-30) REVERT: Y 98 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7435 (mmm160) REVERT: a 139 LEU cc_start: 0.1602 (OUTLIER) cc_final: 0.1205 (tt) REVERT: a 257 MET cc_start: 0.7195 (tmm) cc_final: 0.6663 (ptt) outliers start: 79 outliers final: 34 residues processed: 347 average time/residue: 0.2350 time to fit residues: 134.2449 Evaluate side-chains 286 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 6 MET Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 268 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 400 optimal weight: 6.9990 chunk 471 optimal weight: 30.0000 chunk 218 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 410 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS G 186 GLN W 28 GLN W 73 GLN L 5 ASN R 3 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.070425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047650 restraints weight = 210159.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048283 restraints weight = 113254.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.048391 restraints weight = 73870.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048325 restraints weight = 70210.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048304 restraints weight = 51909.686| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37419 Z= 0.156 Angle : 0.619 12.189 50648 Z= 0.316 Chirality : 0.042 0.168 5902 Planarity : 0.004 0.050 6530 Dihedral : 7.211 132.778 5361 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 12.29 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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 (0.12), residues: 4793 helix: 1.46 (0.10), residues: 2621 sheet: 0.01 (0.23), residues: 498 loop : -0.59 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 99 TYR 0.013 0.001 TYR C 236 PHE 0.047 0.001 PHE S 54 TRP 0.012 0.001 TRP a 186 HIS 0.006 0.001 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00334 (37419) covalent geometry : angle 0.61865 (50648) hydrogen bonds : bond 0.05298 ( 2152) hydrogen bonds : angle 4.52946 ( 6285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 86 MET cc_start: 0.8508 (mtt) cc_final: 0.8123 (mtt) REVERT: B 419 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9105 (pttp) REVERT: C 468 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8841 (tp30) REVERT: C 472 LEU cc_start: 0.9352 (pp) cc_final: 0.9055 (pp) REVERT: D 0 MET cc_start: 0.7758 (ppp) cc_final: 0.7382 (ppp) REVERT: D 63 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (ptm-80) REVERT: D 379 MET cc_start: 0.8362 (tpp) cc_final: 0.7985 (tmm) REVERT: E 287 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8991 (p) REVERT: H 58 HIS cc_start: 0.8350 (m-70) cc_final: 0.8057 (m-70) REVERT: H 75 ASN cc_start: 0.8592 (m-40) cc_final: 0.8285 (t0) REVERT: H 99 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8478 (ptp90) REVERT: H 100 LYS cc_start: 0.7011 (mttm) cc_final: 0.6780 (mttt) REVERT: W 43 MET cc_start: 0.7870 (ttm) cc_final: 0.7637 (tpt) REVERT: I 19 LEU cc_start: 0.8125 (mt) cc_final: 0.7733 (tp) REVERT: J 17 MET cc_start: 0.5718 (mtp) cc_final: 0.4282 (tpp) REVERT: J 61 ASP cc_start: 0.6644 (m-30) cc_final: 0.6364 (p0) REVERT: L 65 MET cc_start: 0.3594 (mmm) cc_final: 0.2880 (ppp) REVERT: M 6 MET cc_start: 0.4296 (mtp) cc_final: 0.3894 (ptt) REVERT: M 16 MET cc_start: 0.2271 (ptm) cc_final: 0.1840 (ppp) REVERT: M 17 MET cc_start: 0.7046 (mtm) cc_final: 0.5811 (tpt) REVERT: N 11 MET cc_start: 0.5655 (tpp) cc_final: 0.5307 (tmm) REVERT: N 65 MET cc_start: 0.4136 (mmm) cc_final: 0.3514 (mmm) REVERT: P 16 MET cc_start: 0.6789 (ttt) cc_final: 0.5815 (tpp) REVERT: P 61 ASP cc_start: 0.1203 (OUTLIER) cc_final: 0.0774 (t0) REVERT: R 53 PHE cc_start: 0.7620 (t80) cc_final: 0.6882 (t80) REVERT: R 57 MET cc_start: 0.7501 (tmm) cc_final: 0.6628 (mmm) REVERT: S 16 MET cc_start: 0.7164 (mtp) cc_final: 0.6866 (ttm) REVERT: S 57 MET cc_start: 0.7233 (tmt) cc_final: 0.7000 (tpt) REVERT: X 48 GLU cc_start: 0.4415 (OUTLIER) cc_final: 0.4048 (tt0) REVERT: X 63 ASP cc_start: 0.4559 (t0) cc_final: 0.3830 (m-30) REVERT: Y 24 TYR cc_start: 0.1252 (OUTLIER) cc_final: 0.0542 (m-80) REVERT: Y 98 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7506 (mtp180) REVERT: Y 113 ARG cc_start: 0.8868 (mtt-85) cc_final: 0.8497 (mmt180) REVERT: a 46 MET cc_start: 0.3746 (mmm) cc_final: 0.3389 (mtt) REVERT: a 139 LEU cc_start: 0.1708 (OUTLIER) cc_final: 0.1496 (tt) REVERT: a 257 MET cc_start: 0.7403 (tmm) cc_final: 0.7056 (ptm) outliers start: 66 outliers final: 28 residues processed: 319 average time/residue: 0.2274 time to fit residues: 120.9584 Evaluate side-chains 273 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 6 MET Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 50 optimal weight: 3.9990 chunk 421 optimal weight: 7.9990 chunk 456 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 391 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN B 420 GLN C 172 GLN F 7 GLN W 73 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN X 37 GLN Y 85 GLN Y 96 GLN a 15 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.068237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.044693 restraints weight = 204339.