Starting phenix.real_space_refine on Sat Mar 7 02:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqv_20454/03_2026/6pqv_20454_neut.cif" } resolution = 3.3 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 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 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: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} 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: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "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: "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: "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: "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: "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: "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: "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: "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: "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} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.18, per 1000 atoms: 0.22 Number of scatterers: 36971 At special positions: 0 Unit cell: (178.035, 221.195, 139.191, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 28 sheets defined 60.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'W' and resid 3 through 21 removed outlier: 3.638A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix removed outlier: 3.632A pdb=" N GLU W 20 " --> pdb=" O ASP W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.825A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.644A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY W 49 " --> pdb=" O GLU W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 70 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: 3.776A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 removed outlier: 4.034A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG W 131 " --> pdb=" O ALA W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 174 removed outlier: 3.711A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 removed outlier: 4.213A pdb=" N GLN C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.580A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.512A pdb=" N ILE C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.607A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.855A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.976A pdb=" N ALA C 285 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.679A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.543A pdb=" N GLU C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.559A pdb=" N ASP C 336 " --> pdb=" O GLN C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.956A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.931A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.050A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.731A pdb=" N VAL C 447 " --> pdb=" O GLN C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.666A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.584A pdb=" N GLY C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.694A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.765A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.552A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) 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 237 removed outlier: 3.711A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.627A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.617A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.525A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.921A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (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 377 through 382 removed outlier: 3.696A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.569A pdb=" N LYS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 4.122A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 432 removed outlier: 3.509A pdb=" N LYS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.636A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 478 removed outlier: 3.990A pdb=" N ALA B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.524A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'A' and resid 6 through 20 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.551A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.517A pdb=" N SER A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.737A pdb=" N LYS A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) 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 251 Proline residue: A 239 - end of helix removed outlier: 3.622A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.527A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.626A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.508A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.742A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.695A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 4.011A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.800A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.183A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.641A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU X 16 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA X 21 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.737A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA X 90 " --> pdb=" O ILE X 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 155 removed outlier: 4.182A pdb=" N LYS X 151 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.584A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.679A pdb=" N SER G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 3.835A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.832A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.647A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.694A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.694A 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 203 removed outlier: 3.775A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.866A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.574A pdb=" N THR F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'F' and resid 130 through 137 removed outlier: 3.659A pdb=" N ASP F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.508A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 removed outlier: 4.130A pdb=" N ASP F 200 " --> pdb=" O ASN F 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.618A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG F 218 " --> pdb=" O GLY F 214 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.051A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 259 No H-bonds generated for 'chain 'F' and resid 257 through 259' Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.731A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 3.554A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 386 through 400 removed outlier: 3.540A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 removed outlier: 3.653A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.614A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.662A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.765A pdb=" N GLU E 192 " --> pdb=" O ASP E 188 " (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: 3.626A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.615A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.883A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.556A pdb=" N ASP E 301 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 4.207A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.642A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 removed outlier: 3.745A pdb=" N GLU E 432 