Starting phenix.real_space_refine on Mon Jul 6 15:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbq_27298/07_2026/8dbq_27298.cif" } resolution = 4.0 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= 0.003 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 23342 2.51 5 N 6275 2.21 5 O 6921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 36737 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3863 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} 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: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "F" 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: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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} Time building chain proxies: 6.83, per 1000 atoms: 0.19 Number of scatterers: 36737 At special positions: 0 Unit cell: (180.193, 223.353, 137.033, 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 6921 8.00 N 6275 7.00 C 23342 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8756 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 21 sheets defined 61.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.691A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.971A 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 289 through 299 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.745A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 4.032A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.291A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 479 removed outlier: 4.067A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.559A 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 4 through 19 removed outlier: 3.844A pdb=" N ILE B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.510A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.680A pdb=" N ASP B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.967A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.512A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 288 through 299 removed outlier: 4.360A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.678A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 410 removed outlier: 3.916A pdb=" N ALA B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.593A pdb=" N LYS B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.776A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.540A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.549A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.524A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) 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 216 through 219 removed outlier: 3.767A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.755A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.970A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.011A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 411 removed outlier: 4.348A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.891A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 196 through 197 No H-bonds generated for 'chain 'D' and resid 196 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 233 removed outlier: 4.162A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.733A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 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 457 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.582A pdb=" N LEU E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.532A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 3.512A pdb=" N ASP E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 170 removed outlier: 3.791A pdb=" N MET E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.675A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) 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 233 removed outlier: 4.611A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.727A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.599A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 305 through 313 removed outlier: 4.157A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 378 removed outlier: 7.087A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 357 " --> pdb=" O HIS E 353 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 419 through 432 removed outlier: 4.735A pdb=" N ARG E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'F' and resid 80 through 84 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 171 removed outlier: 3.630A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 4.644A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 259 removed outlier: 3.594A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 313 removed outlier: 4.249A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 4.001A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 401 removed outlier: 3.915A pdb=" N SER F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'G' and resid 2 through 40 Processing helix chain 'G' and resid 41 through 57 removed outlier: 3.863A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.594A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.643A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.749A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.851A 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 198 through 202 Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.822A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.750A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.797A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.720A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.001A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.610A 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: 4.112A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.686A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.656A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.739A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 78 removed outlier: 3.540A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.977A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.655A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 removed outlier: 3.760A pdb=" N ILE N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.117A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.800A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.643A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 4.040A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.851A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.781A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.851A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY Q 58 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.628A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.568A pdb=" N THR R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 76 removed outlier: 3.659A pdb=" N ILE R 66 " --> pdb=" O ALA R 62 " (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: 3.603A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.517A pdb=" N GLN S 52 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 78 removed outlier: 3.650A pdb=" N MET S 65 " --> pdb=" O ASP S 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 21 Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.628A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 removed outlier: 3.578A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 64 Processing helix chain 'W' and resid 71 through 83 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: 3.943A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.069A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 4.165A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.678A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 156 removed outlier: 3.615A pdb=" N LEU X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 25 Processing helix chain 'Y' and resid 27 through 38 removed outlier: 4.065A pdb=" N ALA Y 31 " --> pdb=" O PRO Y 27 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA Y 32 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 140 removed outlier: 3.947A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 156 Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.639A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 67 removed outlier: 3.509A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.606A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.557A 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 132 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 4.035A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.772A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL a 198 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.757A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.785A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.875A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.396A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.823A 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 59 through 66 removed outlier: 6.078A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 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 45 removed outlier: 6.686A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.708A 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 46 removed outlier: 6.772A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.398A 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 99 removed outlier: 3.751A pdb=" N GLY A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 109 current: chain 'A' and resid 221 through 226 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 226 current: chain 'A' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 331 current: chain 'A' and resid 374 through 375 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 35 removed outlier: 6.562A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.879A 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 60 through 66 removed outlier: 6.491A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 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: 6.890A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.254A 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 135 through 142 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 142 current: chain 'W' and resid 157 through 162 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.467A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.508A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.530A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.500A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.706A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.453A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.535A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.572A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.117A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N TYR E 297 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.129A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.123A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.848A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE G 169 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLN G 186 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER G 171 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE G 184 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS G 173 " --> pdb=" O PRO G 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 207 through 208 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 207 through 208 current: chain 'H' and resid 16 through 26 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 31 through 34 current: chain 'H' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 64 current: chain 'H' and resid 75 through 80 Processing sheet with id=AC3, first strand: chain 'a' and resid 20 through 21 removed outlier: 4.519A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2174 hydrogen bonds defined for protein. 6348 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: 7.07 Time building geometry restraints manager: 3.72 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: 6791 1.32 - 1.45: 8377 1.45 - 1.57: 21745 1.57 - 1.69: 25 1.69 - 1.82: 356 Bond restraints: 37294 Sorted by residual: bond pdb=" C PRO E 138 " pdb=" O PRO E 138 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" N ARG D 24 " pdb=" CA ARG D 24 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.31e-02 5.83e+03 7.01e+00 bond pdb=" CA ALA E 137 " pdb=" CB ALA E 137 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.32e-02 5.74e+03 6.52e+00 bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.25e-02 6.40e+03 5.95e+00 bond pdb=" N SER E 419 " pdb=" CA SER E 419 " ideal model delta sigma weight residual 1.453 1.482 -0.030 1.31e-02 5.83e+03 5.08e+00 ... (remaining 37289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 48812 2.26 - 4.51: 1488 4.51 - 6.77: 160 6.77 - 9.02: 17 9.02 - 11.28: 8 Bond angle restraints: 50485 Sorted by residual: angle pdb=" C LYS E 131 " pdb=" CA LYS E 131 " pdb=" CB LYS E 131 " ideal model delta sigma weight residual 110.88 100.86 10.02 1.57e+00 4.06e-01 4.07e+01 angle pdb=" C ALA O 62 " pdb=" N ILE O 63 " pdb=" CA ILE O 63 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.21e+01 angle pdb=" N LEU a 125 " pdb=" CA LEU a 125 " pdb=" C LEU a 125 " ideal model delta sigma weight residual 110.97 115.29 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" CA ILE Q 63 " pdb=" CB ILE Q 63 " pdb=" CG2 ILE Q 63 " ideal model delta sigma weight residual 110.50 116.96 -6.46 1.70e+00 3.46e-01 1.45e+01 angle pdb=" C1' ADP F 500 " pdb=" C2' ADP F 500 " pdb=" C3' ADP F 500 " ideal model delta sigma weight residual 111.00 99.98 11.02 3.00e+00 1.11e-01 1.35e+01 ... (remaining 50480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 21923 30.68 - 61.37: 535 61.37 - 92.05: 80 92.05 - 122.73: 2 122.73 - 153.42: 2 Dihedral angle restraints: 22542 sinusoidal: 8853 harmonic: 13689 Sorted by residual: dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 146.59 153.42 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 167.56 132.44 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 -173.19 113.18 1 2.00e+01 2.50e-03 3.34e+01 ... (remaining 22539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 5799 0.142 - 0.284: 77 0.284 - 0.426: 4 0.426 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 5881 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 1.94 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA THR E 128 " pdb=" N THR E 128 " pdb=" C THR E 128 " pdb=" CB THR E 128 " both_signs ideal model delta sigma weight residual False 2.53 2.88 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS E 131 " pdb=" N LYS E 131 " pdb=" C LYS E 131 " pdb=" CB LYS E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5878 not shown) Planarity restraints: 6510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 207 " -0.003 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR G 207 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR G 207 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR G 207 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 207 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR G 207 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 207 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR G 207 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 203 " 0.029 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP G 203 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP G 203 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 203 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 203 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 203 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " 0.008 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR B 195 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.038 2.00e-02 2.50e+03 ... (remaining 6507 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 49 2.51 - 3.11: 27863 3.11 - 3.70: 55187 3.70 - 4.30: 81220 4.30 - 4.90: 133656 Nonbonded interactions: 297975 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.911 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.962 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.964 2.170 nonbonded pdb=" O2G ATP E 500 " pdb="MG MG E 501 " model vdw 2.083 2.170 ... (remaining 297970 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 2 through 408 or resid 410 through 601)) selection = (chain 'B' and (resid 2 through 408 or resid 410 through 601)) selection = (chain 'C' and (resid 2 through 408 or resid 410 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' } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.220 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.005 0.076 37294 Z= 0.242 Angle : 0.889 11.281 50485 Z= 0.492 Chirality : 0.053 0.709 5881 Planarity : 0.010 0.113 6510 Dihedral : 13.992 153.417 13786 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Rotamer: Outliers : 1.26 % Allowed : 6.51 % Favored : 92.