Starting phenix.real_space_refine on Mon Jul 6 15:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbv_27310/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_2026/8dbv_27310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbv_27310/07_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 8.99, per 1000 atoms: 0.24 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: 3.47 Conformation dependent library (CDL) restraints added in 1.3 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: 0.92 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: 7.27 Time building geometry restraints manager: 4.39 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: 21840 29.25 - 58.50: 698 58.50 - 87.76: 79 87.76 - 117.01: 5 117.01 - 146.26: 2 Dihedral angle restraints: 22624 sinusoidal: 8882 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 22621 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 33.580 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 14.508 146.259 13834 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/Z covalent geometry : bond 0.01004 / 0.49 (37419) covalent geometry : angle 1.22898 / 0.77 (50648) hydrogen bonds : bond 0.15937 / 10.75 ( 2152) hydrogen bonds : angle 6.55842 / 4.60 ( 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 : 1.468 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: 0.2534 time to fit residues: 216.8237 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 : 1.289 ------------------------------------------------------------------------------- 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... A 18 GLN 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.070127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046312 restraints weight = 205355.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047389 restraints weight = 105776.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047460 restraints weight = 61292.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.047832 restraints weight = 46851.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.047860 restraints weight = 41428.382| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37419 Z= 0.220 Angle : 0.710 11.529 50648 Z= 0.368 Chirality : 0.045 0.210 5902 Planarity : 0.005 0.057 6530 Dihedral : 6.760 139.677 5252 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.67 % Favored : 98.31 % Rotamer: Outliers : 1.99 % Allowed : 10.83 % Favored : 87.19 % 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: 0.34 (0.12), residues: 4793 helix: 0.98 (0.10), residues: 2609 sheet: -0.15 (0.22), residues: 526 loop : -0.75 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 41 TYR 0.021 0.002 TYR N 10 PHE 0.050 0.002 PHE S 54 TRP 0.020 0.002 TRP a 186 HIS 0.008 0.001 HIS H 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (37419) covalent geometry : angle 0.71033 / 0.37 (50648) hydrogen bonds : bond 0.06038 / 4.03 ( 2152) hydrogen bonds : angle 4.88069 / 3.43 ( 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 359 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 283 time to evaluate : 1.448 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: 0.8059 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: D 379 MET cc_start: 0.8319 (tpp) cc_final: 0.7942 (tmm) REVERT: E 193 MET cc_start: 0.8560 (mtm) cc_final: 0.8220 (mpp) REVERT: F 431 MET cc_start: 0.8618 (mtp) cc_final: 0.8400 (mtp) REVERT: H 52 ILE cc_start: 0.6499 (mm) cc_final: 0.6245 (mm) REVERT: H 58 HIS cc_start: 0.8259 (m-70) cc_final: 0.7872 (m-70) REVERT: H 75 ASN cc_start: 0.8611 (m-40) cc_final: 0.8326 (t0) REVERT: H 81 ASP cc_start: 0.7949 (m-30) cc_final: 0.7146 (t70) REVERT: H 99 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8528 (mmp-170) REVERT: H 100 LYS cc_start: 0.7148 (mttm) cc_final: 0.6913 (mttt) REVERT: H 109 HIS cc_start: 0.8298 (t70) cc_final: 0.8065 (m90) REVERT: W 16 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8159 (p0) REVERT: W 73 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: I 19 LEU cc_start: 0.8105 (mt) cc_final: 0.7684 (tp) REVERT: J 17 MET cc_start: 0.5786 (mtp) cc_final: 0.4181 (tpp) REVERT: J 61 ASP cc_start: 0.7039 (m-30) cc_final: 0.6507 (p0) REVERT: L 65 MET cc_start: 0.3320 (mmm) cc_final: 0.2493 (ppp) REVERT: M 6 MET cc_start: 0.4225 (mtp) cc_final: 0.3841 (ptt) REVERT: M 17 MET cc_start: 0.6965 (mtm) cc_final: 0.5261 (tpt) REVERT: M 42 GLN cc_start: 0.8179 (pt0) cc_final: 0.7567 (pp30) REVERT: N 11 MET cc_start: 0.5803 (tpp) cc_final: 0.5510 (tmm) REVERT: N 17 MET cc_start: 0.5774 (tpt) cc_final: 0.5531 (tpt) REVERT: O 53 PHE cc_start: 0.7930 (t80) cc_final: 0.7477 (t80) REVERT: P 61 ASP cc_start: 0.0759 (OUTLIER) cc_final: 0.0278 (t0) REVERT: S 16 MET cc_start: 0.6976 (mtp) cc_final: 0.6704 (ttm) REVERT: S 57 MET cc_start: 0.7161 (tmt) cc_final: 0.6875 (tpt) REVERT: S 75 MET cc_start: 0.2906 (ttt) cc_final: 0.2700 (mmt) REVERT: X 48 GLU cc_start: 0.4061 (OUTLIER) cc_final: 0.3590 (tt0) REVERT: X 63 ASP cc_start: 0.4236 (t0) cc_final: 0.3524 (m-30) REVERT: Y 96 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8252 (tm-30) REVERT: Y 98 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7452 (mtp180) REVERT: a 30 ASP cc_start: 0.6338 (t70) cc_final: 0.6125 (t0) REVERT: a 139 LEU cc_start: 0.1610 (OUTLIER) cc_final: 0.1215 (tt) REVERT: a 257 MET cc_start: 0.7197 (tmm) cc_final: 0.6663 (ptt) outliers start: 76 outliers final: 32 residues processed: 346 average time/residue: 0.2279 time to fit residues: 129.3487 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 : 1.130 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 155 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 chunk 471 optimal weight: 40.0000 chunk 218 optimal weight: 4.9990 chunk 158 optimal weight: 0.0270 chunk 410 optimal weight: 40.0000 chunk 129 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS G 186 GLN W 28 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN R 3 ASN a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.069892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047084 restraints weight = 210563.