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 448 through 457 removed outlier: 4.612A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 171 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.592A pdb=" N TYR D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) 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: 4.915A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.527A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.617A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 378 removed outlier: 7.909A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 385 through 400 removed outlier: 3.510A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 removed outlier: 3.708A pdb=" N GLU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 removed outlier: 4.004A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.892A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 13 " --> pdb=" O LEU J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.555A pdb=" N ILE J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 56 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 removed outlier: 4.141A pdb=" N ILE J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 40 removed outlier: 4.045A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 31 " --> pdb=" O GLY L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 44 No H-bonds generated for 'chain 'L' and resid 42 through 44' Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.501A pdb=" N LEU L 49 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.611A pdb=" N ALA M 20 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 28 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU M 37 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.989A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL M 60 " --> pdb=" O VAL M 56 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP M 61 " --> pdb=" O MET M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.063A pdb=" N GLY M 69 " --> pdb=" O MET M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 6 Processing helix chain 'N' and resid 7 through 41 removed outlier: 4.682A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.586A pdb=" N GLN N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.094A pdb=" N MET O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN O 42 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 4.474A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.990A pdb=" N GLY O 69 " --> pdb=" O MET O 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL O 74 " --> pdb=" O LEU O 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 42 removed outlier: 3.900A pdb=" N MET P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 61 removed outlier: 3.561A pdb=" N THR P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 76 Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.620A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Q 21 " --> pdb=" O MET Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 62 removed outlier: 3.625A pdb=" N LEU Q 49 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.873A pdb=" N GLY Q 69 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 42 removed outlier: 3.910A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 4.018A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL R 60 " --> pdb=" O VAL R 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.621A pdb=" N LEU Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 104 removed outlier: 4.394A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Y 67 " --> pdb=" O ASP Y 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 140 removed outlier: 3.823A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER Y 139 " --> pdb=" O ILE Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 154 removed outlier: 3.797A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Y 152 " --> pdb=" O ILE Y 148 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL Y 153 " --> pdb=" O VAL Y 149 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.606A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.834A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS a 65 " --> pdb=" O ARG a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.890A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 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 removed outlier: 3.590A pdb=" N ILE a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 4.325A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.713A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL a 198 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER a 199 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.585A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET a 215 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.120A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.492A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA a 267 " --> pdb=" O TYR a 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.539A pdb=" N LEU I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 77 Processing helix chain 'S' and resid 7 through 42 removed outlier: 3.947A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA S 14 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU S 31 " --> pdb=" O GLY S 27 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 4.144A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL S 60 " --> pdb=" O VAL S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 6.396A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU B 66 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 13.676A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 35 removed outlier: 4.810A pdb=" N ASP E 27 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA E 28 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 9 removed outlier: 3.704A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 89 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 67 removed outlier: 4.120A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 40 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.500A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.395A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.481A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 322 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.458A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.380A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB4, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AB5, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.565A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.425A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.501A pdb=" N ILE H 23 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 18 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 14 through 27 removed outlier: 7.225A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY H 27 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.316A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.695A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.539A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.469A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.742A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.789A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.371A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.390A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.591A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.147A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 21 through 22 2154 hydrogen bonds defined for protein. 