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.11), residues: 4775 helix: 0.22 (0.09), residues: 2582 sheet: 0.15 (0.22), residues: 475 loop : -0.52 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG C 139 TYR 0.042 0.007 TYR G 207 PHE 0.026 0.003 PHE a 38 TRP 0.064 0.004 TRP G 203 HIS 0.008 0.002 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (37294) covalent geometry : angle 0.88914 / 0.49 (50485) hydrogen bonds : bond 0.15083 / 10.45 ( 2174) hydrogen bonds : angle 6.31513 / 4.53 ( 6348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 658 time to evaluate : 1.285 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: 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: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8937 (mp) cc_final: 0.8537 (mm) REVERT: A 258 ILE cc_start: 0.9124 (tt) cc_final: 0.8806 (tt) REVERT: C 95 LEU cc_start: 0.8904 (tp) cc_final: 0.8615 (tp) REVERT: C 417 THR cc_start: 0.9027 (m) cc_final: 0.8823 (p) REVERT: D 189 PHE cc_start: 0.8829 (t80) cc_final: 0.8383 (t80) REVERT: D 379 MET cc_start: 0.7500 (tpt) cc_final: 0.7083 (tpt) REVERT: D 382 LEU cc_start: 0.8399 (mt) cc_final: 0.7759 (mt) REVERT: D 445 MET cc_start: 0.8770 (mmm) cc_final: 0.8078 (mmm) REVERT: E 136 MET cc_start: 0.9040 (mmm) cc_final: 0.8645 (mmm) REVERT: E 139 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7354 (p90) REVERT: E 209 MET cc_start: 0.8931 (ptp) cc_final: 0.8561 (ptp) REVERT: F 79 VAL cc_start: 0.8351 (m) cc_final: 0.8050 (m) REVERT: F 159 MET cc_start: 0.8607 (mtp) cc_final: 0.8164 (tmm) REVERT: F 254 VAL cc_start: 0.9063 (t) cc_final: 0.8839 (p) REVERT: F 342 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7708 (tpp-160) REVERT: F 379 MET cc_start: 0.9035 (mtp) cc_final: 0.8431 (tpp) REVERT: F 397 GLN cc_start: 0.8956 (tt0) cc_final: 0.8353 (tm-30) REVERT: G 31 MET cc_start: 0.7653 (ttp) cc_final: 0.6716 (tmm) REVERT: G 32 ARG cc_start: 0.8232 (mmt180) cc_final: 0.8016 (mmt180) REVERT: G 48 MET cc_start: 0.8834 (ttm) cc_final: 0.8493 (ttm) REVERT: G 102 MET cc_start: 0.8749 (ttp) cc_final: 0.7982 (ptm) REVERT: H 8 VAL cc_start: 0.8795 (t) cc_final: 0.7749 (p) REVERT: H 61 PHE cc_start: 0.7931 (m-80) cc_final: 0.7617 (m-10) REVERT: I 16 MET cc_start: 0.7541 (ttm) cc_final: 0.6621 (tpt) REVERT: I 53 PHE cc_start: 0.6100 (t80) cc_final: 0.5582 (t80) REVERT: I 54 PHE cc_start: 0.5537 (m-10) cc_final: 0.5166 (t80) REVERT: J 6 MET cc_start: 0.6977 (mtp) cc_final: 0.6733 (pmm) REVERT: J 15 VAL cc_start: 0.7950 (t) cc_final: 0.7710 (p) REVERT: J 16 MET cc_start: 0.6554 (ttt) cc_final: 0.6152 (tpt) REVERT: J 22 ILE cc_start: 0.6836 (mm) cc_final: 0.6606 (mm) REVERT: L 26 ILE cc_start: 0.8569 (mt) cc_final: 0.8328 (mp) REVERT: L 49 LEU cc_start: 0.8490 (mt) cc_final: 0.8262 (mt) REVERT: L 57 MET cc_start: 0.7724 (tmm) cc_final: 0.6264 (ptm) REVERT: M 53 PHE cc_start: 0.8332 (t80) cc_final: 0.7771 (t80) REVERT: M 65 MET cc_start: 0.6298 (mtp) cc_final: 0.5767 (mmt) REVERT: N 31 LEU cc_start: 0.6701 (tp) cc_final: 0.6214 (mt) REVERT: O 6 MET cc_start: 0.5746 (ttm) cc_final: 0.5371 (pmm) REVERT: P 11 MET cc_start: 0.8422 (tpp) cc_final: 0.8025 (mtp) REVERT: Q 63 ILE cc_start: 0.7590 (tt) cc_final: 0.7163 (tt) REVERT: Q 76 PHE cc_start: 0.6962 (m-80) cc_final: 0.6317 (t80) REVERT: R 6 MET cc_start: 0.5805 (mmt) cc_final: 0.5403 (ttm) REVERT: R 68 VAL cc_start: 0.6051 (t) cc_final: 0.5709 (m) REVERT: S 6 MET cc_start: 0.6404 (mmt) cc_final: 0.6118 (pmm) REVERT: S 75 MET cc_start: 0.5173 (ttt) cc_final: 0.4874 (tpt) REVERT: X 49 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8134 (tpt90) REVERT: X 64 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7793 (mm110) REVERT: Y 62 THR cc_start: 0.5997 (m) cc_final: 0.5746 (p) REVERT: Y 99 THR cc_start: 0.8693 (p) cc_final: 0.8481 (p) REVERT: a 46 MET cc_start: 0.2038 (mmm) cc_final: 0.1712 (mtp) outliers start: 48 outliers final: 9 residues processed: 699 average time/residue: 0.2142 time to fit residues: 240.7216 Evaluate side-chains 374 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 364 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS B 294 HIS C 147 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN E 197 ASN E 294 GLN E 353 HIS E 437 HIS ** G 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN W 73 GLN Y 123 GLN a 14 HIS a 132 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.059808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043461 restraints weight = 244559.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044486 restraints weight = 140712.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044532 restraints weight = 79169.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044738 restraints weight = 72232.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044761 restraints weight = 64066.201| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 37294 Z= 0.211 Angle : 0.732 13.365 50485 Z= 0.379 Chirality : 0.046 0.468 5881 Planarity : 0.005 0.056 6510 Dihedral : 6.459 133.875 5220 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.55 % Favored : 98.43 % Rotamer: Outliers : 2.15 % Allowed : 10.57 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4775 helix: 0.86 (0.10), residues: 2616 sheet: 0.09 (0.21), residues: 524 loop : -0.44 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 113 TYR 0.017 0.002 TYR C 400 PHE 0.023 0.002 PHE O 53 TRP 0.021 0.002 TRP G 203 HIS 0.008 0.001 HIS X 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (37294) covalent geometry : angle 0.73159 / 0.38 (50485) hydrogen bonds : bond 0.06476 / 4.42 ( 2174) hydrogen bonds : angle 4.90954 / 3.54 ( 6348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 378 time to evaluate : 1.041 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8111 (mtp) REVERT: B 148 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (t) REVERT: B 245 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8296 (mpp) REVERT: D 136 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8586 (mmm) REVERT: D 274 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7560 (mt-10) REVERT: D 379 MET cc_start: 0.8062 (tpt) cc_final: 0.7742 (tpt) REVERT: D 382 LEU cc_start: 0.8585 (mt) cc_final: 0.8331 (mt) REVERT: D 445 MET cc_start: 0.8898 (mmm) cc_final: 0.8159 (mmm) REVERT: F 79 VAL cc_start: 0.8393 (m) cc_final: 0.7762 (m) REVERT: F 159 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8358 (tmm) REVERT: F 358 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7716 (mmm-85) REVERT: F 379 MET cc_start: 0.9218 (mtp) cc_final: 0.8577 (tpp) REVERT: F 397 GLN cc_start: 0.9023 (tt0) cc_final: 0.8550 (tm-30) REVERT: F 431 MET cc_start: 0.8406 (mtp) cc_final: 0.8200 (ptp) REVERT: G 31 MET cc_start: 0.7933 (ttp) cc_final: 0.7333 (tmm) REVERT: G 32 ARG cc_start: 0.8225 (mmt180) cc_final: 0.7995 (mmp80) REVERT: G 48 MET cc_start: 0.8837 (ttm) cc_final: 0.8374 (ttm) REVERT: G 78 LEU cc_start: 0.9179 (tp) cc_final: 0.8936 (tp) REVERT: G 102 MET cc_start: 0.8748 (ttp) cc_final: 0.7931 (tmm) REVERT: H 61 PHE cc_start: 0.7987 (m-80) cc_final: 0.7687 (m-10) REVERT: I 10 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: I 16 MET cc_start: 0.7407 (ttm) cc_final: 0.7036 (tpt) REVERT: I 53 PHE cc_start: 0.6937 (t80) cc_final: 0.5469 (t80) REVERT: I 54 PHE cc_start: 0.5987 (m-10) cc_final: 0.5340 (t80) REVERT: I 75 MET cc_start: 0.3599 (mmm) cc_final: 0.3352 (mmm) REVERT: J 11 MET cc_start: 0.6263 (tpp) cc_final: 0.6024 (mmp) REVERT: J 16 MET cc_start: 0.6226 (ttt) cc_final: 0.5366 (ttt) REVERT: J 17 MET cc_start: 0.8304 (ptp) cc_final: 0.7915 (mpp) REVERT: L 11 MET cc_start: 0.7975 (mtp) cc_final: 0.6307 (tpt) REVERT: L 16 MET cc_start: 0.6060 (mmm) cc_final: 0.5456 (tpt) REVERT: L 49 LEU cc_start: 0.8344 (mt) cc_final: 0.7960 (tp) REVERT: L 57 MET cc_start: 0.7947 (tmm) cc_final: 0.6644 (ptm) REVERT: M 55 ILE cc_start: 0.8512 (mm) cc_final: 0.8233 (pt) REVERT: M 65 MET cc_start: 0.6383 (mtp) cc_final: 0.5950 (mmt) REVERT: M 68 VAL cc_start: 0.7144 (t) cc_final: 0.6347 (p) REVERT: P 11 MET cc_start: 0.8147 (tpp) cc_final: 0.7827 (mtp) REVERT: P 16 MET cc_start: 0.5431 (mtt) cc_final: 0.5016 (mtt) REVERT: Q 75 MET cc_start: 0.5981 (mmt) cc_final: 0.5778 (mmt) REVERT: Q 76 PHE cc_start: 0.7301 (m-80) cc_final: 0.6380 (t80) REVERT: R 6 MET cc_start: 0.5917 (mmt) cc_final: 0.5439 (ttm) REVERT: S 6 MET cc_start: 0.6403 (mmt) cc_final: 0.6065 (pmm) REVERT: S 75 MET cc_start: 0.5456 (ttt) cc_final: 0.4851 (tpt) REVERT: W 12 LYS cc_start: 0.9511 (ttmm) cc_final: 0.9193 (ttpp) REVERT: X 49 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8192 (tpt90) REVERT: X 64 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7959 (mm-40) REVERT: X 73 GLN cc_start: 0.8725 (mm110) cc_final: 0.8499 (mm-40) REVERT: X 83 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8250 (ttp-110) REVERT: a 115 MET cc_start: 0.6442 (ttp) cc_final: 0.5972 (ttp) REVERT: a 155 LEU cc_start: 0.7264 (mt) cc_final: 0.7004 (pp) REVERT: a 257 MET cc_start: 0.6958 (tmm) cc_final: 0.6325 (ppp) outliers start: 82 outliers final: 33 residues processed: 433 average time/residue: 0.2071 time to fit residues: 148.3636 Evaluate side-chains 347 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 85 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 460 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 376 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN B 511 GLN C 420 GLN ** G 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN O 42 GLN S 42 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.057802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041324 restraints weight = 248531.