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047420 restraints weight = 107434.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.047713 restraints weight = 67984.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047813 restraints weight = 54962.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047804 restraints weight = 49227.782| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 37419 Z= 0.184 Angle : 0.637 12.086 50648 Z= 0.325 Chirality : 0.042 0.166 5902 Planarity : 0.004 0.060 6530 Dihedral : 6.247 134.603 5237 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 1.99 % Allowed : 12.21 % Favored : 85.80 % 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: 0.84 (0.12), residues: 4793 helix: 1.44 (0.10), residues: 2621 sheet: 0.01 (0.23), residues: 498 loop : -0.60 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 221 TYR 0.013 0.001 TYR C 236 PHE 0.046 0.002 PHE S 54 TRP 0.013 0.001 TRP a 186 HIS 0.006 0.001 HIS H 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (37419) covalent geometry : angle 0.63692 / 0.33 (50648) hydrogen bonds : bond 0.05381 / 3.57 ( 2152) hydrogen bonds : angle 4.57627 / 3.22 ( 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 340 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 264 time to evaluate : 1.489 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: 0.8199 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: B 86 MET cc_start: 0.8549 (mtt) cc_final: 0.8135 (mtt) REVERT: B 419 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9180 (ptpp) REVERT: C 468 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8830 (tp30) REVERT: C 472 LEU cc_start: 0.9345 (pp) cc_final: 0.9048 (pp) REVERT: D 0 MET cc_start: 0.7861 (ppp) cc_final: 0.7448 (ppp) REVERT: D 63 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8462 (ptm-80) REVERT: D 379 MET cc_start: 0.8343 (tpp) cc_final: 0.7942 (tmm) REVERT: D 445 MET cc_start: 0.8765 (mmt) cc_final: 0.8525 (mmt) REVERT: E 287 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.9009 (p) REVERT: H 58 HIS cc_start: 0.8336 (m-70) cc_final: 0.8060 (m-70) REVERT: H 75 ASN cc_start: 0.8618 (m-40) cc_final: 0.8316 (t0) REVERT: H 100 LYS cc_start: 0.6990 (mttm) cc_final: 0.6773 (mtmt) REVERT: I 19 LEU cc_start: 0.8115 (mt) cc_final: 0.7721 (tp) REVERT: J 17 MET cc_start: 0.5748 (mtp) cc_final: 0.4373 (tpp) REVERT: J 61 ASP cc_start: 0.6620 (m-30) cc_final: 0.6355 (p0) REVERT: L 65 MET cc_start: 0.3552 (mmm) cc_final: 0.2848 (ppp) REVERT: M 6 MET cc_start: 0.4291 (mtp) cc_final: 0.3885 (ptt) REVERT: M 17 MET cc_start: 0.6936 (mtm) cc_final: 0.5169 (tpt) REVERT: N 11 MET cc_start: 0.5777 (tpp) cc_final: 0.5397 (tmm) REVERT: N 65 MET cc_start: 0.4194 (mmm) cc_final: 0.3534 (mmm) REVERT: P 16 MET cc_start: 0.6882 (ttt) cc_final: 0.5867 (tpp) REVERT: P 17 MET cc_start: 0.7147 (mpp) cc_final: 0.6927 (mmp) REVERT: P 61 ASP cc_start: 0.0953 (OUTLIER) cc_final: 0.0476 (t0) REVERT: R 17 MET cc_start: 0.2409 (mpp) cc_final: 0.2086 (mpp) REVERT: R 57 MET cc_start: 0.7477 (tmm) cc_final: 0.6630 (mmm) REVERT: S 16 MET cc_start: 0.6978 (mtp) cc_final: 0.6719 (ttm) REVERT: S 57 MET cc_start: 0.7208 (tmt) cc_final: 0.6944 (tpt) REVERT: X 48 GLU cc_start: 0.4392 (OUTLIER) cc_final: 0.3977 (tt0) REVERT: X 63 ASP cc_start: 0.4415 (t0) cc_final: 0.3638 (m-30) REVERT: Y 24 TYR cc_start: 0.1326 (OUTLIER) cc_final: 0.0566 (m-80) REVERT: Y 98 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7541 (mtp180) REVERT: Y 113 ARG cc_start: 0.8863 (mtt-85) cc_final: 0.8485 (mmt180) REVERT: a 46 MET cc_start: 0.3938 (mmm) cc_final: 0.3566 (mtt) REVERT: a 139 LEU cc_start: 0.1694 (OUTLIER) cc_final: 0.1443 (tt) REVERT: a 196 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6763 (mt-10) REVERT: a 257 MET cc_start: 0.7416 (tmm) cc_final: 0.7106 (ptm) outliers start: 76 outliers final: 34 residues processed: 325 average time/residue: 0.2279 time to fit residues: 122.9320 Evaluate side-chains 280 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 456 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 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 102 MET Chi-restraints excluded: chain H residue 4 TYR 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 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 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: 10.0000 chunk 421 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 391 optimal weight: 30.0000 chunk 109 optimal weight: 8.9990 chunk 398 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN B 420 GLN C 172 GLN F 7 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN X 37 GLN a 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.068469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.044915 restraints weight = 204421.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.045699 restraints weight = 104766.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045766 restraints weight = 66129.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045970 restraints weight = 47779.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046026 restraints weight = 43404.198| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37419 Z= 0.239 Angle : 0.661 15.279 50648 Z= 0.335 Chirality : 0.043 0.162 5902 Planarity : 0.005 0.049 6530 Dihedral : 5.908 126.784 5235 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 12.87 % Favored : 84.91 % 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: 0.94 (0.12), residues: 4793 helix: 1.57 (0.10), residues: 2619 sheet: -0.07 (0.22), residues: 527 loop : -0.61 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 99 TYR 0.016 0.002 TYR N 10 PHE 0.038 0.002 PHE S 54 TRP 0.011 0.002 TRP a 231 HIS 0.005 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (37419) covalent geometry : angle 0.66106 / 0.34 (50648) hydrogen bonds : bond 0.05129 / 3.42 ( 2152) hydrogen bonds : angle 4.53066 / 3.18 ( 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 340 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 255 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: B 86 MET cc_start: 0.8506 (mtt) cc_final: 0.8040 (mtt) REVERT: B 103 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 156 MET cc_start: 0.9110 (tpp) cc_final: 0.8838 (mmt) REVERT: C 48 MET cc_start: 0.8548 (ptp) cc_final: 0.8244 (ptt) REVERT: D 63 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (ptm-80) REVERT: D 379 MET cc_start: 0.8431 (tpp) cc_final: 0.8062 (tmm) REVERT: E 287 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8980 (p) REVERT: G 155 MET cc_start: 0.8690 (tpp) cc_final: 0.8440 (tpp) REVERT: H 58 HIS cc_start: 0.8188 (m-70) cc_final: 0.7933 (m-70) REVERT: H 75 ASN cc_start: 0.8547 (m-40) cc_final: 0.8219 (t0) REVERT: I 19 LEU cc_start: 0.8050 (mt) cc_final: 0.7649 (tp) REVERT: J 17 MET cc_start: 0.5553 (mtp) cc_final: 0.4206 (tpp) REVERT: L 65 MET cc_start: 0.4129 (mmm) cc_final: 0.3418 (ppp) REVERT: M 6 MET cc_start: 0.4393 (mtp) cc_final: 0.4012 (ptt) REVERT: N 11 MET cc_start: 0.5806 (tpp) cc_final: 0.5537 (tmm) REVERT: N 65 MET cc_start: 0.4611 (mmm) cc_final: 0.3973 (mmm) REVERT: P 16 MET cc_start: 0.6798 (ttt) cc_final: 0.6137 (ttm) REVERT: P 61 ASP cc_start: 0.1512 (OUTLIER) cc_final: 0.1127 (t0) REVERT: S 16 MET cc_start: 0.7109 (mtp) cc_final: 0.6812 (ttm) REVERT: S 57 MET cc_start: 0.7309 (tmt) cc_final: 0.7026 (tpt) REVERT: X 48 GLU cc_start: 0.4470 (OUTLIER) cc_final: 0.4119 (tt0) REVERT: X 63 ASP cc_start: 0.4774 (t0) cc_final: 0.3974 (m-30) REVERT: Y 24 TYR cc_start: 0.1234 (OUTLIER) cc_final: 0.0522 (m-80) REVERT: Y 98 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7519 (mtp180) REVERT: Y 113 ARG cc_start: 0.8939 (mtt-85) cc_final: 0.8537 (mmt180) REVERT: a 46 MET cc_start: 0.3834 (mmm) cc_final: 0.3438 (mtt) REVERT: a 115 MET cc_start: 0.1709 (ttm) cc_final: 0.0671 (ptp) REVERT: a 168 MET cc_start: 0.3506 (mmm) cc_final: 0.3079 (mtt) REVERT: a 196 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6854 (mt-10) outliers start: 85 outliers final: 40 residues processed: 326 average time/residue: 0.2317 time to fit residues: 124.7971 Evaluate side-chains 282 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 420 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 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 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 100 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 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 102 MET Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR 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 O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 16 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 146 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 349 optimal weight: 40.0000 chunk 459 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 GLN I 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN Y 85 GLN a 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.068496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044731 restraints weight = 203972.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.045895 restraints weight = 104903.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.045888 restraints weight = 68073.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.046303 restraints weight = 51963.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046404 restraints weight = 44727.610| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37419 Z= 0.203 Angle : 0.620 11.015 50648 Z= 0.314 Chirality : 0.042 0.241 5902 Planarity : 0.004 0.051 6530 Dihedral : 5.642 130.455 5232 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 2.12 % Allowed : 13.52 % Favored : 84.36 % 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: 1.06 (0.12), residues: 4793 helix: 1.69 (0.10), residues: 2619 sheet: -0.08 (0.22), residues: 527 loop : -0.59 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 121 TYR 0.013 0.001 TYR C 236 PHE 0.031 0.001 PHE S 54 TRP 0.011 0.001 TRP G 203 HIS 0.005 0.001 HIS G 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (37419) covalent geometry : angle 0.61975 / 0.31 (50648) hydrogen bonds : bond 0.04847 / 3.23 ( 2152) hydrogen bonds : angle 4.41259 / 3.11 ( 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 327 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 246 time to evaluate : 1.494 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 18 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8581 (pt0) REVERT: A 262 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: B 86 MET cc_start: 0.8445 (mtt) cc_final: 0.8038 (mtt) REVERT: B 103 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 156 MET cc_start: 0.9139 (tpp) cc_final: 0.8846 (mmt) REVERT: C 48 MET cc_start: 0.8472 (ptp) cc_final: 0.8264 (ptt) REVERT: D 0 MET cc_start: 0.7832 (ppp) cc_final: 0.7385 (ppp) REVERT: D 63 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8423 (ptm-80) REVERT: D 371 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8104 (mtmm) REVERT: D 379 MET cc_start: 0.8485 (tpp) cc_final: 0.8061 (tmm) REVERT: E 246 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8418 (mtt90) REVERT: E 287 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8912 (p) REVERT: F 86 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8309 (mtp180) REVERT: F 136 MET cc_start: 0.9345 (mmm) cc_final: 0.9123 (mmm) REVERT: H 58 HIS cc_start: 0.8245 (m-70) cc_final: 0.8020 (m-70) REVERT: W 73 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: I 19 LEU cc_start: 0.7978 (mt) cc_final: 0.7561 (tp) REVERT: J 17 MET cc_start: 0.5537 (mtp) cc_final: 0.4211 (tpp) REVERT: L 65 MET cc_start: 0.4467 (mmm) cc_final: 0.3852 (ppp) REVERT: M 6 MET cc_start: 0.4477 (mtp) cc_final: 0.4067 (ptt) REVERT: N 11 MET cc_start: 0.5655 (tpp) cc_final: 0.5434 (tmm) REVERT: P 16 MET cc_start: 0.6686 (ttt) cc_final: 0.6112 (ttm) REVERT: P 17 MET cc_start: 0.6693 (mmm) cc_final: 0.6325 (mmm) REVERT: P 61 ASP cc_start: 0.1640 (OUTLIER) cc_final: 0.1228 (t0) REVERT: P 68 VAL cc_start: 0.5385 (t) cc_final: 0.5077 (p) REVERT: R 28 ILE cc_start: 0.7784 (mt) cc_final: 0.7440 (tp) REVERT: S 16 MET cc_start: 0.7110 (mtp) cc_final: 0.6816 (ttp) REVERT: S 57 MET cc_start: 0.7226 (tmt) cc_final: 0.6914 (tpt) REVERT: S 61 ASP cc_start: 0.3044 (OUTLIER) cc_final: 0.2457 (p0) REVERT: X 48 GLU cc_start: 0.4543 (OUTLIER) cc_final: 0.3479 (tp30) REVERT: X 63 ASP cc_start: 0.4756 (t0) cc_final: 0.3953 (m-30) REVERT: Y 24 TYR cc_start: 0.1349 (OUTLIER) cc_final: 0.0641 (m-80) REVERT: Y 98 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7541 (mtp180) REVERT: Y 113 ARG cc_start: 0.8969 (mtt-85) cc_final: 0.8691 (mmt-90) REVERT: a 32 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5673 (mp10) REVERT: a 46 MET cc_start: 0.3825 (mmm) cc_final: 0.3477 (mtp) REVERT: a 196 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6887 (mt-10) outliers start: 81 outliers final: 36 residues processed: 320 average time/residue: 0.2173 time to fit residues: 115.3426 Evaluate side-chains 288 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 146 VAL 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 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 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 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 101 GLU Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 16 MET 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 44 LEU Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 32 GLN 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: 7.9990 chunk 297 optimal weight: 8.9990 chunk 382 optimal weight: 40.0000 chunk 84 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 359 optimal weight: 6.9990 chunk 263 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 5 ASN X 51 HIS a 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.069362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046559 restraints weight = 208325.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047343 restraints weight = 103515.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.047412 restraints weight = 61888.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047618 restraints weight = 49546.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047638 restraints weight = 43764.946| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37419 Z= 0.129 Angle : 0.584 10.325 50648 Z= 0.294 Chirality : 0.041 0.158 5902 Planarity : 0.004 0.054 6530 Dihedral : 5.386 132.307 5232 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 1.70 % Allowed : 14.02 % Favored : 84.28 % 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: 1.27 (0.12), residues: 4793 helix: 1.86 (0.10), residues: 2620 sheet: 0.08 (0.23), residues: 514 loop : -0.53 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 99 TYR 0.012 0.001 TYR a 11 PHE 0.029 0.001 PHE S 54 TRP 0.009 0.001 TRP G 203 HIS 0.004 0.001 HIS G 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (37419) covalent geometry : angle 0.58376 / 0.29 (50648) hydrogen bonds : bond 0.04491 / 2.98 ( 2152) hydrogen bonds : angle 4.25409 / 3.00 ( 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: 65 poor density : 259 time to evaluate : 1.495 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 18 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: A 262 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 448 LEU cc_start: 0.9591 (mt) cc_final: 0.9370 (mt) REVERT: B 86 MET cc_start: 0.8472 (mtt) cc_final: 0.8058 (mtt) REVERT: B 103 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8652 (pp) REVERT: C 48 MET cc_start: 0.8423 (ptp) cc_final: 0.8209 (ptt) REVERT: C 318 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8587 (mtmt) REVERT: C 468 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8695 (tp30) REVERT: D 0 MET cc_start: 0.7818 (ppp) cc_final: 0.7380 (ppp) REVERT: D 63 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8358 (ptm-80) REVERT: D 371 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8083 (mtmm) REVERT: D 379 MET cc_start: 0.8516 (tpp) cc_final: 0.8078 (tmm) REVERT: E 287 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8867 (p) REVERT: E 445 MET cc_start: 0.8501 (mmm) cc_final: 0.8134 (mmm) REVERT: F 86 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8240 (mtp180) REVERT: F 136 MET cc_start: 0.9361 (mmm) cc_final: 0.9092 (mmm) REVERT: G 5 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7729 (p0) REVERT: G 116 MET cc_start: 0.7191 (mmp) cc_final: 0.6921 (mmp) REVERT: G 155 MET cc_start: 0.8769 (tpp) cc_final: 0.8523 (tpp) REVERT: W 73 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: I 19 LEU cc_start: 0.7964 (mt) cc_final: 0.7600 (tp) REVERT: J 17 MET cc_start: 0.5661 (mtp) cc_final: 0.4468 (tpp) REVERT: L 65 MET cc_start: 0.4719 (mmm) cc_final: 0.4140 (ppp) REVERT: M 6 MET cc_start: 0.4427 (mtp) cc_final: 0.3874 (ptt) REVERT: N 11 MET cc_start: 0.5687 (tpp) cc_final: 0.5442 (tmm) REVERT: P 16 MET cc_start: 0.6971 (ttt) cc_final: 0.6309 (ttm) REVERT: P 17 MET cc_start: 0.6882 (mmm) cc_final: 0.6494 (mmm) REVERT: P 61 ASP cc_start: 0.1871 (OUTLIER) cc_final: 0.1487 (t0) REVERT: P 68 VAL cc_start: 0.5365 (t) cc_final: 0.5041 (p) REVERT: R 28 ILE cc_start: 0.7834 (mt) cc_final: 0.7531 (tp) REVERT: S 16 MET cc_start: 0.7157 (mtp) cc_final: 0.6865 (ttp) REVERT: S 57 MET cc_start: 0.7156 (tmt) cc_final: 0.6864 (tpt) REVERT: S 61 ASP cc_start: 0.3264 (OUTLIER) cc_final: 0.2697 (p0) REVERT: X 48 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.3449 (tp30) REVERT: X 63 ASP cc_start: 0.4847 (t0) cc_final: 0.4060 (m-30) REVERT: X 82 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8111 (mmm160) REVERT: Y 24 TYR cc_start: 0.1294 (OUTLIER) cc_final: 0.0576 (m-80) REVERT: Y 98 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7564 (mtp180) REVERT: Y 113 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8603 (mmt180) REVERT: a 6 MET cc_start: 0.3901 (ppp) cc_final: 0.2828 (tmm) REVERT: a 46 MET cc_start: 0.3757 (mmm) cc_final: 0.3404 (mtp) REVERT: a 168 MET cc_start: 0.3464 (mmm) cc_final: 0.3020 (mtt) REVERT: a 196 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6958 (mt-10) outliers start: 65 outliers final: 31 