6267 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: 7.91 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6332 1.30 - 1.43: 8616 1.43 - 1.56: 22196 1.56 - 1.69: 24 1.69 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.09e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.83e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 50608 4.72 - 9.44: 183 9.44 - 14.16: 0 14.16 - 18.88: 1 18.88 - 23.60: 5 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.99 22.88 1.00e+00 1.00e+00 5.23e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.66 22.21 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.59 20.24 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 117.70 19.13 1.00e+00 1.00e+00 3.66e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 22116 31.70 - 63.40: 606 63.40 - 95.10: 66 95.10 - 126.80: 4 126.80 - 158.50: 2 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 98.51 -158.50 1 2.00e+01 2.50e-03 4.63e+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 300.00 168.92 131.07 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 59.50 -119.50 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5494 0.095 - 0.190: 406 0.190 - 0.285: 16 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ARG a 24 " pdb=" N ARG a 24 " pdb=" C ARG a 24 " pdb=" CB ARG a 24 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.023 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C ALA D 264 " -0.081 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 262 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C PRO E 262 " -0.077 2.00e-02 2.50e+03 pdb=" O PRO E 262 " 0.030 2.00e-02 2.50e+03 pdb=" N SER E 263 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 336 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ASP B 336 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP B 336 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL B 337 " -0.024 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 62 2.39 - 3.01: 23382 3.01 - 3.64: 53281 3.64 - 4.27: 83876 4.27 - 4.90: 141887 Nonbonded interactions: 302488 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.757 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.780 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.830 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.862 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.871 2.170 ... (remaining 302483 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 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 500) selection = (chain 'E' and resid 2 through 500) selection = (chain 'F' and resid 2 through 500) } 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 individual isotropic 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.630 Find NCS groups from input model: 0.750 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.009 0.078 37528 Z= 0.446 Angle : 0.928 23.601 50797 Z= 0.616 Chirality : 0.053 0.475 5920 Planarity : 0.005 0.061 6550 Dihedral : 14.821 158.502 13976 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 2.58 % Allowed : 8.45 % Favored : 88.97 % 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: -2.75 (0.10), residues: 4807 helix: -2.00 (0.08), residues: 2575 sheet: -0.73 (0.20), residues: 513 loop : -1.54 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 164 TYR 0.042 0.002 TYR B 492 PHE 0.030 0.002 PHE D 139 TRP 0.020 0.002 TRP G 203 HIS 0.008 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00876 (37528) covalent geometry : angle 0.92844 (50797) hydrogen bonds : bond 0.16681 ( 2154) hydrogen bonds : angle 7.28666 ( 6267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 740 time to evaluate : 1.361 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: W 109 ASP cc_start: 0.8308 (m-30) cc_final: 0.8105 (m-30) REVERT: W 143 ASP cc_start: 0.8309 (t0) cc_final: 0.8077 (t0) REVERT: W 156 ASP cc_start: 0.7647 (p0) cc_final: 0.6780 (p0) REVERT: W 159 ILE cc_start: 0.8826 (mp) cc_final: 0.8308 (tt) REVERT: C 236 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.7439 (t80) REVERT: C 484 GLN cc_start: 0.8448 (tp40) cc_final: 0.7773 (tp-100) REVERT: C 488 GLN cc_start: 0.8932 (tt0) cc_final: 0.8498 (tt0) REVERT: B 86 MET cc_start: 0.8774 (mtt) cc_final: 0.8517 (mtt) REVERT: B 295 SER cc_start: 0.9324 (t) cc_final: 0.9102 (p) REVERT: A 401 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8382 (ttm-80) REVERT: A 415 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8081 (t70) REVERT: A 511 GLN cc_start: 0.3928 (OUTLIER) cc_final: 0.3692 (tp-100) REVERT: X 29 LEU cc_start: 0.9018 (mt) cc_final: 0.8744 (mt) REVERT: X 42 ASP cc_start: 0.7112 (m-30) cc_final: 0.6842 (m-30) REVERT: X 129 VAL cc_start: 0.9197 (t) cc_final: 0.8978 (p) REVERT: H 62 ILE cc_start: 0.8816 (mt) cc_final: 0.8476 (mm) REVERT: H 72 GLN cc_start: 0.8026 (mt0) cc_final: 0.7777 (mm110) REVERT: G 31 MET cc_start: 0.8448 (ttp) cc_final: 0.8154 (ttp) REVERT: G 155 MET cc_start: 0.9270 (mmm) cc_final: 0.9067 (mmt) REVERT: G 259 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7755 (mp0) REVERT: F 209 MET cc_start: 0.8669 (ptp) cc_final: 0.8276 (ptp) REVERT: F 211 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8439 (mt-10) REVERT: F 372 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: E 242 ASP cc_start: 0.7583 (t0) cc_final: 0.7348 (t0) REVERT: E 323 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7713 (mmm-85) REVERT: E 368 GLN cc_start: 0.8636 (tp40) cc_final: 0.8095 (tp40) REVERT: D 88 MET cc_start: 0.9106 (mtm) cc_final: 0.8904 (mtp) REVERT: D 343 GLN cc_start: 0.8284 (mp10) cc_final: 0.7941 (mt0) REVERT: D 379 MET cc_start: 0.8300 (ttt) cc_final: 0.8098 (tpp) REVERT: D 384 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: L 6 MET cc_start: 0.7537 (ttp) cc_final: 0.7260 (mmt) REVERT: L 11 MET cc_start: 0.7388 (tpt) cc_final: 0.7092 (tpt) REVERT: L 57 MET cc_start: 0.8996 (tmm) cc_final: 0.8543 (tmm) REVERT: L 63 ILE cc_start: 0.7548 (mm) cc_final: 0.7340 (mm) REVERT: L 76 PHE cc_start: 0.7488 (m-80) cc_final: 0.7187 (m-80) REVERT: M 11 MET cc_start: 0.8405 (tpt) cc_final: 0.7995 (tpp) REVERT: M 16 MET cc_start: 0.8420 (ttp) cc_final: 0.8209 (ttm) REVERT: M 17 MET cc_start: 0.8455 (mtm) cc_final: 0.8132 (mtm) REVERT: M 41 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7566 (mtm-85) REVERT: M 42 GLN cc_start: 0.7319 (pt0) cc_final: 0.7082 (pt0) REVERT: M 65 MET cc_start: 0.8402 (mtp) cc_final: 0.8113 (ptt) REVERT: N 76 PHE cc_start: 0.6368 (m-80) cc_final: 0.5447 (t80) REVERT: O 8 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6018 (tp) REVERT: P 36 LEU cc_start: 0.8567 (mt) cc_final: 0.8338 (tt) REVERT: P 55 ILE cc_start: 0.8806 (mm) cc_final: 0.8597 (mt) REVERT: Q 34 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7836 (mmtt) REVERT: Q 75 MET cc_start: 0.8997 (mtm) cc_final: 0.8671 (mtp) REVERT: R 10 TYR cc_start: 0.8054 (m-80) cc_final: 0.7420 (m-80) REVERT: R 11 MET cc_start: 0.8312 (tpt) cc_final: 0.7768 (tpt) REVERT: R 16 MET cc_start: 0.8503 (mtp) cc_final: 0.7884 (ttm) REVERT: R 57 MET cc_start: 0.9081 (ttp) cc_final: 0.8853 (tmm) REVERT: R 63 ILE cc_start: 0.8832 (mm) cc_final: 0.8496 (mt) REVERT: R 65 MET cc_start: 0.9070 (mmm) cc_final: 0.8868 (mmm) REVERT: R 75 MET cc_start: 0.7765 (ttt) cc_final: 0.7469 (tpp) REVERT: R 76 PHE cc_start: 0.7086 (m-80) cc_final: 0.6574 (m-10) REVERT: Y 20 PHE cc_start: 0.8097 (t80) cc_final: 0.7785 (t80) REVERT: Y 38 LYS cc_start: 0.8836 (tptt) cc_final: 0.8628 (tmtt) REVERT: Y 56 LEU cc_start: 0.7469 (mp) cc_final: 0.7176 (tp) REVERT: Y 96 GLN cc_start: 0.8661 (tt0) cc_final: 0.8446 (tp40) REVERT: a 33 ASN cc_start: 0.4643 (OUTLIER) cc_final: 0.4376 (p0) REVERT: a 61 ARG cc_start: 0.6190 (tpt170) cc_final: 0.5601 (mtm110) REVERT: a 65 LYS cc_start: 0.5875 (tttt) cc_final: 0.5343 (mmtm) REVERT: a 94 TYR cc_start: 0.5315 (t80) cc_final: 0.5005 (t80) REVERT: a 116 ASN cc_start: 0.7931 (m-40) cc_final: 0.7661 (m-40) REVERT: a 215 MET cc_start: 