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042538 restraints weight = 146102.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042935 restraints weight = 77978.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043123 restraints weight = 67009.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043052 restraints weight = 55784.386| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 37294 Z= 0.232 Angle : 0.683 9.559 50485 Z= 0.357 Chirality : 0.044 0.306 5881 Planarity : 0.005 0.081 6510 Dihedral : 5.962 131.039 5209 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.07 % Rotamer: Outliers : 2.52 % Allowed : 12.46 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4775 helix: 1.21 (0.10), residues: 2622 sheet: 0.00 (0.21), residues: 516 loop : -0.45 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 161 TYR 0.018 0.002 TYR G 222 PHE 0.028 0.002 PHE J 54 TRP 0.021 0.002 TRP a 111 HIS 0.009 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (37294) covalent geometry : angle 0.68305 / 0.36 (50485) hydrogen bonds : bond 0.06140 / 4.18 ( 2174) hydrogen bonds : angle 4.77445 / 3.44 ( 6348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 319 time to evaluate : 1.148 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: A 48 MET cc_start: 0.8306 (ptp) cc_final: 0.8035 (ptp) REVERT: A 225 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8233 (m) REVERT: C 52 MET cc_start: 0.8027 (mtp) cc_final: 0.7645 (mtp) REVERT: D 445 MET cc_start: 0.8883 (mmm) cc_final: 0.8199 (mmm) REVERT: E 139 PHE cc_start: 0.8834 (p90) cc_final: 0.8600 (p90) REVERT: F 56 MET cc_start: 0.9271 (mmp) cc_final: 0.8774 (mmm) REVERT: F 159 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8272 (tmm) REVERT: F 209 MET cc_start: 0.8680 (mtp) cc_final: 0.8214 (mmm) REVERT: F 379 MET cc_start: 0.9273 (mtp) cc_final: 0.8513 (tpp) REVERT: F 397 GLN cc_start: 0.9045 (tt0) cc_final: 0.8550 (tm-30) REVERT: F 431 MET cc_start: 0.8245 (mtp) cc_final: 0.6914 (ptp) REVERT: F 445 MET cc_start: 0.7056 (mmp) cc_final: 0.6848 (mmm) REVERT: G 48 MET cc_start: 0.8969 (ttm) cc_final: 0.8462 (ttm) REVERT: G 78 LEU cc_start: 0.9188 (tp) cc_final: 0.8921 (tp) REVERT: G 102 MET cc_start: 0.8744 (ttp) cc_final: 0.7928 (tmm) REVERT: G 125 PHE cc_start: 0.8778 (m-80) cc_final: 0.8538 (m-80) REVERT: I 10 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: I 22 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7007 (mt) REVERT: I 53 PHE cc_start: 0.6434 (t80) cc_final: 0.5545 (t80) REVERT: I 54 PHE cc_start: 0.5937 (m-10) cc_final: 0.5095 (t80) REVERT: I 57 MET cc_start: 0.4044 (mtm) cc_final: 0.3796 (mtp) REVERT: I 75 MET cc_start: 0.3578 (mmm) cc_final: 0.3375 (mmm) REVERT: J 16 MET cc_start: 0.6312 (ttt) cc_final: 0.5685 (ttt) REVERT: J 17 MET cc_start: 0.8356 (ptp) cc_final: 0.7778 (mpp) REVERT: J 54 PHE cc_start: 0.8117 (m-80) cc_final: 0.7905 (m-80) REVERT: L 11 MET cc_start: 0.7885 (mtp) cc_final: 0.6038 (tpt) REVERT: L 49 LEU cc_start: 0.8370 (mt) cc_final: 0.8003 (tp) REVERT: L 57 MET cc_start: 0.7752 (tmm) cc_final: 0.6648 (ptm) REVERT: L 75 MET cc_start: 0.8012 (tpp) cc_final: 0.6877 (tpt) REVERT: M 55 ILE cc_start: 0.8550 (mm) cc_final: 0.8292 (pt) REVERT: M 64 PRO cc_start: 0.7080 (Cg_exo) cc_final: 0.6771 (Cg_endo) REVERT: M 65 MET cc_start: 0.6532 (mtp) cc_final: 0.6036 (mmp) REVERT: M 68 VAL cc_start: 0.6836 (t) cc_final: 0.6473 (p) REVERT: P 57 MET cc_start: 0.4909 (ppp) cc_final: 0.4297 (ttm) REVERT: R 6 MET cc_start: 0.6186 (mmt) cc_final: 0.5629 (ttm) REVERT: S 75 MET cc_start: 0.5626 (ttt) cc_final: 0.4991 (tpt) REVERT: W 12 LYS cc_start: 0.9517 (ttmm) cc_final: 0.9186 (ttpp) REVERT: W 157 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7988 (mmm) REVERT: X 49 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8254 (tpt90) REVERT: X 83 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8077 (tmm-80) REVERT: a 60 PHE cc_start: 0.7265 (m-80) cc_final: 0.7028 (m-80) REVERT: a 155 LEU cc_start: 0.7345 (mt) cc_final: 0.6714 (tt) outliers start: 96 outliers final: 45 residues processed: 392 average time/residue: 0.1922 time to fit residues: 126.8268 Evaluate side-chains 331 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 257 optimal weight: 9.9990 chunk 450 optimal weight: 6.9990 chunk 363 optimal weight: 0.0870 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 426 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 408 optimal weight: 30.0000 chunk 220 optimal weight: 6.9990 overall best weight: 3.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN D 32 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN G 64 HIS ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 ASN W 71 ASN ** a 18 ASN ** 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 = 0.3508 r_free = 0.3508 target = 0.057973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041558 restraints weight = 248220.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.042470 restraints weight = 152947.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.042885 restraints weight = 89368.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043034 restraints weight = 68338.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043106 restraints weight = 61294.286| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37294 Z= 0.167 Angle : 0.619 10.215 50485 Z= 0.319 Chirality : 0.042 0.280 5881 Planarity : 0.004 0.068 6510 Dihedral : 5.652 111.581 5207 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 2.39 % Allowed : 13.88 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 4775 helix: 1.49 (0.10), residues: 2612 sheet: 0.02 (0.21), residues: 518 loop : -0.42 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 93 TYR 0.022 0.001 TYR S 73 PHE 0.030 0.002 PHE Q 53 TRP 0.015 0.001 TRP a 111 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (37294) covalent geometry : angle 0.61950 / 0.32 (50485) hydrogen bonds : bond 0.05587 / 3.81 ( 2174) hydrogen bonds : angle 4.54189 / 3.28 ( 6348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 300 time to evaluate : 1.413 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 12 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 48 MET cc_start: 0.8462 (ptp) cc_final: 0.8180 (ptp) REVERT: A 156 MET cc_start: 0.9419 (mmt) cc_final: 0.9058 (mmt) REVERT: C 95 LEU cc_start: 0.9286 (tp) cc_final: 0.9006 (tp) REVERT: D 160 MET cc_start: 0.9216 (mtm) cc_final: 0.8980 (mtm) REVERT: D 445 MET cc_start: 0.8928 (mmm) cc_final: 0.8171 (mmm) REVERT: F 56 MET cc_start: 0.9225 (mmp) cc_final: 0.8672 (mmm) REVERT: F 159 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8267 (tmm) REVERT: F 379 MET cc_start: 0.9304 (mtp) cc_final: 0.8454 (tpp) REVERT: F 397 GLN cc_start: 0.9000 (tt0) cc_final: 0.8489 (tm-30) REVERT: F 445 MET cc_start: 0.7119 (mmp) cc_final: 0.6869 (mmm) REVERT: G 25 MET cc_start: 0.8277 (tpp) cc_final: 0.7966 (tpp) REVERT: G 48 MET cc_start: 0.8925 (ttm) cc_final: 0.8376 (ttm) REVERT: G 78 LEU cc_start: 0.9171 (tp) cc_final: 0.8769 (tt) REVERT: G 102 MET cc_start: 0.8759 (ttp) cc_final: 0.8023 (tmm) REVERT: H 49 MET cc_start: 0.7166 (tpp) cc_final: 0.6878 (tpp) REVERT: I 10 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: I 53 PHE cc_start: 0.6287 (t80) cc_final: 0.5239 (t80) REVERT: I 54 PHE cc_start: 0.5832 (m-10) cc_final: 0.4966 (t80) REVERT: I 57 MET cc_start: 0.4449 (mtm) cc_final: 0.4247 (mtp) REVERT: J 16 MET cc_start: 0.6509 (ttt) cc_final: 0.5263 (ttt) REVERT: J 54 PHE cc_start: 0.8188 (m-80) cc_final: 0.7859 (m-80) REVERT: L 11 MET cc_start: 0.7903 (mtp) cc_final: 0.6194 (tpt) REVERT: L 49 LEU cc_start: 0.8392 (mt) cc_final: 0.8084 (tp) REVERT: L 57 MET cc_start: 0.7716 (tmm) cc_final: 0.6665 (ptm) REVERT: L 75 MET cc_start: 0.7985 (tpp) cc_final: 0.7423 (mmt) REVERT: M 17 MET cc_start: 0.5389 (tpp) cc_final: 0.4723 (ptm) REVERT: M 55 ILE cc_start: 0.8531 (mm) cc_final: 0.8314 (pt) REVERT: M 68 VAL cc_start: 0.6920 (t) cc_final: 0.6502 (p) REVERT: N 11 MET cc_start: 0.7283 (mmm) cc_final: 0.7019 (mmm) REVERT: N 17 MET cc_start: 0.5730 (tpp) cc_final: 0.5412 (tpp) REVERT: O 16 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (tpt) REVERT: P 11 MET cc_start: 0.7448 (mtt) cc_final: 0.7017 (mmm) REVERT: P 57 MET cc_start: 0.5341 (ppp) cc_final: 0.4481 (ttm) REVERT: Q 34 LYS cc_start: 0.6317 (mmpt) cc_final: 0.6090 (mmmt) REVERT: R 6 MET cc_start: 0.6100 (mmt) cc_final: 0.5543 (ttm) REVERT: S 16 MET cc_start: 0.7385 (mmt) cc_final: 0.6886 (mmm) REVERT: S 57 MET cc_start: 0.7928 (tpt) cc_final: 0.7195 (tmm) REVERT: S 75 MET cc_start: 0.5498 (ttt) cc_final: 0.4815 (tpp) REVERT: W 12 LYS cc_start: 0.9522 (ttmm) cc_final: 0.9194 (ttpp) REVERT: X 49 ARG cc_start: 0.8716 (mtt180) cc_final: 0.8253 (tpt90) REVERT: Y 1 MET cc_start: 0.6916 (mmm) cc_final: 0.4075 (ppp) REVERT: a 6 MET cc_start: 0.3836 (mmt) cc_final: 0.3495 (mmp) REVERT: a 60 PHE cc_start: 0.7252 (m-80) cc_final: 0.7022 (m-80) REVERT: a 125 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6376 (tp) REVERT: a 155 LEU cc_start: 0.7600 (mt) cc_final: 0.7104 (tt) REVERT: a 209 LEU cc_start: 0.8614 (mm) cc_final: 0.8352 (mm) REVERT: a 215 MET cc_start: 0.6340 (mmm) cc_final: 0.6091 (mmm) REVERT: a 257 MET cc_start: 0.6985 (tmm) cc_final: 0.6611 (tmm) outliers start: 91 outliers final: 44 residues processed: 369 average time/residue: 0.1914 time to fit residues: 120.5676 Evaluate side-chains 333 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 452 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 372 optimal weight: 20.0000 chunk 195 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 346 optimal weight: 7.9990 chunk 459 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.057198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040942 restraints weight = 249555.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041731 restraints weight = 157187.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.042242 restraints weight = 90168.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.042332 restraints weight = 68602.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042385 restraints weight = 60733.435| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37294 Z= 0.195 Angle : 0.633 10.789 50485 Z= 0.325 Chirality : 0.043 0.312 5881 Planarity : 0.004 0.070 6510 Dihedral : 5.499 100.512 5206 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 14.22 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.00 (0.12), residues: 4775 helix: 1.56 (0.10), residues: 2620 sheet: -0.05 (0.21), residues: 516 loop : -0.47 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 93 TYR 0.015 0.001 TYR B 150 PHE 0.058 0.002 PHE X 17 TRP 0.011 0.001 TRP a 232 HIS 0.007 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (37294) covalent geometry : angle 0.63326 / 0.33 (50485) hydrogen bonds : bond 0.05477 / 3.73 ( 2174) hydrogen bonds : angle 4.53732 / 3.27 ( 6348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 293 time to evaluate : 1.526 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 12 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 156 MET cc_start: 0.9454 (mmt) cc_final: 0.9037 (mmt) REVERT: C 95 LEU cc_start: 0.9277 (tp) cc_final: 0.9043 (tp) REVERT: D 136 MET cc_start: 0.9279 (mmm) cc_final: 0.9047 (mmp) REVERT: D 193 MET cc_start: 0.8428 (mmm) cc_final: 0.8166 (mmm) REVERT: D 445 MET cc_start: 0.8923 (mmm) cc_final: 0.8206 (mmm) REVERT: F 56 MET cc_start: 0.9229 (mmp) cc_final: 0.8730 (mmm) REVERT: F 159 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8294 (tmm) REVERT: F 379 MET cc_start: 0.9297 (mtp) cc_final: 0.8419 (tpp) REVERT: F 397 GLN cc_start: 0.8978 (tt0) cc_final: 0.8409 (tm-30) REVERT: G 25 MET cc_start: 0.8359 (tpp) cc_final: 0.7979 (tpp) REVERT: G 48 MET cc_start: 0.8996 (ttm) cc_final: 0.8377 (ttm) REVERT: G 78 LEU cc_start: 0.9151 (tp) cc_final: 0.8730 (tt) REVERT: G 102 MET cc_start: 0.8810 (ttp) cc_final: 0.8100 (tmm) REVERT: H 49 MET cc_start: 0.7232 (tpp) cc_final: 0.6953 (tpp) REVERT: I 10 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: I 53 PHE cc_start: 0.6149 (t80) cc_final: 0.4990 (t80) REVERT: I 54 PHE cc_start: 0.6324 (m-10) cc_final: 0.5217 (t80) REVERT: I 75 MET cc_start: 0.3653 (mmm) cc_final: 0.3376 (mmm) REVERT: J 11 MET cc_start: 0.3519 (mmp) cc_final: 0.2093 (tpp) REVERT: J 16 MET cc_start: 0.6738 (ttt) cc_final: 0.6219 (ttt) REVERT: J 17 MET cc_start: 0.7940 (mtm) cc_final: 0.7706 (mpp) REVERT: J 54 PHE cc_start: 0.8242 (m-80) cc_final: 0.7770 (m-80) REVERT: L 11 MET cc_start: 0.7837 (mtp) cc_final: 0.6011 (tpt) REVERT: L 15 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7426 (p) REVERT: L 49 LEU cc_start: 0.8437 (mt) cc_final: 0.8143 (tp) REVERT: L 57 MET cc_start: 0.7665 (tmm) cc_final: 0.6627 (ptm) REVERT: L 75 MET cc_start: 0.7915 (tpp) cc_final: 0.7080 (tpt) REVERT: M 55 ILE cc_start: 0.8549 (mm) cc_final: 0.8290 (pt) REVERT: M 57 MET cc_start: 0.5468 (ptp) cc_final: 0.5239 (ptp) REVERT: M 65 MET cc_start: 0.6177 (mtp) cc_final: 0.5375 (mmt) REVERT: M 68 VAL cc_start: 0.6992 (t) cc_final: 0.6617 (p) REVERT: N 11 MET cc_start: 0.7312 (mmm) cc_final: 0.7010 (mmm) REVERT: O 75 MET cc_start: 0.2257 (ttt) cc_final: 0.2055 (ttt) REVERT: P 57 MET cc_start: 0.5193 (ppp) cc_final: 0.4297 (ttm) REVERT: P 63 ILE cc_start: 0.0150 (OUTLIER) cc_final: -0.0229 (mm) REVERT: Q 16 MET cc_start: 0.1056 (tpt) cc_final: 0.0853 (mmm) REVERT: R 6 MET cc_start: 0.6170 (mmt) cc_final: 0.5581 (ttm) REVERT: R 65 MET cc_start: 0.5203 (tpt) cc_final: 0.4660 (mtt) REVERT: S 57 MET cc_start: 0.8071 (tpt) cc_final: 0.7372 (tmm) REVERT: S 75 MET cc_start: 0.5446 (ttt) cc_final: 0.4832 (tpp) REVERT: W 12 LYS cc_start: 0.9536 (ttmm) cc_final: 0.9206 (ttpp) REVERT: X 49 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8180 (tpt90) REVERT: X 83 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.8192 (ttp-110) REVERT: a 60 PHE cc_start: 0.7226 (m-80) cc_final: 0.6978 (m-80) REVERT: a 125 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6389 (tp) REVERT: a 155 LEU cc_start: 0.7430 (mt) cc_final: 0.6987 (tt) REVERT: a 201 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7904 (pp) REVERT: a 209 LEU cc_start: 0.8714 (mm) cc_final: 0.8466 (mm) REVERT: a 257 MET cc_start: 0.7080 (tmm) cc_final: 0.6854 (tmm) outliers start: 90 outliers final: 52 residues processed: 367 average time/residue: 0.1802 time to fit residues: 114.4874 Evaluate side-chains 335 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 18 ASN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 146 optimal weight: 10.0000 chunk 418 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 424 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 442 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 484 GLN D 7 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.056348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040187 restraints weight = 251449.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041310 restraints weight = 139298.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041478 restraints weight = 79826.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041704 restraints weight = 63987.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041776 restraints weight = 53494.015| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37294 Z= 0.226 Angle : 0.665 12.450 50485 Z= 0.341 Chirality : 0.043 0.314 5881 Planarity : 0.005 0.072 6510 Dihedral : 5.521 105.551 5206 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.54 % Allowed : 14.95 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.12), residues: 4775 helix: 1.54 (0.10), residues: 2616 sheet: -0.13 (0.22), residues: 516 loop : -0.53 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 93 TYR 0.024 0.002 TYR a 94 PHE 0.028 0.002 PHE Q 53 TRP 0.013 0.002 TRP a 232 HIS 0.008 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (37294) covalent geometry : angle 0.66468 / 0.34 (50485) hydrogen bonds : bond 0.05514 / 3.76 ( 2174) hydrogen bonds : angle 4.60242 / 3.31 ( 6348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 281 time to evaluate : 1.435 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 12 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 48 MET cc_start: 0.8335 (ptp) cc_final: 0.8039 (ptp) REVERT: A 156 MET cc_start: 0.9416 (mmt) cc_final: 0.8923 (mmt) REVERT: C 95 LEU cc_start: 0.9083 (tp) cc_final: 0.8807 (tp) REVERT: D 136 MET cc_start: 0.9328 (mmm) cc_final: 0.9080 (mmp) REVERT: D 445 MET cc_start: 0.8894 (mmm) cc_final: 0.8163 (mmm) REVERT: E 459 LEU cc_start: 