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.045407 restraints weight = 104865.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045462 restraints weight = 70365.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045661 restraints weight = 50086.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.045797 restraints weight = 44046.404| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 37419 Z= 0.281 Angle : 0.691 12.095 50648 Z= 0.352 Chirality : 0.044 0.164 5902 Planarity : 0.005 0.056 6530 Dihedral : 7.032 125.772 5359 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 2.14 % Allowed : 12.76 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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 (0.12), residues: 4793 helix: 1.49 (0.10), residues: 2623 sheet: -0.07 (0.22), residues: 527 loop : -0.63 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 99 TYR 0.016 0.002 TYR N 10 PHE 0.043 0.002 PHE N 54 TRP 0.011 0.002 TRP a 186 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00626 (37419) covalent geometry : angle 0.69083 (50648) hydrogen bonds : bond 0.05277 ( 2152) hydrogen bonds : angle 4.60729 ( 6285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: B 86 MET cc_start: 0.8562 (mtt) cc_final: 0.8070 (mtt) REVERT: B 103 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8619 (pp) REVERT: B 156 MET cc_start: 0.9060 (tpp) cc_final: 0.8620 (tpp) REVERT: B 419 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9048 (pttm) REVERT: D 63 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8556 (ptm-80) REVERT: D 275 MET cc_start: 0.9041 (tpp) cc_final: 0.8839 (tpp) REVERT: D 379 MET cc_start: 0.8426 (tpp) cc_final: 0.8042 (tmm) REVERT: E 287 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.9012 (p) REVERT: F 193 MET cc_start: 0.9105 (mmm) cc_final: 0.8568 (mmm) REVERT: H 58 HIS cc_start: 0.8232 (m-70) cc_final: 0.7967 (m-70) REVERT: H 75 ASN cc_start: 0.8571 (m-40) cc_final: 0.8256 (t0) REVERT: H 95 MET cc_start: 0.7286 (tpt) cc_final: 0.6538 (tpp) REVERT: H 100 LYS cc_start: 0.6822 (mttm) cc_final: 0.6619 (mttt) REVERT: I 19 LEU cc_start: 0.8041 (mt) cc_final: 0.7625 (tp) REVERT: J 17 MET cc_start: 0.5525 (mtp) cc_final: 0.4313 (tpp) REVERT: J 61 ASP cc_start: 0.6791 (m-30) cc_final: 0.6278 (p0) REVERT: L 65 MET cc_start: 0.4180 (mmm) cc_final: 0.3417 (ppp) REVERT: M 6 MET cc_start: 0.4303 (mtp) cc_final: 0.3904 (ptt) REVERT: N 11 MET cc_start: 0.5669 (tpp) cc_final: 0.5369 (tmm) REVERT: N 17 MET cc_start: 0.5536 (tpt) cc_final: 0.5304 (tpt) REVERT: N 65 MET cc_start: 0.4233 (mmm) cc_final: 0.3643 (mmm) REVERT: P 16 MET cc_start: 0.6819 (ttt) cc_final: 0.6532 (ttm) REVERT: P 61 ASP cc_start: 0.1496 (OUTLIER) cc_final: 0.1076 (t0) REVERT: S 16 MET cc_start: 0.7137 (mtp) cc_final: 0.6813 (ttm) REVERT: S 17 MET cc_start: 0.2692 (ptt) cc_final: 0.2453 (ptt) REVERT: S 57 MET cc_start: 0.7215 (tmt) cc_final: 0.6934 (tpt) REVERT: X 48 GLU cc_start: 0.4381 (OUTLIER) cc_final: 0.4030 (tt0) REVERT: X 63 ASP cc_start: 0.4797 (t0) cc_final: 0.4004 (m-30) REVERT: Y 24 TYR cc_start: 0.1326 (OUTLIER) cc_final: 0.0640 (m-80) REVERT: Y 98 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7475 (mtp180) REVERT: Y 113 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8531 (mmt180) REVERT: a 6 MET cc_start: 0.2712 (OUTLIER) cc_final: 0.2318 (ppp) REVERT: a 46 MET cc_start: 0.3868 (mmm) cc_final: 0.3493 (mtt) REVERT: a 115 MET cc_start: 0.1622 (ttm) cc_final: 0.0571 (ptp) REVERT: a 168 MET cc_start: 0.3521 (mmm) cc_final: 0.3108 (mtt) REVERT: a 196 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6781 (mt-10) REVERT: a 257 MET cc_start: 0.7464 (tmm) cc_final: 0.7239 (ptt) outliers start: 82 outliers final: 37 residues processed: 321 average time/residue: 0.2342 time to fit residues: 124.8499 Evaluate side-chains 281 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 146 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 349 optimal weight: 30.0000 chunk 459 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN W 73 GLN I 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN X 37 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.068127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.043569 restraints weight = 202553.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.044580 restraints weight = 100490.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.045204 restraints weight = 63507.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045619 restraints weight = 48274.