0.8652 (mmt) cc_final: 0.8392 (mmm) REVERT: a 220 LEU cc_start: 0.8744 (tp) cc_final: 0.8478 (mt) REVERT: I 16 MET cc_start: 0.7256 (ttm) cc_final: 0.7033 (ttm) REVERT: S 6 MET cc_start: 0.7644 (mmt) cc_final: 0.7438 (mmp) REVERT: S 63 ILE cc_start: 0.8855 (mm) cc_final: 0.8614 (mt) REVERT: S 73 TYR cc_start: 0.8079 (t80) cc_final: 0.7252 (t80) outliers start: 99 outliers final: 49 residues processed: 822 average time/residue: 0.2351 time to fit residues: 309.5163 Evaluate side-chains 600 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 544 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 139 ASN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain Q residue 11 MET Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain a residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN C 58 ASN C 200 GLN B 18 GLN B 42 HIS B 58 ASN B 186 GLN B 333 GLN B 443 GLN A 65 ASN A 147 GLN A 344 ASN A 484 GLN A 493 ASN X 2 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 57 HIS G 64 HIS G 91 ASN G 126 ASN G 252 ASN G 265 ASN G 269 GLN F 7 GLN E 353 HIS D 215 ASN J 52 GLN L 42 GLN M 5 ASN M 52 GLN N 5 ASN ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 184 ASN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070228 restraints weight = 80718.710| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.02 r_work: 0.2870 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37528 Z= 0.146 Angle : 0.651 9.217 50797 Z= 0.341 Chirality : 0.045 0.304 5920 Planarity : 0.004 0.048 6550 Dihedral : 8.612 164.845 5425 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 11.76 % Favored : 85.64 % 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: -0.69 (0.12), residues: 4807 helix: -0.15 (0.10), residues: 2586 sheet: -0.32 (0.21), residues: 535 loop : -0.73 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 138 TYR 0.021 0.001 TYR B 236 PHE 0.027 0.002 PHE O 54 TRP 0.017 0.001 TRP a 111 HIS 0.007 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00306 (37528) covalent geometry : angle 0.65099 (50797) hydrogen bonds : bond 0.05407 ( 2154) hydrogen bonds : angle 5.06618 ( 6267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 623 time to evaluate : 1.306 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: W 143 ASP cc_start: 0.8350 (t0) cc_final: 0.8025 (t0) REVERT: W 156 ASP cc_start: 0.8062 (p0) cc_final: 0.7420 (p0) REVERT: C 245 MET cc_start: 0.9233 (mtt) cc_final: 0.8976 (mtt) REVERT: C 484 GLN cc_start: 0.8873 (tp40) cc_final: 0.8349 (tp-100) REVERT: C 488 GLN cc_start: 0.9182 (tt0) cc_final: 0.8900 (tt0) REVERT: A 172 GLN cc_start: 0.9016 (tt0) cc_final: 0.8667 (tt0) REVERT: A 180 ILE cc_start: 0.9427 (pt) cc_final: 0.9152 (mm) REVERT: A 401 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8405 (ttm-80) REVERT: X 42 ASP cc_start: 0.7059 (m-30) cc_final: 0.6736 (m-30) REVERT: H 23 ILE cc_start: 0.9074 (pt) cc_final: 0.8700 (mm) REVERT: H 129 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7961 (mtm-85) REVERT: H 132 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: G 31 MET cc_start: 0.8885 (ttp) cc_final: 0.8663 (ttp) REVERT: G 155 MET cc_start: 0.9263 (mmm) cc_final: 0.9045 (mmp) REVERT: F 209 MET cc_start: 0.9012 (ptp) cc_final: 0.8741 (ptp) REVERT: E 368 GLN cc_start: 0.8789 (tp40) cc_final: 0.8120 (tp-100) REVERT: D 166 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8972 (mp) REVERT: J 37 GLU cc_start: 0.8937 (tp30) cc_final: 0.8692 (tp30) REVERT: L 11 MET cc_start: 0.7152 (tpt) cc_final: 0.6760 (tpt) REVERT: L 17 MET cc_start: 0.7975 (mtm) cc_final: 0.7562 (mtt) REVERT: L 34 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8078 (mmpt) REVERT: L 63 ILE cc_start: 0.7922 (mm) cc_final: 0.7642 (mt) REVERT: L 75 MET cc_start: 0.7870 (mmm) cc_final: 0.7366 (tpt) REVERT: L 76 PHE cc_start: 0.7509 (m-80) cc_final: 0.7013 (m-80) REVERT: M 34 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8256 (mmtt) REVERT: M 42 GLN cc_start: 0.7512 (pt0) cc_final: 0.7234 (pt0) REVERT: M 54 PHE cc_start: 0.8656 (m-80) cc_final: 0.8417 (m-80) REVERT: M 65 MET cc_start: 0.8340 (mtp) cc_final: 0.8053 (ptt) REVERT: N 10 TYR cc_start: 0.6970 (m-80) cc_final: 0.6740 (m-80) REVERT: N 41 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7942 (mtt90) REVERT: N 75 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7626 (tmm) REVERT: N 76 PHE cc_start: 0.6179 (m-80) cc_final: 0.5395 (t80) REVERT: O 6 MET cc_start: 0.6091 (mpp) cc_final: 0.5247 (mpp) REVERT: O 10 TYR cc_start: 0.7032 (m-10) cc_final: 0.6346 (m-10) REVERT: O 11 MET cc_start: 0.7521 (tpp) cc_final: 0.6099 (mtt) REVERT: O 17 MET cc_start: 0.8087 (ttm) cc_final: 0.7313 (tpp) REVERT: O 72 LEU cc_start: 0.8523 (pp) cc_final: 0.8317 (mm) REVERT: P 36 LEU cc_start: 0.8667 (mt) cc_final: 0.8443 (tt) REVERT: P 42 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7622 (mp10) REVERT: P 51 THR cc_start: 0.8361 (p) cc_final: 0.8151 (t) REVERT: P 55 ILE cc_start: 0.8890 (mm) cc_final: 0.8639 (mt) REVERT: Q 11 MET cc_start: 0.8542 (ttm) cc_final: 0.7535 (tpt) REVERT: Q 35 PHE cc_start: 0.8829 (t80) cc_final: 0.8270 (t80) REVERT: Q 54 PHE cc_start: 0.7830 (m-80) cc_final: 0.7458 (m-80) REVERT: Q 75 MET cc_start: 0.9162 (mtm) cc_final: 0.8952 (mtp) REVERT: R 10 TYR cc_start: 0.8099 (m-80) cc_final: 0.7760 (m-80) REVERT: R 16 MET cc_start: 0.8499 (mtp) cc_final: 0.8037 (ttm) REVERT: Y 16 LEU cc_start: 0.7488 (mm) cc_final: 0.7097 (mt) REVERT: Y 20 PHE cc_start: 0.7875 (t80) cc_final: 0.7611 (t80) REVERT: Y 30 MET cc_start: 0.8363 (ptm) cc_final: 0.8114 (mmm) REVERT: Y 38 LYS cc_start: 0.8921 (tptt) cc_final: 0.8717 (tmtt) REVERT: Y 82 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8253 (tpp-160) REVERT: Y 98 ARG cc_start: 0.7305 (mtp-110) cc_final: 0.7074 (ttm-80) REVERT: a 55 LEU cc_start: 0.7014 (mm) cc_final: 0.6791 (mt) REVERT: a 65 LYS cc_start: 0.5504 (tttt) cc_final: 0.4948 (mtpt) REVERT: a 118 MET cc_start: 0.7844 (mmt) cc_final: 0.7626 (mmt) REVERT: a 215 MET cc_start: 0.8507 (mmt) cc_final: 0.7769 (mmm) REVERT: a 220 LEU cc_start: 0.8629 (tp) cc_final: 0.8338 (mt) REVERT: a 241 TRP cc_start: 0.8221 (t-100) cc_final: 0.7833 (t-100) REVERT: a 252 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8502 (mm-40) REVERT: S 37 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7998 (mm-30) REVERT: S 57 MET cc_start: 0.9127 (tmm) cc_final: 0.8860 (tmm) REVERT: S 73 TYR cc_start: 0.7616 (t80) cc_final: 0.7292 (t80) outliers start: 100 outliers final: 54 residues processed: 692 average time/residue: 0.2220 time to fit residues: 249.5547 Evaluate side-chains 584 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 527 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 chunk 431 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN X 2 ASN G 57 HIS F 7 GLN F 187 ASN D 210 ASN L 5 ASN a 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068341 restraints weight = 81282.896| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.11 r_work: 0.2831 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 37528 Z= 0.216 Angle : 0.641 10.180 50797 Z= 0.333 Chirality : 0.045 0.179 5920 Planarity : 0.004 0.057 6550 Dihedral : 7.930 165.007 5369 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.81 % Allowed : 13.71 % Favored : 82.48 % 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: -0.17 (0.12), residues: 4807 helix: 0.35 (0.10), residues: 2621 sheet: -0.09 (0.21), residues: 533 loop : -0.69 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 41 TYR 0.026 0.001 TYR a 263 PHE 0.037 0.002 PHE E 189 TRP 0.013 0.001 TRP a 111 HIS 0.006 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00509 (37528) covalent geometry : angle 0.64133 (50797) hydrogen bonds : bond 0.05098 ( 2154) hydrogen bonds : angle 4.84458 ( 