residues processed: 312 average time/residue: 0.2164 time to fit residues: 111.4691 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 : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 146 VAL 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 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 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 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 H residue 4 TYR Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 16 MET 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 32 GLN 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: 0.9980 chunk 24 optimal weight: 7.9990 chunk 464 optimal weight: 0.3980 chunk 245 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 182 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 372 optimal weight: 0.0470 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 479 HIS H 5 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS a 15 HIS a 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.070185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.047365 restraints weight = 208973.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.048117 restraints weight = 105822.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.048344 restraints weight = 66040.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048628 restraints weight = 48117.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048615 restraints weight = 42709.998| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37419 Z= 0.110 Angle : 0.579 10.115 50648 Z= 0.288 Chirality : 0.040 0.158 5902 Planarity : 0.004 0.055 6530 Dihedral : 5.128 132.463 5232 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % 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: 1.41 (0.12), residues: 4793 helix: 1.98 (0.10), residues: 2627 sheet: 0.08 (0.23), residues: 534 loop : -0.46 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 246 TYR 0.014 0.001 TYR F 247 PHE 0.025 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/Z covalent geometry : bond 0.00221 / 0.11 (37419) covalent geometry : angle 0.57934 / 0.29 (50648) hydrogen bonds : bond 0.04121 / 2.72 ( 2152) hydrogen bonds : angle 4.09960 / 2.89 ( 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 322 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.406 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: A 18 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: A 48 MET cc_start: 0.8545 (mmm) cc_final: 0.8138 (mmm) REVERT: A 262 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: A 448 LEU cc_start: 0.9596 (mt) cc_final: 0.9369 (mt) REVERT: B 86 MET cc_start: 0.8459 (mtt) cc_final: 0.8057 (mtt) REVERT: B 103 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8497 (pp) REVERT: C 468 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8734 (tp30) REVERT: D 0 MET cc_start: 0.7836 (ppp) cc_final: 0.7371 (ppp) REVERT: D 63 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8180 (ptm-80) REVERT: D 371 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8093 (mtmm) REVERT: D 379 MET cc_start: 0.8486 (tpp) cc_final: 0.8079 (tmm) REVERT: E 287 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8807 (p) REVERT: F 86 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8189 (mtp180) REVERT: F 136 MET cc_start: 0.9384 (mmm) cc_final: 0.9057 (mmm) REVERT: G 5 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7721 (p0) REVERT: G 116 MET cc_start: 0.7206 (mmp) cc_final: 0.7003 (mmp) REVERT: G 155 MET cc_start: 0.8836 (tpp) cc_final: 0.8567 (tpp) REVERT: I 11 MET cc_start: 0.6200 (tmm) cc_final: 0.5930 (tpt) REVERT: I 19 LEU cc_start: 0.7947 (mt) cc_final: 0.7618 (tp) REVERT: J 17 MET cc_start: 0.5755 (mtp) cc_final: 0.4567 (tpp) REVERT: L 65 MET cc_start: 0.4745 (mmm) cc_final: 0.4253 (ppp) REVERT: M 6 MET cc_start: 0.4320 (mtp) cc_final: 0.3841 (ptt) REVERT: N 11 MET cc_start: 0.5730 (tpp) cc_final: 0.5477 (tmm) REVERT: N 65 MET cc_start: 0.5221 (mmm) cc_final: 0.4887 (mmm) REVERT: P 16 MET cc_start: 0.7046 (ttt) cc_final: 0.6387 (ttm) REVERT: P 17 MET cc_start: 0.6983 (mmm) cc_final: 0.6464 (mmm) REVERT: P 68 VAL cc_start: 0.5654 (t) cc_final: 0.5351 (p) REVERT: Q 17 MET cc_start: 0.1690 (ptp) cc_final: 0.1294 (tmm) REVERT: R 28 ILE cc_start: 0.7801 (mt) cc_final: 0.7468 (tp) REVERT: S 16 MET cc_start: 0.7022 (mtp) cc_final: 0.6699 (ttp) REVERT: S 35 PHE cc_start: 0.6714 (t80) cc_final: 0.6191 (t80) REVERT: S 57 MET cc_start: 0.7152 (tmt) cc_final: 0.6872 (tpt) REVERT: S 61 ASP cc_start: 0.3472 (OUTLIER) cc_final: 0.2951 (p0) REVERT: X 1 MET cc_start: 0.2575 (mtm) cc_final: 0.2196 (mtm) REVERT: X 48 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4035 (tp30) REVERT: X 63 ASP cc_start: 0.4958 (t0) cc_final: 0.4202 (m-30) REVERT: X 82 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8104 (mmm160) REVERT: Y 24 TYR cc_start: 0.1241 (OUTLIER) cc_final: 0.0525 (m-80) REVERT: Y 98 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7520 (mtp180) REVERT: Y 113 ARG cc_start: 0.8957 (mtt-85) cc_final: 0.8572 (mmt180) REVERT: a 6 MET cc_start: 0.3957 (ppp) cc_final: 0.2815 (tmm) REVERT: a 7 THR cc_start: 0.5035 (OUTLIER) cc_final: 0.4652 (t) REVERT: a 32 GLN cc_start: 0.6235 (mp10) cc_final: 0.6020 (mp10) REVERT: a 46 MET cc_start: 0.3742 (mmm) cc_final: 0.3349 (mtp) REVERT: a 93 MET cc_start: 0.6870 (mmm) cc_final: 0.6440 (mtm) REVERT: a 168 MET cc_start: 0.3453 (mmm) cc_final: 0.3010 (mtt) REVERT: a 196 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6905 (mt-10) outliers start: 58 outliers final: 30 residues processed: 316 average time/residue: 0.2246 time to fit residues: 117.7204 Evaluate side-chains 284 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 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 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 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 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 H residue 4 TYR Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain N residue 63 ILE 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 7 THR 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: 0.0050 chunk 434 optimal weight: 8.9990 chunk 95 optimal weight: 0.0020 chunk 126 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 448 optimal weight: 50.0000 chunk 198 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 overall best weight: 2.