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.045786 restraints weight = 41041.394| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37419 Z= 0.218 Angle : 0.637 11.072 50648 Z= 0.323 Chirality : 0.042 0.159 5902 Planarity : 0.004 0.060 6530 Dihedral : 6.751 130.086 5356 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 2.20 % Allowed : 13.49 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4793 helix: 1.63 (0.10), residues: 2620 sheet: -0.07 (0.22), residues: 527 loop : -0.61 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 129 TYR 0.013 0.001 TYR C 236 PHE 0.032 0.002 PHE S 54 TRP 0.012 0.001 TRP G 203 HIS 0.005 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00481 (37419) covalent geometry : angle 0.63694 (50648) hydrogen bonds : bond 0.04932 ( 2152) hydrogen bonds : angle 4.45037 ( 6285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 251 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: A 262 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: A 439 MET cc_start: 0.8807 (mtp) cc_final: 0.8596 (mtm) REVERT: B 86 MET cc_start: 0.8537 (mtt) cc_final: 0.8038 (mtt) REVERT: B 103 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8644 (pp) REVERT: B 156 MET cc_start: 0.9156 (tpp) cc_final: 0.8864 (mmt) REVERT: B 419 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9055 (ptpp) REVERT: D 0 MET cc_start: 0.7881 (ppp) cc_final: 0.7406 (ppp) REVERT: D 63 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8464 (ptm-80) REVERT: D 371 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8076 (mtmm) REVERT: D 379 MET cc_start: 0.8486 (tpp) cc_final: 0.8034 (tmm) REVERT: E 287 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8986 (p) REVERT: E 445 MET cc_start: 0.8451 (mmm) cc_final: 0.7989 (mmm) REVERT: F 86 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8188 (mtp180) REVERT: F 136 MET cc_start: 0.9403 (mmm) cc_final: 0.9185 (mmm) REVERT: G 155 MET cc_start: 0.8715 (tpp) cc_final: 0.8476 (tpp) REVERT: H 58 HIS cc_start: 0.8074 (m-70) cc_final: 0.7824 (m-70) REVERT: H 95 MET cc_start: 0.7126 (tpt) cc_final: 0.6760 (tpp) REVERT: H 100 LYS cc_start: 0.6756 (mttm) cc_final: 0.6529 (mttt) REVERT: I 19 LEU cc_start: 0.7979 (mt) cc_final: 0.7619 (tp) REVERT: J 17 MET cc_start: 0.5483 (mtp) cc_final: 0.4175 (tpp) REVERT: L 65 MET cc_start: 0.4466 (mmm) cc_final: 0.3864 (ppp) REVERT: M 6 MET cc_start: 0.4477 (mtp) cc_final: 0.4083 (ptt) REVERT: N 17 MET cc_start: 0.5048 (tpt) cc_final: 0.4810 (tpt) REVERT: N 65 MET cc_start: 0.4589 (mmm) cc_final: 0.4061 (mmm) REVERT: P 16 MET cc_start: 0.6468 (ttt) cc_final: 0.6249 (ttm) REVERT: P 61 ASP cc_start: 0.1558 (OUTLIER) cc_final: 0.1185 (t0) REVERT: R 28 ILE cc_start: 0.7756 (mt) cc_final: 0.7358 (tp) REVERT: S 16 MET cc_start: 0.7138 (mtp) cc_final: 0.6694 (ttm) REVERT: S 57 MET cc_start: 0.7112 (tmt) cc_final: 0.6814 (tpt) REVERT: S 61 ASP cc_start: 0.3039 (OUTLIER) cc_final: 0.2433 (p0) REVERT: X 48 GLU cc_start: 0.4291 (OUTLIER) cc_final: 0.4031 (tt0) REVERT: X 63 ASP cc_start: 0.4956 (t0) cc_final: 0.4219 (m-30) REVERT: Y 24 TYR cc_start: 0.1356 (OUTLIER) cc_final: 0.0803 (m-80) REVERT: Y 98 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7596 (mtp180) REVERT: Y 113 ARG cc_start: 0.8920 (mtt-85) cc_final: 0.8656 (mmt-90) REVERT: a 6 MET cc_start: 0.3327 (ttp) cc_final: 0.2768 (ppp) REVERT: a 46 MET cc_start: 0.3916 (mmm) cc_final: 0.3604 (mtp) REVERT: a 115 MET cc_start: 0.1873 (ttm) cc_final: 0.0804 (ptp) REVERT: a 196 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6882 (mt-10) outliers start: 84 outliers final: 36 residues processed: 327 average time/residue: 0.2246 time to fit residues: 121.4297 Evaluate side-chains 286 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 355 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 382 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 359 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 318 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 5 ASN X 51 HIS a 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.069020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.045053 restraints weight = 207885.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.046097 restraints weight = 98487.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046835 restraints weight = 61906.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.047216 restraints weight = 46378.