6267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 548 time to evaluate : 1.417 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: W 143 ASP cc_start: 0.8365 (t0) cc_final: 0.7989 (t0) REVERT: W 156 ASP cc_start: 0.8050 (p0) cc_final: 0.7363 (p0) REVERT: C 236 TYR cc_start: 0.9420 (OUTLIER) cc_final: 0.7892 (t80) REVERT: C 484 GLN cc_start: 0.8966 (tp40) cc_final: 0.8456 (tp-100) REVERT: C 488 GLN cc_start: 0.9204 (tt0) cc_final: 0.8935 (tt0) REVERT: B 171 ARG cc_start: 0.9176 (ptt90) cc_final: 0.8967 (ptt-90) REVERT: X 42 ASP cc_start: 0.7100 (m-30) cc_final: 0.6805 (m-30) REVERT: X 121 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7765 (mtp85) REVERT: H 23 ILE cc_start: 0.9137 (pt) cc_final: 0.8726 (mm) REVERT: H 65 SER cc_start: 0.8636 (m) cc_final: 0.8039 (t) REVERT: H 127 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8056 (tp40) REVERT: H 129 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8005 (mtm-85) REVERT: H 132 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: G 31 MET cc_start: 0.8931 (ttp) cc_final: 0.8688 (ttp) REVERT: G 155 MET cc_start: 0.9274 (mmm) cc_final: 0.9065 (mmp) REVERT: G 187 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8850 (pp) REVERT: F 125 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8847 (mp) REVERT: F 209 MET cc_start: 0.9063 (ptp) cc_final: 0.8863 (ptp) REVERT: E 323 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8140 (mtt-85) REVERT: E 368 GLN cc_start: 0.8887 (tp40) cc_final: 0.8371 (tp40) REVERT: D 166 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8930 (mp) REVERT: L 6 MET cc_start: 0.6630 (mmt) cc_final: 0.5682 (mmt) REVERT: L 11 MET cc_start: 0.7198 (tpt) cc_final: 0.6773 (tpt) REVERT: L 17 MET cc_start: 0.7913 (mtm) cc_final: 0.7561 (mtt) REVERT: L 37 GLU cc_start: 0.7891 (pp20) cc_final: 0.7456 (mm-30) REVERT: L 41 ARG cc_start: 0.7055 (mmp80) cc_final: 0.6750 (mmp80) REVERT: L 63 ILE cc_start: 0.7696 (mm) cc_final: 0.7338 (mm) REVERT: L 75 MET cc_start: 0.7963 (mmm) cc_final: 0.7557 (tpt) REVERT: L 76 PHE cc_start: 0.7379 (m-80) cc_final: 0.7004 (m-80) REVERT: M 42 GLN cc_start: 0.7510 (pt0) cc_final: 0.7239 (pt0) REVERT: M 46 ILE cc_start: 0.9372 (mt) cc_final: 0.9167 (mp) REVERT: M 54 PHE cc_start: 0.8634 (m-80) cc_final: 0.8418 (m-80) REVERT: M 65 MET cc_start: 0.8317 (mtp) cc_final: 0.8074 (ptt) REVERT: M 75 MET cc_start: 0.8152 (ttt) cc_final: 0.7787 (tmm) REVERT: N 75 MET cc_start: 0.8362 (tmm) cc_final: 0.7497 (tpp) REVERT: O 17 MET cc_start: 0.8241 (ttm) cc_final: 0.7236 (tpp) REVERT: P 36 LEU cc_start: 0.8712 (mt) cc_final: 0.8427 (tt) REVERT: P 37 GLU cc_start: 0.8360 (tp30) cc_final: 0.8146 (tp30) REVERT: P 42 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7690 (mp10) REVERT: P 64 PRO cc_start: 0.7980 (Cg_exo) cc_final: 0.7670 (Cg_endo) REVERT: Q 11 MET cc_start: 0.8417 (ttm) cc_final: 0.7480 (tpt) REVERT: Q 41 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.6837 (mtm110) REVERT: Q 54 PHE cc_start: 0.7850 (m-80) cc_final: 0.7628 (m-80) REVERT: Q 75 MET cc_start: 0.9124 (mtm) cc_final: 0.8865 (mtp) REVERT: R 10 TYR cc_start: 0.8309 (m-80) cc_final: 0.7910 (m-80) REVERT: R 16 MET cc_start: 0.8512 (mtp) cc_final: 0.8158 (ttt) REVERT: R 55 ILE cc_start: 0.9141 (tt) cc_final: 0.8712 (pt) REVERT: R 75 MET cc_start: 0.8189 (tpp) cc_final: 0.7467 (tpp) REVERT: Y 16 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6843 (mt) REVERT: Y 20 PHE cc_start: 0.7748 (t80) cc_final: 0.7401 (t80) REVERT: Y 38 LYS cc_start: 0.8962 (tptt) cc_final: 0.8742 (tmtt) REVERT: Y 82 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8295 (tpp-160) REVERT: Y 119 GLU cc_start: 0.9108 (tp30) cc_final: 0.8802 (tm-30) REVERT: a 65 LYS cc_start: 0.5532 (tttt) cc_final: 0.5122 (pptt) REVERT: a 94 TYR cc_start: 0.6173 (t80) cc_final: 0.5905 (t80) REVERT: a 215 MET cc_start: 0.8539 (mmt) cc_final: 0.8208 (mmm) REVERT: a 220 LEU cc_start: 0.8639 (tp) cc_final: 0.8371 (mt) REVERT: a 241 TRP cc_start: 0.8224 (t-100) cc_final: 0.7850 (t-100) REVERT: I 50 ARG cc_start: 0.8965 (mtm110) cc_final: 0.8720 (mtm110) REVERT: I 75 MET cc_start: 0.7911 (ptm) cc_final: 0.7708 (ptp) REVERT: S 7 ASP cc_start: 0.5431 (p0) cc_final: 0.5216 (p0) outliers start: 146 outliers final: 89 residues processed: 654 average time/residue: 0.2167 time to fit residues: 232.8233 Evaluate side-chains 615 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 520 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 267 optimal weight: 0.9990 chunk 362 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 331 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 394 optimal weight: 6.9990 chunk 292 optimal weight: 0.6980 chunk 379 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN X 2 ASN X 73 GLN H 55 GLN G 57 HIS F 7 GLN D 210 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN a 185 HIS I 52 GLN S 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071176 restraints weight = 80214.755| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.96 r_work: 0.2902 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37528 Z= 0.118 Angle : 0.574 9.477 50797 Z= 0.295 Chirality : 0.042 0.199 5920 Planarity : 0.004 0.057 6550 Dihedral : 7.351 159.472 5367 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.08 % Allowed : 15.30 % Favored : 81.62 % 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: 0.33 (0.12), residues: 4807 helix: 0.85 (0.10), residues: 2598 sheet: 0.04 (0.22), residues: 516 loop : -0.56 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 41 TYR 0.036 0.001 TYR P 10 PHE 0.026 0.001 PHE I 53 TRP 0.020 0.001 TRP a 111 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00246 (37528) covalent geometry : angle 0.57362 (50797) hydrogen bonds : bond 0.04313 ( 2154) hydrogen bonds : angle 4.51571 ( 6267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 581 time to evaluate : 1.404 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: W 143 ASP cc_start: 0.8246 (t0) cc_final: 0.7985 (t0) REVERT: W 156 ASP cc_start: 0.8045 (p0) cc_final: 0.7423 (p0) REVERT: C 236 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.7710 (t80) REVERT: C 484 GLN cc_start: 0.8967 (tp40) cc_final: 0.8524 (tp-100) REVERT: C 488 GLN cc_start: 0.9059 (tt0) cc_final: 0.8835 (tt0) REVERT: A 415 ASP cc_start: 0.8247 (m-30) cc_final: 0.7687 (t70) REVERT: X 42 ASP cc_start: 0.7089 (m-30) cc_final: 0.6746 (m-30) REVERT: X 53 ASP cc_start: 0.7556 (t70) cc_final: 0.7308 (t0) REVERT: X 121 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7950 (mtp85) REVERT: H 22 LYS cc_start: 0.8336 (pttm) cc_final: 0.8105 (pttp) REVERT: H 23 ILE cc_start: 0.9023 (pt) cc_final: 0.8798 (mm) REVERT: H 54 LYS cc_start: 0.8661 (mtmm) cc_final: 0.7758 (ptpp) REVERT: H 127 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8102 (tp40) REVERT: H 129 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7952 (mtm-85) REVERT: H 132 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: H 138 MET cc_start: 0.6940 (ttm) cc_final: 0.6389 (ttp) REVERT: G 187 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8708 (pp) REVERT: F 193 MET cc_start: 0.9029 (mmp) cc_final: 0.8809 (mmp) REVERT: E 368 GLN cc_start: 0.8790 (tp40) cc_final: 0.8125 (tp-100) REVERT: D 166 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8841 (mp) REVERT: J 11 MET cc_start: 0.8185 (mmm) cc_final: 0.7889 (mmm) REVERT: J 53 PHE cc_start: 0.8909 (t80) cc_final: 0.8595 (t80) REVERT: J 65 MET cc_start: 0.8479 (mmp) cc_final: 0.8125 (mmp) REVERT: L 6 MET cc_start: 0.6663 (mmt) cc_final: 0.5894 (mmt) REVERT: L 17 MET cc_start: 0.7905 (mtm) cc_final: 0.7526 (mtt) REVERT: L 41 ARG cc_start: 0.7115 (mmp80) cc_final: 0.6779 (mmp80) REVERT: L 51 THR cc_start: 0.8713 (p) cc_final: 0.8494 (t) REVERT: L 63 