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS E 243 ASN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN a 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.069372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045325 restraints weight = 208174.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.046489 restraints weight = 96760.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.047173 restraints weight = 59409.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.047608 restraints weight = 44337.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.047821 restraints weight = 37454.725| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37419 Z= 0.142 Angle : 0.593 10.682 50648 Z= 0.295 Chirality : 0.041 0.176 5902 Planarity : 0.004 0.051 6530 Dihedral : 5.096 132.366 5232 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 1.67 % Allowed : 14.51 % Favored : 83.81 % 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: 1.46 (0.12), residues: 4793 helix: 2.04 (0.10), residues: 2628 sheet: 0.02 (0.22), residues: 538 loop : -0.43 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 129 TYR 0.013 0.001 TYR H 63 PHE 0.021 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/Z covalent geometry : bond 0.00310 / 0.14 (37419) covalent geometry : angle 0.59296 / 0.29 (50648) hydrogen bonds : bond 0.04184 / 2.78 ( 2152) hydrogen bonds : angle 4.11797 / 2.90 ( 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 317 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 1.376 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: A 18 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: A 48 MET cc_start: 0.8484 (mmm) cc_final: 0.8019 (mmm) REVERT: A 262 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: A 448 LEU cc_start: 0.9578 (mt) cc_final: 0.9360 (mt) REVERT: B 86 MET cc_start: 0.8466 (mtt) cc_final: 0.8139 (mtt) REVERT: B 103 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8612 (pp) REVERT: C 318 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8488 (mtmt) REVERT: C 468 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8620 (tp30) REVERT: D 0 MET cc_start: 0.7828 (ppp) cc_final: 0.7354 (ppp) REVERT: D 63 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8256 (ptm-80) REVERT: D 371 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8165 (mtmm) REVERT: D 379 MET cc_start: 0.8447 (tpp) cc_final: 0.8086 (tmm) REVERT: E 287 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8860 (p) REVERT: F 86 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8284 (mtp180) REVERT: F 136 MET cc_start: 0.9400 (mmm) cc_final: 0.9049 (mmm) REVERT: F 209 MET cc_start: 0.8559 (ptp) cc_final: 0.8058 (mtm) REVERT: W 73 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: W 76 ILE cc_start: 0.8987 (pt) cc_final: 0.8516 (mp) REVERT: I 11 MET cc_start: 0.6508 (tmm) cc_final: 0.6151 (tpt) REVERT: I 19 LEU cc_start: 0.8052 (mt) cc_final: 0.7742 (tp) REVERT: J 17 MET cc_start: 0.5349 (mtp) cc_final: 0.4274 (tpp) REVERT: L 65 MET cc_start: 0.4769 (mmm) cc_final: 0.4319 (ppp) REVERT: M 6 MET cc_start: 0.4330 (mtp) cc_final: 0.3892 (ptt) REVERT: M 17 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.4227 (tmm) REVERT: N 65 MET cc_start: 0.5030 (mmm) cc_final: 0.4641 (mmm) REVERT: P 16 MET cc_start: 0.6629 (ttt) cc_final: 0.6035 (ttm) REVERT: P 17 MET cc_start: 0.6987 (mmm) cc_final: 0.6699 (mmm) REVERT: P 68 VAL cc_start: 0.5068 (t) cc_final: 0.4750 (m) REVERT: R 28 ILE cc_start: 0.7771 (mt) cc_final: 0.7446 (tp) REVERT: S 16 MET cc_start: 0.7126 (mtp) cc_final: 0.6622 (ttp) REVERT: S 35 PHE cc_start: 0.6435 (t80) cc_final: 0.5925 (t80) REVERT: S 57 MET cc_start: 0.6964 (tmt) cc_final: 0.6691 (tpt) REVERT: S 61 ASP cc_start: 0.3048 (OUTLIER) cc_final: 0.2498 (p0) REVERT: X 1 MET cc_start: 0.3538 (mtm) cc_final: 0.2884 (mtm) REVERT: X 48 GLU cc_start: 0.4703 (OUTLIER) cc_final: 0.3943 (tp30) REVERT: X 63 ASP cc_start: 0.5374 (t0) cc_final: 0.4678 (m-30) REVERT: X 82 ARG cc_start: 0.8636 (ttt180) cc_final: 0.8092 (mmm160) REVERT: Y 24 TYR cc_start: 0.1282 (OUTLIER) cc_final: 0.0776 (m-80) REVERT: Y 98 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7701 (mtp180) REVERT: Y 113 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8580 (mmt180) REVERT: a 6 MET cc_start: 0.4645 (ppp) cc_final: 0.3080 (tmm) REVERT: a 46 MET cc_start: 0.3849 (mmm) cc_final: 0.3470 (mtp) REVERT: a 93 MET cc_start: 0.6847 (mmm) cc_final: 0.6288 (mtm) REVERT: a 115 MET cc_start: 0.1525 (ttt) cc_final: 0.1213 (mmm) REVERT: a 196 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6824 (mt-10) outliers start: 64 outliers final: 33 residues processed: 312 average time/residue: 0.2096 time to fit residues: 108.6952 Evaluate side-chains 289 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 504 LEU 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 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 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 282 ILE Chi-restraints excluded: chain F residue 370 LEU 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 H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain N residue 63 ILE 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: 9.9990 chunk 41 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 287 optimal weight: 0.2980 chunk 349 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 451 optimal weight: 7.9990 chunk 415 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.068546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045143 restraints weight = 205125.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.046677 restraints weight = 102938.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.046339 restraints weight = 49587.