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.047402 restraints weight = 39237.607| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37419 Z= 0.151 Angle : 0.601 11.347 50648 Z= 0.303 Chirality : 0.041 0.248 5902 Planarity : 0.004 0.056 6530 Dihedral : 6.503 132.257 5356 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 1.83 % Allowed : 13.91 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4793 helix: 1.79 (0.10), residues: 2618 sheet: 0.05 (0.23), residues: 513 loop : -0.58 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 121 TYR 0.012 0.001 TYR C 236 PHE 0.030 0.001 PHE S 54 TRP 0.010 0.001 TRP G 203 HIS 0.004 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00328 (37419) covalent geometry : angle 0.60149 (50648) hydrogen bonds : bond 0.04625 ( 2152) hydrogen bonds : angle 4.32013 ( 6285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 254 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: A 448 LEU cc_start: 0.9578 (mt) cc_final: 0.9364 (mt) REVERT: B 86 MET cc_start: 0.8471 (mtt) cc_final: 0.8073 (mtt) REVERT: B 103 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8581 (pp) REVERT: B 419 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8964 (pttm) REVERT: C 318 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8549 (mtmt) REVERT: C 468 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8569 (tp30) REVERT: D 0 MET cc_start: 0.7802 (ppp) cc_final: 0.7394 (ppp) REVERT: D 63 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8425 (ptm-80) REVERT: D 371 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8092 (mtmm) REVERT: D 379 MET cc_start: 0.8502 (tpp) cc_final: 0.8119 (tmm) REVERT: E 287 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8918 (p) REVERT: F 86 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8217 (mtp180) REVERT: F 136 MET cc_start: 0.9367 (mmm) cc_final: 0.9122 (mmm) REVERT: G 116 MET cc_start: 0.6960 (mmp) cc_final: 0.6706 (mmp) REVERT: G 155 MET cc_start: 0.8694 (tpp) cc_final: 0.8446 (tpp) REVERT: H 95 MET cc_start: 0.6879 (tpt) cc_final: 0.6198 (tpp) REVERT: W 73 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: I 19 LEU cc_start: 0.7983 (mt) cc_final: 0.7583 (tp) REVERT: J 17 MET cc_start: 0.5464 (mtp) cc_final: 0.4231 (tpp) REVERT: L 65 MET cc_start: 0.4719 (mmm) cc_final: 0.4123 (ppp) REVERT: M 6 MET cc_start: 0.4425 (mtp) cc_final: 0.3902 (ptt) REVERT: M 57 MET cc_start: 0.7370 (mmm) cc_final: 0.6994 (mmm) REVERT: N 17 MET cc_start: 0.5025 (tpt) cc_final: 0.4743 (tpt) REVERT: N 75 MET cc_start: 0.2017 (mmt) cc_final: 0.1785 (mmp) REVERT: P 16 MET cc_start: 0.6446 (ttt) cc_final: 0.6042 (ttm) REVERT: P 61 ASP cc_start: 0.1766 (OUTLIER) cc_final: 0.1418 (t0) REVERT: R 28 ILE cc_start: 0.7704 (mt) cc_final: 0.7297 (tp) REVERT: S 16 MET cc_start: 0.7105 (mtp) cc_final: 0.6697 (ttp) REVERT: S 57 MET cc_start: 0.7035 (tmt) cc_final: 0.6779 (tpt) REVERT: X 48 GLU cc_start: 0.4376 (OUTLIER) cc_final: 0.3478 (tp30) REVERT: X 63 ASP cc_start: 0.5048 (t0) cc_final: 0.4288 (m-30) REVERT: X 82 ARG cc_start: 0.8627 (ttt180) cc_final: 0.8085 (mmm160) REVERT: Y 24 TYR cc_start: 0.1280 (OUTLIER) cc_final: 0.0773 (m-80) REVERT: Y 98 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7580 (mtp180) REVERT: Y 113 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8566 (mmt180) REVERT: a 6 MET cc_start: 0.3485 (ttp) cc_final: 0.2679 (ppp) REVERT: a 46 MET cc_start: 0.3915 (mmm) cc_final: 0.3617 (mtp) REVERT: a 115 MET cc_start: 0.1853 (ttm) cc_final: 0.0786 (ptp) REVERT: a 168 MET cc_start: 0.3343 (mmm) cc_final: 0.2998 (mtt) REVERT: a 196 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6908 (mt-10) outliers start: 70 outliers final: 40 residues processed: 317 average time/residue: 0.2379 time to fit residues: 124.3957 Evaluate side-chains 288 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 135 optimal weight: 0.9990 chunk 200 optimal weight: 0.0030 chunk 24 optimal weight: 7.9990 chunk 464 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 252 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 182 optimal weight: 0.0070 chunk 134 optimal weight: 2.9990 chunk 372 optimal weight: 0.0980 overall best weight: 0.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS W 73 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.070159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047199 restraints weight = 208624.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048547 restraints weight = 101487.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048430 restraints weight = 53143.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048622 restraints weight = 48610.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.048639 restraints weight = 43195.625| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 37419 Z= 0.114 Angle : 0.587 10.114 50648 Z= 0.293 Chirality : 0.041 0.229 5902 Planarity : 0.004 0.051 6530 Dihedral : 6.134 132.546 5356 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 1.54 % Allowed : 14.38 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 4793 helix: 1.96 (0.10), residues: 2623 sheet: 0.08 (0.23), residues: 526 loop : -0.48 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 129 TYR 0.012 0.001 TYR A 474 PHE 0.027 0.001 PHE S 54 TRP 0.008 0.001 TRP G 203 HIS 0.003 0.000 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00225 (37419) covalent geometry : angle 0.58727 (50648) hydrogen bonds : bond 0.04176 ( 2152) hydrogen bonds : angle 4.14397 ( 