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7152 (mm) REVERT: L 75 MET cc_start: 0.7839 (mmm) cc_final: 0.7490 (tpt) REVERT: L 76 PHE cc_start: 0.7377 (m-80) cc_final: 0.6909 (m-80) REVERT: M 75 MET cc_start: 0.8076 (ttt) cc_final: 0.7763 (tmm) REVERT: N 41 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7825 (mtt-85) REVERT: O 11 MET cc_start: 0.7173 (mmm) cc_final: 0.5291 (mtt) REVERT: O 17 MET cc_start: 0.7987 (ttm) cc_final: 0.7170 (tpp) REVERT: P 10 TYR cc_start: 0.6845 (m-80) cc_final: 0.6519 (m-10) REVERT: P 36 LEU cc_start: 0.8693 (mt) cc_final: 0.8430 (tt) REVERT: P 41 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7961 (ttp-110) REVERT: P 42 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7697 (mp10) REVERT: P 55 ILE cc_start: 0.8806 (mm) cc_final: 0.8554 (mt) REVERT: Q 11 MET cc_start: 0.8495 (ttm) cc_final: 0.7540 (tpt) REVERT: Q 35 PHE cc_start: 0.8826 (t80) cc_final: 0.8327 (t80) REVERT: Q 42 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7442 (mm-40) REVERT: Q 54 PHE cc_start: 0.7916 (m-80) cc_final: 0.7652 (m-80) REVERT: R 10 TYR cc_start: 0.8343 (m-80) cc_final: 0.7743 (m-80) REVERT: R 11 MET cc_start: 0.8124 (tpp) cc_final: 0.7788 (tpt) REVERT: R 16 MET cc_start: 0.8514 (mtp) cc_final: 0.8040 (ttm) REVERT: R 55 ILE cc_start: 0.9167 (tt) cc_final: 0.8690 (pt) REVERT: R 57 MET cc_start: 0.8942 (ttp) cc_final: 0.8644 (ptm) REVERT: R 65 MET cc_start: 0.8791 (mmm) cc_final: 0.8578 (mmm) REVERT: Y 1 MET cc_start: 0.4544 (ptt) cc_final: 0.3525 (tpt) REVERT: Y 16 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6960 (mt) REVERT: Y 20 PHE cc_start: 0.7715 (t80) cc_final: 0.7412 (t80) REVERT: Y 38 LYS cc_start: 0.9015 (tptt) cc_final: 0.8776 (tmtt) REVERT: Y 64 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8424 (pp30) REVERT: Y 82 ARG cc_start: 0.8674 (tpp-160) cc_final: 0.8411 (tpp-160) REVERT: Y 119 GLU cc_start: 0.9030 (tp30) cc_final: 0.8696 (tm-30) REVERT: a 65 LYS cc_start: 0.5375 (tttt) cc_final: 0.4983 (pptt) REVERT: a 94 TYR cc_start: 0.6322 (t80) cc_final: 0.6059 (t80) REVERT: a 118 MET cc_start: 0.8003 (mmm) cc_final: 0.7752 (mmm) REVERT: a 215 MET cc_start: 0.8483 (mmt) cc_final: 0.8180 (mmm) REVERT: a 252 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8575 (mm-40) REVERT: a 263 TYR cc_start: 0.8881 (m-10) cc_final: 0.8620 (m-80) REVERT: a 264 LEU cc_start: 0.9057 (mt) cc_final: 0.8686 (pp) REVERT: I 43 PRO cc_start: 0.9091 (Cg_endo) cc_final: 0.8758 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8956 (mtm110) cc_final: 0.8711 (mtm110) REVERT: S 16 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.4935 (tmm) outliers start: 118 outliers final: 63 residues processed: 667 average time/residue: 0.2200 time to fit residues: 240.1188 Evaluate side-chains 595 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 524 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain M residue 76 PHE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 404 optimal weight: 10.0000 chunk 445 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 chunk 443 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 362 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS X 2 ASN G 57 HIS F 7 GLN J 3 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069974 restraints weight = 80023.826| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.97 r_work: 0.2877 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37528 Z= 0.156 Angle : 0.585 9.841 50797 Z= 0.300 Chirality : 0.043 0.158 5920 Planarity : 0.004 0.056 6550 Dihedral : 7.216 160.023 5365 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.55 % Allowed : 15.98 % Favored : 80.47 % 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: 0.52 (0.12), residues: 4807 helix: 1.05 (0.10), residues: 2606 sheet: 0.03 (0.22), residues: 534 loop : -0.53 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.029 0.001 TYR a 216 PHE 0.028 0.001 PHE L 35 TRP 0.009 0.001 TRP a 111 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00361 (37528) covalent geometry : angle 0.58462 (50797) hydrogen bonds : bond 0.04338 ( 2154) hydrogen bonds : angle 4.51675 ( 6267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 540 time to evaluate : 1.391 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: W 143 ASP cc_start: 0.8320 (t0) cc_final: 0.8018 (t0) REVERT: W 156 ASP cc_start: 0.7886 (p0) cc_final: 0.7316 (p0) REVERT: C 236 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.7784 (t80) REVERT: C 484 GLN cc_start: 0.9017 (tp40) cc_final: 0.8542 (tp-100) REVERT: A 415 ASP cc_start: 0.8413 (m-30) cc_final: 0.7745 (t70) REVERT: X 16 LEU cc_start: 0.8970 (mp) cc_final: 0.8700 (pp) REVERT: X 42 ASP cc_start: 0.7017 (m-30) cc_final: 0.6699 (m-30) REVERT: X 53 ASP cc_start: 0.7632 (t70) cc_final: 0.7391 (t0) REVERT: X 121 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7972 (mtp85) REVERT: H 23 ILE cc_start: 0.9148 (pt) cc_final: 0.8887 (mm) REVERT: H 65 SER cc_start: 0.8608 (m) cc_final: 0.8109 (t) REVERT: H 127 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8102 (tp40) REVERT: H 129 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: H 132 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: H 138 MET cc_start: 0.7067 (ttm) cc_final: 0.6544 (ttp) REVERT: G 155 MET cc_start: 0.9231 (mmm) cc_final: 0.9029 (mmp) REVERT: G 187 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8697 (pp) REVERT: G 203 TRP cc_start: 0.8268 (p-90) cc_final: 0.7949 (p-90) REVERT: F 224 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9179 (tt) REVERT: E 368 GLN cc_start: 0.8831 (tp40) cc_final: 0.8102 (tp-100) REVERT: D 166 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8822 (mp) REVERT: J 53 PHE cc_start: 0.8923 (t80) cc_final: 0.8495 (t80) REVERT: J 65 MET cc_start: 0.8567 (mmp) cc_final: 0.8254 (mmp) REVERT: L 6 MET cc_start: 0.6782 (mmt) cc_final: 0.6257 (mmt) REVERT: L 11 MET cc_start: 0.7024 (tpt) cc_final: 0.6524 (tpt) REVERT: L 17 MET cc_start: 0.7855 (mtm) cc_final: 0.7477 (mtt) REVERT: L 37 GLU cc_start: 0.7797 (pp20) cc_final: 0.7398 (mm-30) REVERT: L 76 PHE cc_start: 0.7382 (m-80) cc_final: 0.6895 (m-80) REVERT: M 64 PRO cc_start: 0.8132 (Cg_exo) cc_final: 0.7920 (Cg_endo) REVERT: M 75 MET cc_start: 0.8078 (ttt) cc_final: 0.7758 (tmm) REVERT: O 17 MET cc_start: 0.8189 (ttm) cc_final: 0.7139 (tpp) REVERT: P 10 TYR cc_start: 0.6896 (m-80) cc_final: 0.6658 (m-10) REVERT: P 41 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.7997 (ttp-110) REVERT: P 42 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7795 (mp10) REVERT: P 55 ILE cc_start: 0.8814 (mm) cc_final: 0.8566 (mt) REVERT: P 66 ILE cc_start: 0.8499 (mt) cc_final: 0.8279 (mp) REVERT: Q 41 ARG cc_start: 0.7268 (mtm-85) cc_final: 0.6598 (mtm110) REVERT: Q 54 PHE cc_start: 0.7912 (m-80) cc_final: 0.7687 (m-80) REVERT: R 10 TYR cc_start: 0.8311 (m-80) cc_final: 0.7734 (m-80) REVERT: R 11 MET cc_start: 0.8324 (tpp) cc_final: 0.7982 (tpt) REVERT: R 16 MET cc_start: 0.8500 (mtp) cc_final: 0.8170 (ttm) REVERT: R 57 MET cc_start: 0.8856 (ttp) cc_final: 0.8571 (ptm) REVERT: R 65 MET cc_start: 0.8817 (mmm) cc_final: 0.8586 (mmm) REVERT: Y 1 MET cc_start: 0.4532 (ptt) cc_final: 0.3579 (tpt) REVERT: Y 16 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7048 (mt) REVERT: Y 20 PHE cc_start: 0.7776 (t80) cc_final: 0.7545 (t80) REVERT: Y 64 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: Y 82 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8530 (tpp-160) REVERT: Y 119 GLU cc_start: 0.9008 (tp30) cc_final: 0.8770 (tm-30) REVERT: a 65 LYS cc_start: 0.5545 (tttt) cc_final: 0.5164 (pptt) REVERT: a 214 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7943 (p0) REVERT: a 215 MET cc_start: 0.8444 (mmt) cc_final: 0.7934 (mmm) REVERT: a 252 