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046522 restraints weight = 47291.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.046536 restraints weight = 43949.032| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37419 Z= 0.174 Angle : 0.625 10.760 50648 Z= 0.310 Chirality : 0.042 0.184 5902 Planarity : 0.004 0.052 6530 Dihedral : 5.136 132.630 5230 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 1.36 % Allowed : 15.14 % Favored : 83.50 % 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: 1.43 (0.12), residues: 4793 helix: 2.01 (0.10), residues: 2623 sheet: -0.00 (0.22), residues: 538 loop : -0.44 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 129 TYR 0.019 0.001 TYR a 216 PHE 0.019 0.001 PHE E 189 TRP 0.010 0.001 TRP a 235 HIS 0.006 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (37419) covalent geometry : angle 0.62451 / 0.31 (50648) hydrogen bonds : bond 0.04305 / 2.86 ( 2152) hydrogen bonds : angle 4.21072 / 2.97 ( 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 302 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 1.463 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 18 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: A 48 MET cc_start: 0.8496 (mmm) cc_final: 0.8052 (mmm) REVERT: A 262 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 448 LEU cc_start: 0.9615 (mt) cc_final: 0.9399 (mt) REVERT: B 103 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8605 (pp) REVERT: C 318 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8558 (mtmt) REVERT: C 468 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8716 (tp30) REVERT: D 0 MET cc_start: 0.7811 (ppp) cc_final: 0.7423 (ppp) REVERT: D 63 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8285 (ptm-80) REVERT: D 371 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8036 (mtmm) REVERT: D 379 MET cc_start: 0.8414 (tpp) cc_final: 0.7961 (tmm) REVERT: E 287 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8849 (p) REVERT: F 86 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8260 (mtp180) REVERT: F 136 MET cc_start: 0.9402 (mmm) cc_final: 0.9042 (mmm) REVERT: F 209 MET cc_start: 0.8525 (ptp) cc_final: 0.8162 (mtm) REVERT: G 5 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7802 (p0) REVERT: G 116 MET cc_start: 0.7235 (mmp) cc_final: 0.7032 (mmp) REVERT: W 73 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: W 76 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8762 (mp) REVERT: W 128 MET cc_start: 0.8877 (mmt) cc_final: 0.8621 (mmp) REVERT: I 11 MET cc_start: 0.6379 (tmm) cc_final: 0.6090 (tpt) REVERT: I 19 LEU cc_start: 0.7889 (mt) cc_final: 0.7517 (tp) REVERT: J 17 MET cc_start: 0.5365 (mtp) cc_final: 0.4298 (tpp) REVERT: L 63 ILE cc_start: 0.6239 (mm) cc_final: 0.5067 (mt) REVERT: L 65 MET cc_start: 0.4688 (mmm) cc_final: 0.4329 (ppp) REVERT: M 6 MET cc_start: 0.4624 (mtp) cc_final: 0.4165 (ptt) REVERT: N 65 MET cc_start: 0.5406 (mmm) cc_final: 0.4867 (mmm) REVERT: P 16 MET cc_start: 0.6834 (ttt) cc_final: 0.6188 (ttm) REVERT: P 68 VAL cc_start: 0.4655 (t) cc_final: 0.4432 (p) REVERT: Q 17 MET cc_start: 0.1204 (ptp) cc_final: 0.0624 (tmm) REVERT: R 28 ILE cc_start: 0.7793 (mt) cc_final: 0.7459 (tp) REVERT: S 16 MET cc_start: 0.6999 (mtp) cc_final: 0.6658 (ttp) REVERT: S 57 MET cc_start: 0.7159 (tmt) cc_final: 0.6874 (tpt) REVERT: S 61 ASP cc_start: 0.3274 (OUTLIER) cc_final: 0.2686 (p0) REVERT: X 1 MET cc_start: 0.2915 (mtm) cc_final: 0.2483 (mtm) REVERT: X 48 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4106 (tp30) REVERT: X 63 ASP cc_start: 0.5257 (t0) cc_final: 0.4529 (m-30) REVERT: X 82 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8132 (mmm160) REVERT: Y 24 TYR cc_start: 0.1123 (OUTLIER) cc_final: 0.0439 (m-80) REVERT: Y 98 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7494 (mtp180) REVERT: Y 113 ARG cc_start: 0.8988 (mtt-85) cc_final: 0.8625 (mmt180) REVERT: a 6 MET cc_start: 0.4665 (ppp) cc_final: 0.3097 (tmm) REVERT: a 46 MET cc_start: 0.3700 (mmm) cc_final: 0.3255 (mtp) REVERT: a 97 LYS cc_start: 0.5456 (mttt) cc_final: 0.5204 (pptt) REVERT: a 115 MET cc_start: 0.1510 (ttt) cc_final: 0.1201 (mmm) REVERT: a 168 MET cc_start: 0.3336 (mmm) cc_final: 0.2899 (mtt) REVERT: a 196 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6988 (mt-10) outliers start: 52 outliers final: 32 residues processed: 299 average time/residue: 0.2266 time to fit residues: 112.6041 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 : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 412 ASP 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 132 VAL 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 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 W residue 39 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 76 ILE Chi-restraints excluded: chain N residue 63 ILE 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: 0.5980 chunk 271 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 399 optimal weight: 50.0000 chunk 463 optimal weight: 7.9990 chunk 381 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 32 GLN a 185 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.068530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045354 restraints weight = 203778.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.046317 restraints weight = 110592.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.046170 restraints weight = 61509.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046271 restraints weight = 54958.