0.8395 (mp) cc_final: 0.8125 (tt) REVERT: F 56 MET cc_start: 0.9280 (mmp) cc_final: 0.8870 (mmm) REVERT: F 159 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8331 (tmm) REVERT: F 379 MET cc_start: 0.9209 (mtp) cc_final: 0.8271 (tpp) REVERT: F 397 GLN cc_start: 0.8937 (tt0) cc_final: 0.8376 (tm-30) REVERT: G 25 MET cc_start: 0.8297 (tpp) cc_final: 0.7935 (tpp) REVERT: G 48 MET cc_start: 0.9070 (ttm) cc_final: 0.8387 (ttm) REVERT: G 102 MET cc_start: 0.8763 (ttp) cc_final: 0.8109 (tmm) REVERT: G 243 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8938 (tpp) REVERT: H 49 MET cc_start: 0.7394 (tpp) cc_final: 0.7165 (tpp) REVERT: I 10 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: I 45 LEU cc_start: 0.6221 (tp) cc_final: 0.5837 (mm) REVERT: I 53 PHE cc_start: 0.5698 (t80) cc_final: 0.4960 (t80) REVERT: I 54 PHE cc_start: 0.6429 (m-10) cc_final: 0.5195 (t80) REVERT: I 57 MET cc_start: 0.4278 (mtp) cc_final: 0.4033 (mtp) REVERT: I 75 MET cc_start: 0.3487 (mmm) cc_final: 0.3183 (mmm) REVERT: J 11 MET cc_start: 0.3518 (mmp) cc_final: 0.2335 (tpp) REVERT: J 16 MET cc_start: 0.6865 (ttt) cc_final: 0.6541 (ttm) REVERT: J 54 PHE cc_start: 0.8327 (m-80) cc_final: 0.7915 (m-80) REVERT: L 7 ASP cc_start: 0.5182 (OUTLIER) cc_final: 0.4557 (p0) REVERT: L 11 MET cc_start: 0.7749 (mtp) cc_final: 0.6147 (tpt) REVERT: L 49 LEU cc_start: 0.8467 (mt) cc_final: 0.8168 (tp) REVERT: L 57 MET cc_start: 0.7720 (tmm) cc_final: 0.6694 (ptm) REVERT: M 65 MET cc_start: 0.6229 (mtp) cc_final: 0.5645 (mmp) REVERT: M 68 VAL cc_start: 0.6943 (t) cc_final: 0.6675 (p) REVERT: N 11 MET cc_start: 0.7381 (mmm) cc_final: 0.7028 (mmm) REVERT: P 11 MET cc_start: 0.7470 (mtp) cc_final: 0.7105 (tpt) REVERT: P 57 MET cc_start: 0.5173 (ppp) cc_final: 0.4335 (ttm) REVERT: P 63 ILE cc_start: -0.0687 (OUTLIER) cc_final: -0.0910 (mm) REVERT: Q 16 MET cc_start: 0.1428 (tpt) cc_final: 0.1139 (mmm) REVERT: R 6 MET cc_start: 0.6140 (mmt) cc_final: 0.5590 (ttm) REVERT: S 57 MET cc_start: 0.7964 (tpt) cc_final: 0.7260 (tmm) REVERT: S 75 MET cc_start: 0.5518 (ttt) cc_final: 0.4948 (tpt) REVERT: W 12 LYS cc_start: 0.9529 (ttmm) cc_final: 0.9196 (ttpp) REVERT: X 18 VAL cc_start: 0.6516 (m) cc_final: 0.6300 (t) REVERT: X 49 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8194 (tpt90) REVERT: X 83 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.8241 (ttp80) REVERT: X 141 ASP cc_start: 0.8445 (p0) cc_final: 0.8080 (t0) REVERT: a 46 MET cc_start: 0.3745 (mmm) cc_final: 0.3414 (mmm) REVERT: a 60 PHE cc_start: 0.7418 (m-80) cc_final: 0.7199 (m-80) REVERT: a 93 MET cc_start: 0.8038 (tmm) cc_final: 0.7510 (tmm) REVERT: a 155 LEU cc_start: 0.7559 (mt) cc_final: 0.7173 (tt) REVERT: a 201 LEU cc_start: 0.8379 (tt) cc_final: 0.8044 (pp) REVERT: a 257 MET cc_start: 0.7359 (tmm) cc_final: 0.6841 (tpp) outliers start: 97 outliers final: 62 residues processed: 361 average time/residue: 0.1843 time to fit residues: 115.0431 Evaluate side-chains 342 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 220 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 244 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 114 optimal weight: 0.0670 chunk 252 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN E 121 ASN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.057932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.041633 restraints weight = 245561.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.042892 restraints weight = 136608.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043028 restraints weight = 73694.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043270 restraints weight = 60755.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043308 restraints weight = 50980.204| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37294 Z= 0.124 Angle : 0.611 11.745 50485 Z= 0.307 Chirality : 0.042 0.290 5881 Planarity : 0.004 0.068 6510 Dihedral : 5.161 94.898 5206 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.68 % Allowed : 15.79 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.24 (0.12), residues: 4775 helix: 1.78 (0.10), residues: 2622 sheet: 0.00 (0.22), residues: 520 loop : -0.40 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 210 TYR 0.036 0.001 TYR a 94 PHE 0.042 0.001 PHE Q 53 TRP 0.008 0.001 TRP E 107 HIS 0.005 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (37294) covalent geometry : angle 0.61083 / 0.31 (50485) hydrogen bonds : bond 0.05025 / 3.42 ( 2174) hydrogen bonds : angle 4.33140 / 3.13 ( 6348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 1.460 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: A 12 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 156 MET cc_start: 0.9465 (mmt) cc_final: 0.9169 (mmt) REVERT: C 52 MET cc_start: 0.8834 (tpp) cc_final: 0.8615 (tpp) REVERT: D 160 MET cc_start: 0.9052 (mtm) cc_final: 0.8820 (mtm) REVERT: D 193 MET cc_start: 0.8308 (mmm) cc_final: 0.8022 (mmm) REVERT: D 209 MET cc_start: 0.8545 (mpp) cc_final: 0.8281 (mpp) REVERT: D 445 MET cc_start: 0.8834 (mmm) cc_final: 0.8107 (mmm) REVERT: E 88 MET cc_start: 0.8074 (mpp) cc_final: 0.7525 (mpp) REVERT: E 275 MET cc_start: 0.8246 (mmm) cc_final: 0.8040 (tpp) REVERT: E 459 LEU cc_start: 0.8320 (mp) cc_final: 0.8031 (tt) REVERT: F 56 MET cc_start: 0.9305 (mmp) cc_final: 0.8745 (mmm) REVERT: F 159 MET cc_start: 0.8983 (mtp) cc_final: 0.8285 (tmm) REVERT: F 209 MET cc_start: 0.8745 (mtp) cc_final: 0.8473 (mtm) REVERT: F 311 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9320 (t) REVERT: F 379 MET cc_start: 0.9144 (mtp) cc_final: 0.8409 (tpp) REVERT: F 397 GLN cc_start: 0.8918 (tt0) cc_final: 0.8254 (tm-30) REVERT: F 431 MET cc_start: 0.7772 (mtp) cc_final: 0.7436 (ptp) REVERT: G 25 MET cc_start: 0.8269 (tpp) cc_final: 0.7898 (tpp) REVERT: G 48 MET cc_start: 0.8996 (ttm) cc_final: 0.8375 (ttm) REVERT: G 78 LEU cc_start: 0.9049 (tp) cc_final: 0.8555 (tt) REVERT: G 102 MET cc_start: 0.8777 (ttp) cc_final: 0.8116 (tmm) REVERT: G 243 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: H 49 MET cc_start: 0.7180 (tpp) cc_final: 0.6938 (tpp) REVERT: I 10 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: I 45 LEU cc_start: 0.5974 (tp) cc_final: 0.5639 (mm) REVERT: I 53 PHE cc_start: 0.6156 (t80) cc_final: 0.5317 (t80) REVERT: I 54 PHE cc_start: 0.6320 (m-10) cc_final: 0.5089 (t80) REVERT: I 57 MET cc_start: 0.4385 (mtp) cc_final: 0.4098 (mtp) REVERT: I 75 MET cc_start: 0.3683 (mmm) cc_final: 0.3381 (mmm) REVERT: J 11 MET cc_start: 0.3584 (mmp) cc_final: 0.2677 (tpp) REVERT: J 16 MET cc_start: 0.6719 (ttt) cc_final: 0.6084 (ttm) REVERT: J 17 MET cc_start: 0.8217 (ptp) cc_final: 0.7543 (mpp) REVERT: J 54 PHE cc_start: 0.8366 (m-80) cc_final: 0.8016 (m-80) REVERT: L 7 ASP cc_start: 0.5290 (OUTLIER) cc_final: 0.4772 (p0) REVERT: L 11 MET cc_start: 0.7102 (mtp) cc_final: 0.5687 (tpt) REVERT: L 16 MET cc_start: 0.4749 (mmm) cc_final: 0.4111 (mmp) REVERT: L 49 LEU cc_start: 0.8491 (mt) cc_final: 0.8223 (tp) REVERT: L 57 MET cc_start: 0.7633 (tmm) cc_final: 0.6670 (ptm) REVERT: L 75 MET cc_start: 0.7219 (tpp) cc_final: 0.5926 (tpt) REVERT: M 65 MET cc_start: 0.6185 (mtp) cc_final: 0.5622 (mmp) REVERT: M 68 VAL cc_start: 0.6949 (t) cc_final: 0.6712 (t) REVERT: N 11 MET cc_start: 0.7443 (mmm) cc_final: 0.6958 (mmp) REVERT: N 16 MET cc_start: 0.2846 (tpp) cc_final: 0.2566 (tpp) REVERT: N 65 MET cc_start: 0.6630 (mmp) cc_final: 0.5530 (tpt) REVERT: P 11 MET cc_start: 0.7544 (mtp) cc_final: 0.7337 (tpt) REVERT: P 57 MET cc_start: 0.5034 (ppp) cc_final: 0.4154 (ttm) REVERT: P 63 ILE cc_start: -0.0863 (OUTLIER) cc_final: -0.1065 (mm) REVERT: Q 16 MET cc_start: 0.1423 (tpt) cc_final: 0.0820 (tpt) REVERT: R 6 MET cc_start: 0.6110 (mmt) cc_final: 0.5560 (ttm) REVERT: R 11 MET cc_start: 0.6511 (ppp) cc_final: 0.4879 (tpt) REVERT: R 65 MET cc_start: 0.4793 (tpt) cc_final: 0.4281 (mtt) REVERT: S 57 MET cc_start: 0.8092 (tpt) cc_final: 0.7374 (tmm) REVERT: S 75 MET cc_start: 0.5669 (ttt) cc_final: 0.5132 (tpt) REVERT: W 147 MET cc_start: 0.9022 (mtm) cc_final: 0.8574 (mpp) REVERT: X 18 VAL cc_start: 0.6552 (m) cc_final: 0.6342 (t) REVERT: X 40 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6457 (pt) REVERT: X 49 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8122 (tpt90) REVERT: X 83 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8183 (ttp-110) REVERT: a 46 MET cc_start: 0.3658 (mmm) cc_final: 0.3306 (mmm) REVERT: a 60 PHE cc_start: 0.7287 (m-80) cc_final: 0.7063 (m-80) REVERT: a 93 MET cc_start: 0.7989 (tmm) cc_final: 0.7475 (tmm) REVERT: a 94 TYR cc_start: 0.5723 (t80) cc_final: 0.5268 (t80) REVERT: a 155 LEU cc_start: 0.7894 (mt) cc_final: 0.7661 (tt) REVERT: a 201 LEU cc_start: 0.8340 (tt) cc_final: 0.8033 (pp) REVERT: a 257 MET cc_start: 0.7558 (tmm) cc_final: 0.7172 (tpp) outliers start: 64 outliers final: 38 residues processed: 352 average time/residue: 0.1883 time to fit residues: 112.4453 Evaluate side-chains 329 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 453 optimal weight: 6.9990 chunk 153 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 416 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.055989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039961 restraints weight = 251517.