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8543 (mm110) REVERT: a 264 LEU cc_start: 0.8976 (mt) cc_final: 0.8604 (pp) REVERT: I 43 PRO cc_start: 0.9090 (Cg_endo) cc_final: 0.8765 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8668 (mtm110) REVERT: I 54 PHE cc_start: 0.8642 (m-80) cc_final: 0.8407 (m-80) REVERT: S 16 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5195 (tmm) REVERT: S 17 MET cc_start: 0.6915 (mmm) cc_final: 0.6646 (mmm) outliers start: 136 outliers final: 87 residues processed: 634 average time/residue: 0.2223 time to fit residues: 230.7600 Evaluate side-chains 614 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 518 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain M residue 76 PHE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain a residue 214 ASN Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 326 optimal weight: 0.1980 chunk 395 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 chunk 422 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 2 ASN H 24 GLN G 57 HIS D 243 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS a 245 HIS I 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071060 restraints weight = 81712.525| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.08 r_work: 0.2867 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37528 Z= 0.157 Angle : 0.586 10.214 50797 Z= 0.300 Chirality : 0.043 0.164 5920 Planarity : 0.004 0.056 6550 Dihedral : 7.199 164.170 5364 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.42 % Allowed : 16.50 % Favored : 80.08 % 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: 0.63 (0.12), residues: 4807 helix: 1.15 (0.10), residues: 2607 sheet: 0.08 (0.22), residues: 531 loop : -0.52 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 98 TYR 0.032 0.001 TYR L 10 PHE 0.028 0.001 PHE L 35 TRP 0.009 0.001 TRP a 39 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00364 (37528) covalent geometry : angle 0.58642 (50797) hydrogen bonds : bond 0.04275 ( 2154) hydrogen bonds : angle 4.48069 ( 6267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 540 time to evaluate : 1.334 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: W 143 ASP cc_start: 0.8338 (t0) cc_final: 0.8031 (t0) REVERT: W 156 ASP cc_start: 0.7982 (p0) cc_final: 0.7424 (p0) REVERT: C 236 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 484 GLN cc_start: 0.9017 (tp40) cc_final: 0.8436 (tp-100) REVERT: C 488 GLN cc_start: 0.9121 (tt0) cc_final: 0.8876 (tt0) REVERT: A 252 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8922 (mtt180) REVERT: A 386 MET cc_start: 0.9254 (mmm) cc_final: 0.8915 (mmt) REVERT: X 42 ASP cc_start: 0.7050 (m-30) cc_final: 0.6699 (m-30) REVERT: X 53 ASP cc_start: 0.7619 (t70) cc_final: 0.7409 (t0) REVERT: X 121 ARG cc_start: 0.8218 (mtp85) cc_final: 0.8006 (mtp85) REVERT: H 23 ILE cc_start: 0.9136 (pt) cc_final: 0.8893 (mm) REVERT: H 65 SER cc_start: 0.8591 (m) cc_final: 0.8068 (t) REVERT: H 127 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8141 (tp40) REVERT: H 129 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: H 132 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: H 138 MET cc_start: 0.7137 (ttm) cc_final: 0.6593 (ttp) REVERT: G 155 MET cc_start: 0.9255 (mmm) cc_final: 0.9036 (mmp) REVERT: G 187 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8681 (pp) REVERT: G 203 TRP cc_start: 0.8298 (p-90) cc_final: 0.7996 (p-90) REVERT: F 125 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (mp) REVERT: F 224 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9199 (tt) REVERT: E 368 GLN cc_start: 0.8848 (tp40) cc_final: 0.8151 (tp-100) REVERT: D 166 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8836 (mp) REVERT: D 374 ILE cc_start: 0.9470 (mt) cc_final: 0.9249 (mt) REVERT: J 11 MET cc_start: 0.8252 (mmm) cc_final: 0.8021 (mmm) REVERT: J 53 PHE cc_start: 0.8868 (t80) cc_final: 0.8380 (t80) REVERT: L 6 MET cc_start: 0.6635 (mmt) cc_final: 0.6254 (mmt) REVERT: L 11 MET cc_start: 0.6933 (tpt) cc_final: 0.6401 (tpt) REVERT: L 17 MET cc_start: 0.7812 (mtm) cc_final: 0.7351 (mtm) REVERT: L 41 ARG cc_start: 0.6931 (mmp80) cc_final: 0.6616 (mmp80) REVERT: L 75 MET cc_start: 0.7367 (tpt) cc_final: 0.7093 (tpt) REVERT: L 76 PHE cc_start: 0.7319 (m-80) cc_final: 0.6779 (m-80) REVERT: M 75 MET cc_start: 0.7928 (ttt) cc_final: 0.7525 (tmm) REVERT: N 52 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7707 (mp10) REVERT: N 57 MET cc_start: 0.8659 (ttp) cc_final: 0.8412 (ttm) REVERT: O 11 MET cc_start: 0.6595 (mmm) cc_final: 0.4682 (mtt) REVERT: O 17 MET cc_start: 0.7890 (ttm) cc_final: 0.7024 (tpp) REVERT: O 34 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8147 (mmmm) REVERT: P 10 TYR cc_start: 0.6969 (m-80) cc_final: 0.6717 (m-10) REVERT: P 41 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8082 (ttp-110) REVERT: P 42 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7812 (mp10) REVERT: P 55 ILE cc_start: 0.8808 (mm) cc_final: 0.8559 (mt) REVERT: Q 6 MET cc_start: 0.2739 (mpp) cc_final: 0.1916 (ttt) REVERT: Q 8 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.5657 (tt) REVERT: Q 35 PHE cc_start: 0.8801 (t80) cc_final: 0.8348 (t80) REVERT: R 10 TYR cc_start: 0.8272 (m-80) cc_final: 0.7648 (m-80) REVERT: R 11 MET cc_start: 0.8282 (tpp) cc_final: 0.8046 (tpt) REVERT: R 16 MET cc_start: 0.8534 (mtp) cc_final: 0.8243 (ttm) REVERT: R 52 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: R 57 MET cc_start: 0.8888 (ttp) cc_final: 0.8631 (ptm) REVERT: R 65 MET cc_start: 0.8835 (mmm) cc_final: 0.8624 (mmm) REVERT: Y 1 MET cc_start: 0.4308 (ptt) cc_final: 0.3576 (tpt) REVERT: Y 16 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6945 (mt) REVERT: Y 20 PHE cc_start: 0.7781 (t80) cc_final: 0.7528 (t80) REVERT: Y 64 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (pp30) REVERT: Y 82 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.8520 (tpp-160) REVERT: Y 119 GLU cc_start: 0.9035 (tp30) cc_final: 0.8765 (tm-30) REVERT: a 65 LYS cc_start: 0.5577 (tttt) cc_final: 0.5190 (pptt) REVERT: a 264 LEU cc_start: 0.9009 (mt) cc_final: 0.8651 (pp) REVERT: I 42 GLN cc_start: 0.7976 (mm110) cc_final: 0.7159 (tp40) REVERT: I 43 PRO cc_start: 0.9108 (Cg_endo) cc_final: 0.8743 (Cg_exo) REVERT: I 54 PHE cc_start: 0.8610 (m-80) cc_final: 0.8364 (m-80) outliers start: 131 outliers final: 85 residues processed: 625 average time/residue: 0.2195 time to fit residues: 225.7506 Evaluate side-chains 613 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 517 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain M residue 76 PHE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 141 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 435 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 82 optimal weight: 0.0000 chunk 342 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 2 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS D 243 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070186 restraints weight = 80451.834| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.07 r_work: 0.2876 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37528 Z= 0.149 Angle : 0.584 11.680 50797 Z= 0.298 Chirality : 0.043 0.209 5920 Planarity : 0.004 0.057 6550 Dihedral : 7.062 166.960 5360 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.95 % Allowed : 16.92 % Favored : 80.14 % 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: 0.68 (0.12), residues: 4807 helix: 1.18 (0.10), residues: 2651 sheet: 0.11 (0.22), residues: 528 loop : -0.53 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 50 TYR 0.023 0.001 TYR a 94 PHE 0.026 0.001 PHE L 35 TRP 0.009 0.001 TRP a 111 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00345 (37528) covalent geometry : angle 