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046353 restraints weight = 49037.884| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37419 Z= 0.152 Angle : 0.628 10.790 50648 Z= 0.311 Chirality : 0.041 0.261 5902 Planarity : 0.004 0.057 6530 Dihedral : 5.096 131.184 5230 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 1.28 % Allowed : 15.59 % Favored : 83.13 % 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: 1.44 (0.12), residues: 4793 helix: 2.02 (0.10), residues: 2624 sheet: 0.08 (0.22), residues: 543 loop : -0.47 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 129 TYR 0.019 0.001 TYR a 216 PHE 0.020 0.001 PHE F 189 TRP 0.011 0.001 TRP a 235 HIS 0.004 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (37419) covalent geometry : angle 0.62764 / 0.31 (50648) hydrogen bonds : bond 0.04207 / 2.80 ( 2152) hydrogen bonds : angle 4.18736 / 2.95 ( 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 298 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 1.424 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 18 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: A 48 MET cc_start: 0.8590 (mmm) cc_final: 0.8073 (mmm) REVERT: A 262 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: A 448 LEU cc_start: 0.9656 (mt) cc_final: 0.9422 (mt) REVERT: B 86 MET cc_start: 0.8552 (mtt) cc_final: 0.8153 (mtt) REVERT: B 103 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8645 (pp) REVERT: C 468 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8745 (tp30) REVERT: D 0 MET cc_start: 0.7993 (ppp) cc_final: 0.7500 (ppp) REVERT: D 63 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8312 (ptm-80) REVERT: D 371 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8038 (mtmm) REVERT: D 379 MET cc_start: 0.8403 (tpp) cc_final: 0.7912 (tmm) REVERT: F 86 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8174 (mtp180) REVERT: F 136 MET cc_start: 0.9448 (mmm) cc_final: 0.9073 (mmm) REVERT: F 209 MET cc_start: 0.8554 (ptp) cc_final: 0.8246 (mtm) REVERT: G 5 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7904 (p0) REVERT: G 116 MET cc_start: 0.7406 (mmp) cc_final: 0.7187 (mmp) REVERT: W 73 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: W 76 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8813 (mp) REVERT: W 128 MET cc_start: 0.8937 (mmt) cc_final: 0.8723 (mmp) REVERT: I 11 MET cc_start: 0.6564 (tmm) cc_final: 0.6300 (tpt) REVERT: I 19 LEU cc_start: 0.7857 (mt) cc_final: 0.7497 (tp) REVERT: J 17 MET cc_start: 0.5256 (mtp) cc_final: 0.4277 (tpp) REVERT: L 63 ILE cc_start: 0.6300 (mm) cc_final: 0.5186 (mt) REVERT: L 65 MET cc_start: 0.4610 (mmm) cc_final: 0.4298 (ppp) REVERT: M 6 MET cc_start: 0.4619 (mtp) cc_final: 0.4158 (ptt) REVERT: M 75 MET cc_start: 0.5366 (tmt) cc_final: 0.4812 (mmp) REVERT: N 65 MET cc_start: 0.5364 (mmm) cc_final: 0.4836 (mmm) REVERT: P 16 MET cc_start: 0.7002 (ttt) cc_final: 0.6728 (ttm) REVERT: P 17 MET cc_start: 0.6470 (mmm) cc_final: 0.6160 (mmm) REVERT: P 68 VAL cc_start: 0.5007 (t) cc_final: 0.4765 (p) REVERT: Q 17 MET cc_start: 0.1177 (ptp) cc_final: 0.0663 (tmm) REVERT: R 28 ILE cc_start: 0.7747 (mt) cc_final: 0.7408 (tp) REVERT: S 16 MET cc_start: 0.6966 (mtp) cc_final: 0.6589 (ttp) REVERT: S 57 MET cc_start: 0.7135 (tmt) cc_final: 0.6746 (tmm) REVERT: X 1 MET cc_start: 0.2655 (mtm) cc_final: 0.2184 (mtm) REVERT: X 48 GLU cc_start: 0.4922 (OUTLIER) cc_final: 0.4326 (tp30) REVERT: X 63 ASP cc_start: 0.5228 (t0) cc_final: 0.4502 (m-30) REVERT: X 82 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8151 (mmm160) REVERT: Y 24 TYR cc_start: 0.1307 (OUTLIER) cc_final: 0.0647 (m-80) REVERT: Y 98 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7602 (mtp180) REVERT: Y 113 ARG cc_start: 0.8998 (mtt-85) cc_final: 0.8626 (mmt180) REVERT: a 6 MET cc_start: 0.4473 (ppp) cc_final: 0.3070 (tmm) REVERT: a 46 MET cc_start: 0.3708 (mmm) cc_final: 0.3264 (mtp) REVERT: a 93 MET cc_start: 0.6665 (mmm) cc_final: 0.6147 (mtm) REVERT: a 97 LYS cc_start: 0.5694 (mttt) cc_final: 0.5400 (pptt) REVERT: a 115 MET cc_start: 0.1643 (ttt) cc_final: 0.1113 (mmm) REVERT: a 153 MET cc_start: 0.0525 (mtm) cc_final: -0.0268 (ttt) REVERT: a 168 MET cc_start: 0.3346 (mmm) cc_final: 0.2916 (mtt) REVERT: a 196 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6995 (mt-10) outliers start: 49 outliers final: 32 residues processed: 295 average time/residue: 0.2204 time to fit residues: 107.9722 Evaluate side-chains 285 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 504 LEU 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 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 348 VAL Chi-restraints excluded: chain D residue 408 GLU 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 W residue 39 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 76 ILE Chi-restraints excluded: chain N residue 63 ILE 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 32 GLN 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: 7.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 440 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 384 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 369 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 376 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.068497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.045255 restraints weight = 204094.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.046289 restraints weight = 110117.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045989 restraints weight = 58840.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046204 restraints weight = 61123.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046231 restraints weight = 49878.999| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 37419 Z= 0.208 Angle : 0.736 59.100 50648 Z= 0.386 Chirality : 0.042 0.349 5902 Planarity : 0.004 0.055 6530 Dihedral : 5.062 131.193 5228 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.31 % Allowed : 15.48 % Favored : 83.21 % Cbeta Deviations : 0.02 % 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: 1.43 (0.12), residues: 4793 helix: 2.01 (0.10), residues: 2624 sheet: 0.08 (0.22), residues: 543 loop : -0.47 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 129 TYR 0.015 0.001 TYR a 216 PHE 0.022 0.001 PHE F 189 TRP 0.011 0.001 TRP a 235 HIS 0.004 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (37419) covalent geometry : angle 0.73555 / 0.39 (50648) hydrogen bonds : bond 0.04238 / 2.82 ( 2152) hydrogen bonds : angle 4.19221 / 2.95 ( 6285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6728.27 seconds wall clock time: 116 minutes 34.05 seconds (6994.05 seconds total)