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.040936 restraints weight = 145125.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041087 restraints weight = 86095.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041296 restraints weight = 72435.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041304 restraints weight = 64827.661| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 37294 Z= 0.236 Angle : 0.693 14.900 50485 Z= 0.351 Chirality : 0.043 0.313 5881 Planarity : 0.004 0.074 6510 Dihedral : 5.377 94.731 5206 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.99 % Allowed : 16.21 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.08 (0.12), residues: 4775 helix: 1.68 (0.10), residues: 2619 sheet: -0.07 (0.22), residues: 519 loop : -0.54 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 93 TYR 0.028 0.002 TYR a 94 PHE 0.042 0.002 PHE Q 53 TRP 0.014 0.002 TRP a 232 HIS 0.008 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (37294) covalent geometry : angle 0.69342 / 0.35 (50485) hydrogen bonds : bond 0.05319 / 3.63 ( 2174) hydrogen bonds : angle 4.57860 / 3.31 ( 6348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 156 MET cc_start: 0.9433 (mmt) cc_final: 0.9060 (mmt) REVERT: C 52 MET cc_start: 0.8887 (tpp) cc_final: 0.8632 (tpp) REVERT: D 209 MET cc_start: 0.8710 (mpp) cc_final: 0.8441 (mpp) REVERT: D 445 MET cc_start: 0.8871 (mmm) cc_final: 0.8080 (mmm) REVERT: E 459 LEU cc_start: 0.8382 (mp) cc_final: 0.8103 (tt) REVERT: F 56 MET cc_start: 0.9210 (mmp) cc_final: 0.8607 (mmm) REVERT: F 159 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8345 (tmm) REVERT: F 209 MET cc_start: 0.8790 (mtp) cc_final: 0.8545 (mtm) REVERT: F 379 MET cc_start: 0.9285 (mtp) cc_final: 0.8226 (tpp) REVERT: F 397 GLN cc_start: 0.8865 (tt0) cc_final: 0.8243 (tm-30) REVERT: F 431 MET cc_start: 0.7936 (mtp) cc_final: 0.7626 (ptp) REVERT: G 25 MET cc_start: 0.8308 (tpp) cc_final: 0.7978 (tpp) REVERT: G 48 MET cc_start: 0.9078 (ttm) cc_final: 0.8354 (ttm) REVERT: G 78 LEU cc_start: 0.9088 (tp) cc_final: 0.8744 (tp) REVERT: G 102 MET cc_start: 0.8715 (ttp) cc_final: 0.8104 (tmm) REVERT: G 125 PHE cc_start: 0.8784 (m-80) cc_final: 0.8494 (m-80) REVERT: I 10 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: I 53 PHE cc_start: 0.5535 (t80) cc_final: 0.4815 (t80) REVERT: I 54 PHE cc_start: 0.6441 (m-10) cc_final: 0.5074 (t80) REVERT: I 57 MET cc_start: 0.4181 (mtp) cc_final: 0.3969 (mtp) REVERT: J 11 MET cc_start: 0.3347 (mmp) cc_final: 0.2678 (tpp) REVERT: J 16 MET cc_start: 0.6772 (ttt) cc_final: 0.6424 (ttm) REVERT: J 54 PHE cc_start: 0.8281 (m-80) cc_final: 0.7694 (m-80) REVERT: L 7 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4762 (p0) REVERT: L 11 MET cc_start: 0.7156 (mtp) cc_final: 0.5726 (tpt) REVERT: L 49 LEU cc_start: 0.8354 (mt) cc_final: 0.8062 (tp) REVERT: L 75 MET cc_start: 0.7296 (tpp) cc_final: 0.5985 (tpt) REVERT: M 65 MET cc_start: 0.6252 (mtp) cc_final: 0.5595 (mmp) REVERT: M 68 VAL cc_start: 0.7105 (t) cc_final: 0.6847 (t) REVERT: N 11 MET cc_start: 0.7194 (mmm) cc_final: 0.6712 (mmm) REVERT: N 65 MET cc_start: 0.6601 (mmp) cc_final: 0.5681 (tpt) REVERT: P 11 MET cc_start: 0.7487 (mtp) cc_final: 0.7256 (tmm) REVERT: P 57 MET cc_start: 0.4993 (ppp) cc_final: 0.3994 (ttm) REVERT: Q 16 MET cc_start: 0.1046 (tpt) cc_final: 0.0471 (tpt) REVERT: R 6 MET cc_start: 0.6222 (mmt) cc_final: 0.5655 (ttm) REVERT: R 11 MET cc_start: 0.6560 (ppp) cc_final: 0.4902 (tpt) REVERT: S 57 MET cc_start: 0.7949 (tpt) cc_final: 0.7304 (tmm) REVERT: S 75 MET cc_start: 0.5695 (ttt) cc_final: 0.5095 (tpt) REVERT: W 12 LYS cc_start: 0.9527 (ttmm) cc_final: 0.9188 (ttpp) REVERT: X 18 VAL cc_start: 0.6758 (m) cc_final: 0.6544 (t) REVERT: X 40 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6522 (pt) REVERT: X 49 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8200 (tpt90) REVERT: X 83 ARG cc_start: 0.8580 (tmm-80) cc_final: 0.8120 (ttp-110) REVERT: X 141 ASP cc_start: 0.8411 (p0) cc_final: 0.8076 (t0) REVERT: a 46 MET cc_start: 0.4216 (mmm) cc_final: 0.3865 (mmm) REVERT: a 60 PHE cc_start: 0.7293 (m-80) cc_final: 0.7052 (m-80) REVERT: a 93 MET cc_start: 0.8079 (tmm) cc_final: 0.7650 (ppp) REVERT: a 155 LEU cc_start: 0.7955 (mt) cc_final: 0.7738 (tt) REVERT: a 201 LEU cc_start: 0.8350 (tt) cc_final: 0.8051 (pp) REVERT: a 257 MET cc_start: 0.7660 (tmm) cc_final: 0.7275 (tpp) outliers start: 76 outliers final: 50 residues processed: 335 average time/residue: 0.1858 time to fit residues: 107.0379 Evaluate side-chains 328 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 165 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 469 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 294 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041161 restraints weight = 249340.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042182 restraints weight = 147157.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042482 restraints weight = 79914.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042596 restraints weight = 70263.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.042636 restraints weight = 62356.009| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37294 Z= 0.134 Angle : 0.643 13.109 50485 Z= 0.318 Chirality : 0.042 0.299 5881 Planarity : 0.004 0.072 6510 Dihedral : 5.159 91.625 5206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 16.71 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 4775 helix: 1.82 (0.10), residues: 2625 sheet: 0.03 (0.22), residues: 523 loop : -0.47 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 93 TYR 0.023 0.001 TYR F 367 PHE 0.052 0.001 PHE Q 53 TRP 0.008 0.001 TRP a 232 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (37294) covalent geometry : angle 0.64277 / 0.32 (50485) hydrogen bonds : bond 0.04992 / 3.38 ( 2174) hydrogen bonds : angle 4.36315 / 3.16 ( 6348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 1.421 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: A 12 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 156 MET cc_start: 0.9461 (mmt) cc_final: 0.9123 (mmt) REVERT: C 52 MET cc_start: 0.8922 (tpp) cc_final: 0.8644 (tpp) REVERT: C 103 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9340 (mm) REVERT: D 193 MET cc_start: 0.8334 (mmm) cc_final: 0.8028 (mmm) REVERT: D 445 MET cc_start: 0.8963 (mmm) cc_final: 0.8190 (mmm) REVERT: E 88 MET cc_start: 0.8259 (mpp) cc_final: 0.7453 (mpp) REVERT: E 459 LEU cc_start: 0.8386 (mp) cc_final: 0.8090 (tt) REVERT: F 56 MET cc_start: 0.9296 (mmp) cc_final: 0.8807 (mmm) REVERT: F 159 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8293 (tmm) REVERT: F 209 MET cc_start: 0.8792 (mtp) cc_final: 0.8549 (mtm) REVERT: F 311 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9275 (t) REVERT: F 379 MET cc_start: 0.9295 (mtp) cc_final: 0.8261 (tpp) REVERT: F 397 GLN cc_start: 0.8836 (tt0) cc_final: 0.8180 (tm-30) REVERT: F 431 MET cc_start: 0.7910 (mtp) cc_final: 0.7598 (ptp) REVERT: F 445 MET cc_start: 0.6913 (mmm) cc_final: 0.6546 (mmm) REVERT: G 25 MET cc_start: 0.8393 (tpp) cc_final: 0.8042 (tpp) REVERT: G 48 MET cc_start: 0.9013 (ttm) cc_final: 0.8344 (ttm) REVERT: G 78 LEU cc_start: 0.9100 (tp) cc_final: 0.8548 (tt) REVERT: G 102 MET cc_start: 0.8735 (ttp) cc_final: 0.8095 (tmm) REVERT: G 125 PHE cc_start: 0.8826 (m-80) cc_final: 0.8527 (m-80) REVERT: G 155 MET cc_start: 0.9123 (mmm) cc_final: 0.8894 (mmt) REVERT: I 45 LEU cc_start: 0.6028 (tp) cc_final: 0.5662 (mm) REVERT: I 53 PHE cc_start: 0.5437 (t80) cc_final: 0.4700 (t80) REVERT: I 54 PHE cc_start: 0.6422 (m-10) cc_final: 0.5043 (t80) REVERT: I 57 MET cc_start: 0.4148 (mtp) cc_final: 0.3937 (mtp) REVERT: J 11 MET cc_start: 0.3276 (mmp) cc_final: 0.2737 (tpp) REVERT: J 16 MET cc_start: 0.6704 (ttt) cc_final: 0.6290 (ttt) REVERT: J 54 PHE cc_start: 0.8192 (m-80) cc_final: 0.7687 (m-80) REVERT: L 7 ASP cc_start: 0.5448 (OUTLIER) cc_final: 0.5099 (p0) REVERT: L 11 MET cc_start: 0.7010 (mtp) cc_final: 0.5722 (tpt) REVERT: L 49 LEU cc_start: 0.8382 (mt) cc_final: 0.8114 (tp) REVERT: L 57 MET cc_start: 0.7611 (tmm) cc_final: 0.6604 (ptm) REVERT: L 75 MET cc_start: 0.7132 (tpp) cc_final: 0.6209 (tpt) REVERT: M 65 MET cc_start: 0.6222 (mtp) cc_final: 0.5588 (mmp) REVERT: N 11 MET cc_start: 0.7296 (mmm) cc_final: 0.6929 (mmt) REVERT: N 16 MET cc_start: 0.2734 (tpp) cc_final: 0.2442 (tpp) REVERT: N 65 MET cc_start: 0.6791 (mmp) cc_final: 0.5817 (tpt) REVERT: P 57 MET cc_start: 0.5023 (ppp) cc_final: 0.3982 (ttm) REVERT: Q 16 MET cc_start: 0.0690 (tpt) cc_final: 0.0239 (mmm) REVERT: R 6 MET cc_start: 0.6213 (mmt) cc_final: 0.5665 (ttm) REVERT: R 11 MET cc_start: 0.6181 (ppp) cc_final: 0.4826 (tpt) REVERT: R 65 MET cc_start: 0.4846 (tpt) cc_final: 0.4339 (mtt) REVERT: S 6 MET cc_start: 0.5830 (ppp) cc_final: 0.5244 (pmm) REVERT: S 57 MET cc_start: 0.8073 (tpt) cc_final: 0.7426 (tmm) REVERT: S 75 MET cc_start: 0.5775 (ttt) cc_final: 0.5266 (tpt) REVERT: W 12 LYS cc_start: 0.9528 (ttmm) cc_final: 0.9170 (ttpp) REVERT: X 30 MET cc_start: 0.5945 (ppp) cc_final: 0.5535 (ppp) REVERT: X 40 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6413 (pt) REVERT: X 49 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8175 (tpt90) REVERT: X 83 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8145 (ttp-110) REVERT: X 141 ASP cc_start: 0.8471 (p0) cc_final: 0.8095 (t0) REVERT: a 46 MET cc_start: 0.4210 (mmm) cc_final: 0.3819 (mmm) REVERT: a 60 PHE cc_start: 0.7321 (m-80) cc_final: 0.7095 (m-80) REVERT: a 93 MET cc_start: 0.8158 (tmm) cc_final: 0.7762 (tmm) REVERT: a 201 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (pp) REVERT: a 257 MET cc_start: 0.7770 (tmm) cc_final: 0.7449 (tpp) outliers start: 59 outliers final: 45 residues processed: 334 average time/residue: 0.1866 time to fit residues: 107.2617 Evaluate side-chains 329 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 305 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 299 optimal weight: 0.4980 chunk 345 optimal weight: 3.9990 chunk 412 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 407 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN A 358 ASN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 294 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.056642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040628 restraints weight = 250853.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041638 restraints weight = 139114.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041852 restraints weight = 86688.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042131 restraints weight = 63131.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042157 restraints weight = 56990.234| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37294 Z= 0.165 Angle : 0.668 14.123 50485 Z= 0.331 Chirality : 0.043 0.431 5881 Planarity : 0.004 0.073 6510 Dihedral : 5.185 92.328 5206 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.44 % Allowed : 16.97 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.25 (0.12), residues: 4775 helix: 1.81 (0.10), residues: 2622 sheet: 0.03 (0.22), residues: 523 loop : -0.46 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 93 TYR 0.021 0.001 TYR F 367 PHE 0.049 0.001 PHE Q 53 TRP 0.011 0.001 TRP a 111 HIS 0.007 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (37294) covalent geometry : angle 0.66753 / 0.33 (50485) hydrogen bonds : bond 0.04994 / 3.38 ( 2174) hydrogen bonds : angle 4.43399 / 3.21 ( 6348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 156 MET cc_start: 0.9451 (mmt) cc_final: 0.9123 (mmt) REVERT: C 52 MET cc_start: 0.8839 (tpp) cc_final: 0.8604 (tpp) REVERT: D 445 MET cc_start: 0.8956 (mmm) cc_final: 0.8202 (mmm) REVERT: E 88 MET cc_start: 0.8245 (mpp) cc_final: 0.7503 (mpp) REVERT: E 459 LEU cc_start: 0.8352 (mp) cc_final: 0.8049 (tt) REVERT: F 56 MET cc_start: 0.9257 (mmp) cc_final: 0.8574 (mmm) REVERT: F 159 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8331 (tmm) REVERT: F 209 MET cc_start: 0.8815 (mtp) cc_final: 0.8582 (mtm) REVERT: F 379 MET cc_start: 0.9226 (mtp) cc_final: 0.8230 (tpp) REVERT: F 397 GLN cc_start: 0.8842 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 431 MET cc_start: 0.7870 (mtp) cc_final: 0.7540 (ptp) REVERT: F 445 MET cc_start: 0.6966 (mmm) cc_final: 0.6636 (mmm) REVERT: G 25 MET cc_start: 0.8295 (tpp) cc_final: 0.7971 (tpp) REVERT: G 48 MET cc_start: 0.9048 (ttm) cc_final: 0.8320 (ttm) REVERT: G 78 LEU cc_start: 0.9094 (tp) cc_final: 0.8723 (tp) REVERT: G 102 MET cc_start: 0.8697 (ttp) cc_final: 0.8000 (tmm) REVERT: G 125 PHE cc_start: 0.8824 (m-80) cc_final: 0.8520 (m-80) REVERT: I 53 PHE cc_start: 0.5475 (t80) cc_final: 0.4718 (t80) REVERT: I 54 PHE cc_start: 0.6599 (m-10) cc_final: 0.5071 (t80) REVERT: I 57 MET cc_start: 0.4104 (mtp) cc_final: 0.3898 (mtp) REVERT: J 11 MET cc_start: 0.3067 (mmp) cc_final: 0.2455 (tpp) REVERT: J 16 MET cc_start: 0.6758 (ttt) cc_final: 0.6103 (ttm) REVERT: J 17 MET cc_start: 0.7454 (ptp) cc_final: 0.6811 (mpp) REVERT: J 54 PHE cc_start: 0.8292 (m-80) cc_final: 0.7748 (m-80) REVERT: L 7 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.5063 (p0) REVERT: L 11 MET cc_start: 0.6854 (mtp) cc_final: 0.5559 (tpt) REVERT: L 49 LEU cc_start: 0.8382 (mt) cc_final: 0.8119 (tp) REVERT: L 57 MET cc_start: 0.7602 (tmm) cc_final: 0.6602 (ptm) REVERT: L 75 MET cc_start: 0.6883 (tpp) cc_final: 0.5954 (tpt) REVERT: M 17 MET cc_start: 0.4970 (tpp) cc_final: 0.4528 (tpp) REVERT: M 65 MET cc_start: 0.6346 (mtp) cc_final: 0.5521 (mmp) REVERT: M 68 VAL cc_start: 0.7120 (t) cc_final: 0.6394 (p) REVERT: N 11 MET cc_start: 0.7367 (mmm) cc_final: 0.7069 (mmt) REVERT: N 65 MET cc_start: 0.6763 (mmp) cc_final: 0.5399 (tpt) REVERT: P 11 MET cc_start: 0.8057 (tmm) cc_final: 0.7445 (mtp) REVERT: P 16 MET cc_start: 0.3707 (mtt) cc_final: 0.3469 (ptp) REVERT: P 57 MET cc_start: 0.5030 (ppp) cc_final: 0.3970 (ttm) REVERT: Q 16 MET cc_start: 0.0740 (tpt) cc_final: 0.0237 (mmm) REVERT: R 6 MET cc_start: 0.6396 (mmt) cc_final: 0.5835 (ttm) REVERT: R 11 MET cc_start: 0.6295 (ppp) cc_final: 0.4223 (tpt) REVERT: R 53 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6981 (t80) REVERT: R 65 MET cc_start: 0.4888 (tpt) cc_final: 0.4397 (mtt) REVERT: S 57 MET cc_start: 0.8088 (tpt) cc_final: 0.7578 (tmm) REVERT: S 75 MET cc_start: 0.5785 (ttt) cc_final: 0.5350 (tpt) REVERT: W 12 LYS cc_start: 0.9531 (ttmm) cc_final: 0.9179 (ttpp) REVERT: X 30 MET cc_start: 0.5890 (ppp) cc_final: 0.5565 (ppp) REVERT: X 40 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6480 (pt) REVERT: X 49 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8172 (tpt90) REVERT: X 83 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8135 (ttp-110) REVERT: X 141 ASP cc_start: 0.8406 (p0) cc_final: 0.8037 (t0) REVERT: a 60 PHE cc_start: 0.7380 (m-80) cc_final: 0.7142 (m-80) REVERT: a 93 MET cc_start: 0.8269 (tmm) cc_final: 0.7916 (ppp) REVERT: a 201 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (pp) REVERT: a 257 MET cc_start: 0.7841 (tmm) cc_final: 0.7545 (tpp) outliers start: 55 outliers final: 43 residues processed: 322 average time/residue: 0.1828 time to fit residues: 100.8987 Evaluate side-chains 322 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 264 optimal weight: 4.9990 chunk 363 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 421 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.056690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040746 restraints weight = 250269.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041790 restraints weight = 147362.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041872 restraints weight = 83630.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042009 restraints weight = 70171.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042199 restraints weight = 63478.602| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37294 Z= 0.162 Angle : 0.665 12.581 50485 Z= 0.330 Chirality : 0.043 0.433 5881 Planarity : 0.004 0.073 6510 Dihedral : 5.167 92.391 5206 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.42 % Allowed : 17.18 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.21 (0.12), residues: 4775 helix: 1.77 (0.10), residues: 2631 sheet: 0.06 (0.22), residues: 515 loop : -0.48 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 93 TYR 0.021 0.001 TYR F 367 PHE 0.048 0.001 PHE Q 53 TRP 0.010 0.001 TRP a 232 HIS 0.007 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (37294) covalent geometry : angle 0.66509 / 0.33 (50485) hydrogen bonds : bond 0.04942 / 3.35 ( 2174) hydrogen bonds : angle 4.44283 / 3.21 ( 6348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.23 seconds wall clock time: 94 minutes 58.43 seconds (5698.43 seconds total)