6285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: A 448 LEU cc_start: 0.9596 (mt) cc_final: 0.9364 (mt) REVERT: B 86 MET cc_start: 0.8454 (mtt) cc_final: 0.8051 (mtt) REVERT: B 103 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 419 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9017 (pttm) REVERT: C 468 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8670 (tp30) REVERT: D 0 MET cc_start: 0.7855 (ppp) cc_final: 0.7391 (ppp) REVERT: D 63 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8277 (ptm-80) REVERT: D 371 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8017 (mtmm) REVERT: D 379 MET cc_start: 0.8483 (tpp) cc_final: 0.8033 (tmm) REVERT: E 287 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (p) REVERT: F 86 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8224 (mtp180) REVERT: F 136 MET cc_start: 0.9391 (mmm) cc_final: 0.9080 (mmm) REVERT: G 5 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7777 (p0) REVERT: G 116 MET cc_start: 0.7211 (mmp) cc_final: 0.7003 (mmp) REVERT: H 95 MET cc_start: 0.6927 (tpt) cc_final: 0.6353 (tpp) REVERT: W 73 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: I 11 MET cc_start: 0.6163 (tmm) cc_final: 0.5906 (tpt) REVERT: I 17 MET cc_start: 0.6166 (ppp) cc_final: 0.5791 (ppp) REVERT: I 19 LEU cc_start: 0.7897 (mt) cc_final: 0.7545 (tp) REVERT: J 17 MET cc_start: 0.5793 (mtp) cc_final: 0.4680 (tpp) REVERT: L 65 MET cc_start: 0.4661 (mmm) cc_final: 0.4142 (ppp) REVERT: M 6 MET cc_start: 0.4319 (mtp) cc_final: 0.3846 (ptt) REVERT: M 28 ILE cc_start: 0.6875 (mm) cc_final: 0.6356 (tt) REVERT: M 57 MET cc_start: 0.7466 (mmm) cc_final: 0.6947 (mmm) REVERT: N 17 MET cc_start: 0.5384 (tpt) cc_final: 0.5179 (tpt) REVERT: N 65 MET cc_start: 0.5500 (mmm) cc_final: 0.5019 (mmm) REVERT: R 17 MET cc_start: 0.2964 (mpp) cc_final: 0.2530 (mpp) REVERT: R 28 ILE cc_start: 0.7704 (mt) cc_final: 0.7345 (tp) REVERT: S 16 MET cc_start: 0.6964 (mtp) cc_final: 0.6691 (ttp) REVERT: S 35 PHE cc_start: 0.6617 (t80) cc_final: 0.6091 (t80) REVERT: S 57 MET cc_start: 0.7170 (tmt) cc_final: 0.6889 (tpt) REVERT: S 61 ASP cc_start: 0.3318 (OUTLIER) cc_final: 0.2813 (p0) REVERT: X 48 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.3922 (tp30) REVERT: X 63 ASP cc_start: 0.4894 (t0) cc_final: 0.4111 (m-30) REVERT: X 82 ARG cc_start: 0.8627 (ttt180) cc_final: 0.8109 (mmm160) REVERT: Y 24 TYR cc_start: 0.1188 (OUTLIER) cc_final: 0.0449 (m-80) REVERT: Y 98 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7603 (mmm160) REVERT: Y 113 ARG cc_start: 0.8948 (mtt-85) cc_final: 0.8594 (mmt180) REVERT: a 6 MET cc_start: 0.2128 (ttp) cc_final: 0.1837 (ppp) REVERT: a 46 MET cc_start: 0.3740 (mmm) cc_final: 0.3339 (mtp) REVERT: a 93 MET cc_start: 0.6798 (mmm) cc_final: 0.6336 (mtm) REVERT: a 168 MET cc_start: 0.3472 (mmm) cc_final: 0.3023 (mtt) REVERT: a 196 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6918 (mt-10) outliers start: 59 outliers final: 33 residues processed: 311 average time/residue: 0.2261 time to fit residues: 117.4284 Evaluate side-chains 287 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 204 optimal weight: 9.9990 chunk 434 optimal weight: 5.9990 chunk 95 optimal weight: 0.0030 chunk 126 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 448 optimal weight: 40.0000 chunk 198 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 196 optimal weight: 0.3980 chunk 281 optimal weight: 1.9990 overall best weight: 2.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 HIS L 5 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS a 14 HIS a 15 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.069124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045767 restraints weight = 208508.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046933 restraints weight = 101128.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047027 restraints weight = 64751.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047328 restraints weight = 47412.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047408 restraints weight = 40273.425| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37419 Z= 0.157 Angle : 0.609 14.576 50648 Z= 0.303 Chirality : 0.041 0.228 5902 Planarity : 0.004 0.050 6530 Dihedral : 6.054 132.646 5356 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.40 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 14.51 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.12), residues: 4793 helix: 2.01 (0.10), residues: 2627 sheet: 0.05 (0.23), residues: 531 loop : -0.47 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 129 TYR 0.031 0.001 TYR H 63 PHE 0.023 0.001 PHE S 54 TRP 0.011 0.001 TRP a 235 HIS 0.005 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00342 (37419) covalent geometry : angle 0.60897 (50648) hydrogen bonds : bond 0.04273 ( 2152) hydrogen bonds : angle 4.16238 ( 6285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: A 448 LEU cc_start: 0.9576 (mt) cc_final: 0.9362 (mt) REVERT: B 86 MET cc_start: 0.8508 (mtt) cc_final: 0.8087 (mtt) REVERT: B 103 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8636 (pp) REVERT: B 419 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8942 (pttm) REVERT: C 468 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8587 (tp30) REVERT: D 0 MET cc_start: 0.7896 (ppp) cc_final: 0.7418 (ppp) REVERT: D 63 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8280 (ptm-80) REVERT: D 371 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8099 (mtmm) REVERT: D 379 MET cc_start: 0.8467 (tpp) cc_final: 0.8083 (tmm) REVERT: E 287 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8858 (p) REVERT: F 86 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8283 (mtp180) REVERT: F 136 MET cc_start: 0.9381 (mmm) cc_final: 0.9043 (mmm) REVERT: F 209 MET cc_start: 0.8644 (ptp) cc_final: 0.8141 (mtm) REVERT: G 5 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7733 (p0) REVERT: H 95 MET cc_start: 0.7042 (tpt) cc_final: 0.6448 (tpp) REVERT: W 73 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: I 11 MET cc_start: 0.6254 (tmm) cc_final: 0.5892 (tpt) REVERT: I 19 LEU cc_start: 0.7956 (mt) cc_final: 0.7612 (tp) REVERT: J 17 MET cc_start: 0.5661 (mtp) cc_final: 0.4472 (tpp) REVERT: L 65 MET cc_start: 0.4745 (mmm) cc_final: 0.4290 (ppp) REVERT: M 6 MET cc_start: 0.4326 (mtp) cc_final: 0.3871 (ptt) REVERT: M 28 ILE cc_start: 0.6981 (mm) cc_final: 0.6452 (tt) REVERT: N 17 MET cc_start: 0.5446 (tpt) cc_final: 0.5150 (tpt) REVERT: N 65 MET cc_start: 0.5205 (mmm) cc_final: 0.4740 (mmm) REVERT: O 57 MET cc_start: 0.2777 (mmm) cc_final: 0.2329 (mmt) REVERT: Q 17 MET cc_start: 0.1020 (ptp) cc_final: -0.0075 (tpp) REVERT: R 17 MET cc_start: 0.2722 (mpp) cc_final: 0.2515 (mpp) REVERT: R 28 ILE cc_start: 0.7679 (mt) cc_final: 0.7314 (tp) REVERT: S 16 MET cc_start: 0.7073 (mtp) cc_final: 0.6648 (ttp) REVERT: S 35 PHE cc_start: 0.6535 (t80) cc_final: 0.6015 (t80) REVERT: S 57 MET cc_start: 0.7098 (tmt) cc_final: 0.6818 (tpt) REVERT: S 61 ASP cc_start: 0.3225 (OUTLIER) cc_final: 0.2602 (p0) REVERT: X 1 MET cc_start: 0.2996 (mtm) cc_final: 0.2706 (mtm) REVERT: X 48 GLU cc_start: 0.4846 (OUTLIER) cc_final: 0.4008 (tp30) REVERT: X 63 ASP cc_start: 0.5045 (t0) cc_final: 0.4309 (m-30) REVERT: X 82 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8123 (mmm160) REVERT: Y 24 TYR cc_start: 0.1283 (OUTLIER) cc_final: 0.0657 (m-80) REVERT: Y 98 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7539 (mtp180) REVERT: Y 113 ARG cc_start: 0.8960 (mtt-85) cc_final: 0.8616 (mmt180) REVERT: a 6 MET cc_start: 0.2183 (ttp) cc_final: 0.1857 (tmm) REVERT: a 46 MET cc_start: 0.3799 (mmm) cc_final: 0.3378 (mtp) REVERT: a 115 MET cc_start: 0.1575 (ttt) cc_final: 0.1262 (mmm) REVERT: a 196 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6928 (mt-10) outliers start: 58 outliers final: 38 residues processed: 305 average time/residue: 0.2311 time to fit residues: 117.8047 Evaluate side-chains 292 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 109 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 287 optimal weight: 30.0000 chunk 349 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 451 optimal weight: 10.0000 chunk 415 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.067914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043804 restraints weight = 205294.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044641 restraints weight = 100608.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045288 restraints weight = 63837.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045701 restraints weight = 48143.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045873 restraints weight = 40834.442| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37419 Z= 0.202 Angle : 0.654 14.504 50648 Z= 0.325 Chirality : 0.042 0.197 5902 Planarity : 0.004 0.051 6530 Dihedral : 6.171 133.166 5356 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.88 % Favored : 97.10 % Rotamer: Outliers : 1.46 % Allowed : 14.64 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.12), residues: 4793 helix: 1.91 (0.10), residues: 2621 sheet: 0.03 (0.22), residues: 536 loop : -0.55 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 129 TYR 0.026 0.001 TYR H 63 PHE 0.018 0.001 PHE S 54 TRP 0.011 0.001 TRP G 203 HIS 0.009 0.001 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00449 (37419) covalent geometry : angle 0.65379 (50648) hydrogen bonds : bond 0.04518 ( 2152) hydrogen bonds : angle 4.28230 ( 6285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: A 448 LEU cc_start: 0.9637 (mt) cc_final: 0.9425 (mt) REVERT: B 86 MET cc_start: 0.8548 (mtt) cc_final: 0.8139 (mtt) REVERT: B 103 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 419 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9021 (pttm) REVERT: D 0 MET cc_start: 0.7884 (ppp) cc_final: 0.7424 (ppp) REVERT: D 63 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8324 (ptm-80) REVERT: D 371 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8137 (mtmm) REVERT: D 379 MET cc_start: 0.8425 (tpp) cc_final: 0.7994 (tmm) REVERT: F 86 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8188 (mtp180) REVERT: F 136 MET cc_start: 0.9409 (mmm) cc_final: 0.9038 (mmm) REVERT: F 209 MET cc_start: 0.8635 (ptp) cc_final: 0.8349 (mtm) REVERT: G 5 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7821 (p0) REVERT: G 116 MET cc_start: 0.7209 (mmp) cc_final: 0.7008 (mmp) REVERT: H 15 MET cc_start: 0.4680 (tpp) cc_final: 0.4246 (tpp) REVERT: H 95 MET cc_start: 0.6895 (tpt) cc_final: 0.6237 (tpp) REVERT: W 76 ILE cc_start: 0.8975 (tp) cc_final: 0.8771 (mp) REVERT: W 128 MET cc_start: 0.8821 (mmt) cc_final: 0.8546 (mmp) REVERT: I 11 MET cc_start: 0.6591 (tmm) cc_final: 0.6268 (tpt) REVERT: I 16 MET cc_start: 0.3268 (tmm) cc_final: 0.2898 (tmm) REVERT: I 19 LEU cc_start: 0.7885 (mt) cc_final: 0.7525 (tp) REVERT: J 17 MET cc_start: 0.4924 (mtp) cc_final: 0.3792 (tpp) REVERT: L 63 ILE cc_start: 0.5877 (mm) cc_final: 0.4701 (mt) REVERT: L 65 MET cc_start: 0.4860 (mmm) cc_final: 0.4434 (ppp) REVERT: M 6 MET cc_start: 0.4600 (mtp) cc_final: 0.4142 (ptt) REVERT: M 28 ILE cc_start: 0.6778 (mm) cc_final: 0.6202 (tt) REVERT: M 42 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6546 (pp30) REVERT: N 16 MET cc_start: 0.5636 (tpp) cc_final: 0.5279 (tpp) REVERT: N 17 MET cc_start: 0.5201 (tpt) cc_final: 0.4951 (tpt) REVERT: N 65 MET cc_start: 0.5043 (mmm) cc_final: 0.4617 (mmm) REVERT: O 57 MET cc_start: 0.2855 (mmm) cc_final: 0.2425 (mmt) REVERT: Q 17 MET cc_start: 0.0453 (ptp) cc_final: -0.0387 (tpp) REVERT: R 28 ILE cc_start: 0.7604 (mt) cc_final: 0.7228 (tp) REVERT: S 16 MET cc_start: 0.6948 (mtp) cc_final: 0.6533 (ttp) REVERT: S 57 MET cc_start: 0.7032 (tmt) cc_final: 0.6766 (tpt) REVERT: S 61 ASP cc_start: 0.3217 (OUTLIER) cc_final: 0.2754 (p0) REVERT: X 1 MET cc_start: 0.3395 (mtm) cc_final: 0.3126 (mtm) REVERT: X 48 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.3747 (tp30) REVERT: X 63 ASP cc_start: 0.5426 (t0) cc_final: 0.4765 (m-30) REVERT: X 82 ARG cc_start: 0.8626 (ttt180) cc_final: 0.8120 (mmm160) REVERT: Y 24 TYR cc_start: 0.1194 (OUTLIER) cc_final: 0.0651 (m-80) REVERT: Y 98 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7608 (mtp180) REVERT: Y 113 ARG cc_start: 0.8948 (mtt-85) cc_final: 0.8595 (mmt180) REVERT: a 6 MET cc_start: 0.2806 (ttp) cc_final: 0.2307 (tmm) REVERT: a 46 MET cc_start: 0.3892 (mmm) cc_final: 0.3502 (mtp) REVERT: a 93 MET cc_start: 0.6105 (mmp) cc_final: 0.5654 (mtm) REVERT: a 97 LYS cc_start: 0.5770 (mttt) cc_final: 0.5490 (pptt) REVERT: a 115 MET cc_start: 0.1626 (ttt) cc_final: 0.1278 (mmm) REVERT: a 168 MET cc_start: 0.3360 (mmm) cc_final: 0.3026 (mtt) REVERT: a 196 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7004 (mt-10) outliers start: 56 outliers final: 35 residues processed: 307 average time/residue: 0.2297 time to fit residues: 117.2424 Evaluate side-chains 290 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 372 optimal weight: 0.0670 chunk 271 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 399 optimal weight: 50.0000 chunk 463 optimal weight: 7.9990 chunk 381 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 331 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 185 HIS a 214 ASN a 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.068768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044419 restraints weight = 203504.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045561 restraints weight = 97968.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046173 restraints weight = 61201.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046655 restraints weight = 46448.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046909 restraints weight = 39116.675| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37419 Z= 0.125 Angle : 0.622 12.772 50648 Z= 0.307 Chirality : 0.041 0.207 5902 Planarity : 0.004 0.052 6530 Dihedral : 5.990 129.915 5354 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 1.15 % Allowed : 15.22 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 4793 helix: 1.98 (0.10), residues: 2624 sheet: -0.02 (0.22), residues: 550 loop : -0.49 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 129 TYR 0.025 0.001 TYR H 63 PHE 0.020 0.001 PHE S 54 TRP 0.011 0.001 TRP a 235 HIS 0.005 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00265 (37419) covalent geometry : angle 0.62249 (50648) hydrogen bonds : bond 0.04188 ( 2152) hydrogen bonds : angle 4.16779 ( 6285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8552 (mmm) cc_final: 0.8155 (mmm) REVERT: A 86 MET cc_start: 0.8035 (ptp) cc_final: 0.7744 (ptp) REVERT: A 262 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: A 448 LEU cc_start: 0.9600 (mt) cc_final: 0.9375 (mt) REVERT: B 86 MET cc_start: 0.8489 (mtt) cc_final: 0.8152 (mtt) REVERT: B 103 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 419 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8953 (pttm) REVERT: C 468 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8478 (tp30) REVERT: D 0 MET cc_start: 0.7934 (ppp) cc_final: 0.7483 (ppp) REVERT: D 63 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8248 (ptm-80) REVERT: D 379 MET cc_start: 0.8420 (tpp) cc_final: 0.8015 (tmm) REVERT: F 86 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8245 (mtp180) REVERT: F 136 MET cc_start: 0.9415 (mmm) cc_final: 0.9067 (mmm) REVERT: F 209 MET cc_start: 0.8548 (ptp) cc_final: 0.8210 (mtm) REVERT: G 5 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7760 (p0) REVERT: H 95 MET cc_start: 0.6957 (tpt) cc_final: 0.6333 (tpp) REVERT: W 73 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: W 128 MET cc_start: 0.8789 (mmt) cc_final: 0.8553 (mmp) REVERT: I 11 MET cc_start: 0.6772 (tmm) cc_final: 0.6442 (tpt) REVERT: I 16 MET cc_start: 0.3294 (tmm) cc_final: 0.2839 (tmm) REVERT: I 19 LEU cc_start: 0.7936 (mt) cc_final: 0.7595 (tp) REVERT: J 17 MET cc_start: 0.4958 (mtp) cc_final: 0.3952 (tpp) REVERT: L 63 ILE cc_start: 0.5757 (mm) cc_final: 0.4712 (mt) REVERT: L 65 MET cc_start: 0.4772 (mmm) cc_final: 0.4402 (ppp) REVERT: M 6 MET cc_start: 0.4600 (mtp) cc_final: 0.4146 (ptt) REVERT: M 28 ILE cc_start: 0.6734 (mm) cc_final: 0.6390 (tt) REVERT: N 17 MET cc_start: 0.5152 (tpt) cc_final: 0.4747 (tpt) REVERT: N 65 MET cc_start: 0.5033 (mmm) cc_final: 0.4611 (mmm) REVERT: P 11 MET cc_start: 0.5175 (mmm) cc_final: 0.4648 (mmm) REVERT: Q 17 MET cc_start: 0.0251 (ptp) cc_final: -0.0637 (tpp) REVERT: R 28 ILE cc_start: 0.7577 (mt) cc_final: 0.7267 (tt) REVERT: S 16 MET cc_start: 0.6901 (mtp) cc_final: 0.6469 (ttp) REVERT: S 57 MET cc_start: 0.6995 (tmt) cc_final: 0.6680 (tmm) REVERT: X 1 MET cc_start: 0.3641 (mtm) cc_final: 0.3373 (mtp) REVERT: X 48 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4099 (tp30) REVERT: X 63 ASP cc_start: 0.5308 (t0) cc_final: 0.4598 (m-30) REVERT: X 82 ARG cc_start: 0.8671 (ttt180) cc_final: 0.8128 (mmm160) REVERT: Y 24 TYR cc_start: 0.1369 (OUTLIER) cc_final: 0.0865 (m-80) REVERT: Y 98 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7702 (mtp180) REVERT: Y 113 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8620 (mmt180) REVERT: a 6 MET cc_start: 0.2831 (ttp) cc_final: 0.2239 (tmm) REVERT: a 46 MET cc_start: 0.3880 (mmm) cc_final: 0.3503 (mtp) REVERT: a 93 MET cc_start: 0.6317 (mmp) cc_final: 0.5786 (mtm) REVERT: a 97 LYS cc_start: 0.5819 (mttt) cc_final: 0.5564 (pptt) REVERT: a 115 MET cc_start: 0.1538 (ttt) cc_final: 0.1066 (mmm) REVERT: a 153 MET cc_start: 0.0509 (mtm) cc_final: -0.0351 (ttt) REVERT: a 168 MET cc_start: 0.3365 (mmm) cc_final: 0.3098 (mtt) REVERT: a 196 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6993 (mt-10) outliers start: 44 outliers final: 29 residues processed: 299 average time/residue: 0.2365 time to fit residues: 117.5258 Evaluate side-chains 282 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 86 ARG Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 53 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 440 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 384 optimal weight: 30.0000 chunk 143 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 376 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN W 21 HIS W 82 ASN L 42 GLN a 15 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.043877 restraints weight = 205217.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.044079 restraints weight = 116852.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044578 restraints weight = 76238.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.044649 restraints weight = 52004.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044726 restraints weight = 54550.773| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 37419 Z= 0.293 Angle : 0.743 13.539 50648 Z= 0.371 Chirality : 0.044 0.186 5902 Planarity : 0.005 0.051 6530 Dihedral : 6.275 131.308 5352 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.20 % Allowed : 15.35 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4793 helix: 1.73 (0.10), residues: 2616 sheet: -0.13 (0.22), residues: 545 loop : -0.58 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 26 TYR 0.021 0.002 TYR H 63 PHE 0.019 0.002 PHE H 61 TRP 0.014 0.002 TRP a 231 HIS 0.008 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00654 (37419) covalent geometry : angle 0.74300 (50648) hydrogen bonds : bond 0.04847 ( 2152) hydrogen bonds : angle 4.48655 ( 6285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7802.63 seconds wall clock time: 134 minutes 51.76 seconds (8091.76 seconds total)