0.58357 (50797) hydrogen bonds : bond 0.04167 ( 2154) hydrogen bonds : angle 4.44169 ( 6267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 534 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.8339 (t0) cc_final: 0.8037 (t0) REVERT: W 156 ASP cc_start: 0.7941 (p0) cc_final: 0.7419 (p0) REVERT: C 236 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.7730 (t80) REVERT: C 484 GLN cc_start: 0.9060 (tp40) cc_final: 0.8482 (tp-100) REVERT: C 488 GLN cc_start: 0.9167 (tt0) cc_final: 0.8948 (tt0) REVERT: B 406 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5896 (m-10) REVERT: A 172 GLN cc_start: 0.9061 (tt0) cc_final: 0.8752 (tp40) REVERT: A 252 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8886 (mtt180) REVERT: A 386 MET cc_start: 0.9169 (mmm) cc_final: 0.8848 (mmt) REVERT: X 42 ASP cc_start: 0.7018 (m-30) cc_final: 0.6676 (m-30) REVERT: H 23 ILE cc_start: 0.9175 (pt) cc_final: 0.8892 (mm) REVERT: H 65 SER cc_start: 0.8631 (m) cc_final: 0.8120 (t) REVERT: H 127 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8182 (tp40) REVERT: H 129 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: H 132 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: H 138 MET cc_start: 0.7086 (ttm) cc_final: 0.6562 (ttp) REVERT: G 31 MET cc_start: 0.8979 (ttp) cc_final: 0.8702 (ttp) REVERT: G 116 MET cc_start: 0.8996 (mmm) cc_final: 0.8753 (mmm) REVERT: G 155 MET cc_start: 0.9227 (mmm) cc_final: 0.9005 (mmp) REVERT: G 187 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8697 (pp) REVERT: G 203 TRP cc_start: 0.8257 (p-90) cc_final: 0.7972 (p-90) REVERT: F 125 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8795 (mp) REVERT: F 224 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9205 (tt) REVERT: E 368 GLN cc_start: 0.8855 (tp40) cc_final: 0.8302 (tp-100) REVERT: D 166 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8792 (mp) REVERT: D 374 ILE cc_start: 0.9467 (mt) cc_final: 0.9253 (mt) REVERT: D 445 MET cc_start: 0.9069 (mmt) cc_final: 0.8856 (mmm) REVERT: J 17 MET cc_start: 0.7918 (mtm) cc_final: 0.7563 (tmm) REVERT: L 11 MET cc_start: 0.7027 (tpt) cc_final: 0.6518 (tpt) REVERT: L 17 MET cc_start: 0.7828 (mtm) cc_final: 0.7407 (mtm) REVERT: L 37 GLU cc_start: 0.7584 (pp20) cc_final: 0.7303 (mm-30) REVERT: L 41 ARG cc_start: 0.7065 (mmp80) cc_final: 0.6798 (mmp-170) REVERT: L 75 MET cc_start: 0.7388 (tpt) cc_final: 0.7162 (tpt) REVERT: L 76 PHE cc_start: 0.7366 (m-80) cc_final: 0.6833 (m-80) REVERT: M 75 MET cc_start: 0.7851 (ttt) cc_final: 0.7473 (tmm) REVERT: N 52 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7731 (mp10) REVERT: O 10 TYR cc_start: 0.6998 (m-80) cc_final: 0.6504 (m-10) REVERT: O 11 MET cc_start: 0.6797 (mmm) cc_final: 0.6011 (mmm) REVERT: O 16 MET cc_start: 0.7587 (mtm) cc_final: 0.7111 (mpp) REVERT: O 17 MET cc_start: 0.7917 (ttm) cc_final: 0.7062 (tpp) REVERT: O 34 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8318 (mmmm) REVERT: P 41 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8088 (ttp-110) REVERT: P 42 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7852 (mp10) REVERT: P 55 ILE cc_start: 0.8809 (mm) cc_final: 0.8551 (mt) REVERT: P 73 TYR cc_start: 0.7651 (t80) cc_final: 0.6032 (m-80) REVERT: Q 8 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.5738 (tt) REVERT: Q 35 PHE cc_start: 0.8807 (t80) cc_final: 0.8408 (t80) REVERT: Q 54 PHE cc_start: 0.7914 (m-80) cc_final: 0.7582 (m-80) REVERT: R 10 TYR cc_start: 0.8207 (m-80) cc_final: 0.7551 (m-80) REVERT: R 16 MET cc_start: 0.8533 (mtp) cc_final: 0.8177 (ttm) REVERT: R 50 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7949 (ttp-110) REVERT: R 57 MET cc_start: 0.8882 (ttp) cc_final: 0.8652 (ptm) REVERT: R 65 MET cc_start: 0.8853 (mmm) cc_final: 0.8650 (mmm) REVERT: Y 1 MET cc_start: 0.4248 (ptt) cc_final: 0.3721 (tpt) REVERT: Y 16 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6973 (mt) REVERT: Y 64 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8428 (pp30) REVERT: Y 67 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8138 (tmtt) REVERT: Y 82 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8520 (tpp-160) REVERT: a 65 LYS cc_start: 0.5584 (tttt) cc_final: 0.5231 (pptt) REVERT: a 264 LEU cc_start: 0.9013 (mt) cc_final: 0.8626 (pp) REVERT: I 43 PRO cc_start: 0.9111 (Cg_endo) cc_final: 0.8782 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8506 (mtm110) REVERT: I 54 PHE cc_start: 0.8621 (m-80) cc_final: 0.8353 (m-80) outliers start: 113 outliers final: 85 residues processed: 606 average time/residue: 0.2243 time to fit residues: 222.3927 Evaluate side-chains 610 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 514 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain M residue 76 PHE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 0.0970 chunk 332 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 434 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 330 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS D 19 GLN D 243 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072220 restraints weight = 80138.963| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.99 r_work: 0.2920 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 37528 Z= 0.116 Angle : 0.571 10.516 50797 Z= 0.290 Chirality : 0.042 0.205 5920 Planarity : 0.004 0.057 6550 Dihedral : 6.814 165.679 5360 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.61 % Allowed : 17.67 % Favored : 79.72 % 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: 0.87 (0.12), residues: 4807 helix: 1.32 (0.10), residues: 2648 sheet: 0.18 (0.22), residues: 524 loop : -0.41 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 140 TYR 0.024 0.001 TYR a 216 PHE 0.027 0.001 PHE L 35 TRP 0.028 0.001 TRP X 26 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00247 (37528) covalent geometry : angle 0.57071 (50797) hydrogen bonds : bond 0.03857 ( 2154) hydrogen bonds : angle 4.31933 ( 6267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 559 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9147 (tptt) cc_final: 0.8888 (tptt) REVERT: W 143 ASP cc_start: 0.8249 (t0) cc_final: 0.7973 (t0) REVERT: W 156 ASP cc_start: 0.7958 (p0) cc_final: 0.7460 (p0) REVERT: C 236 TYR cc_start: 0.9335 (OUTLIER) cc_final: 0.7703 (t80) REVERT: B 448 LEU cc_start: 0.8377 (mm) cc_final: 0.8159 (mm) REVERT: A 172 GLN cc_start: 0.8989 (tt0) cc_final: 0.8666 (tp40) REVERT: A 386 MET cc_start: 0.9182 (mmm) cc_final: 0.8840 (mmt) REVERT: X 16 LEU cc_start: 0.8892 (mp) cc_final: 0.8676 (pp) REVERT: X 36 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7747 (mtm-85) REVERT: X 42 ASP cc_start: 0.6991 (m-30) cc_final: 0.6623 (m-30) REVERT: H 23 ILE cc_start: 0.9118 (pt) cc_final: 0.8824 (mm) REVERT: H 129 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7811 (mtm-85) REVERT: H 132 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: H 138 MET cc_start: 0.7344 (ttm) cc_final: 0.6745 (ttp) REVERT: G 31 MET cc_start: 0.8957 (ttp) cc_final: 0.8577 (ttp) REVERT: G 155 MET cc_start: 0.9253 (mmm) cc_final: 0.9039 (mmp) REVERT: G 187 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8615 (pp) REVERT: G 199 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7346 (mmmt) REVERT: F 224 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9160 (tt) REVERT: F 428 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8974 (ttmm) REVERT: E 368 GLN cc_start: 0.8795 (tp40) cc_final: 0.8127 (tp-100) REVERT: D 166 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8668 (mp) REVERT: D 374 ILE cc_start: 0.9445 (mt) cc_final: 0.9240 (mt) REVERT: D 445 MET cc_start: 0.9021 (mmt) cc_final: 0.8799 (mmm) REVERT: J 11 MET cc_start: 0.7790 (mmm) cc_final: 0.7574 (mmm) REVERT: J 17 MET cc_start: 0.7894 (mtm) cc_final: 0.7580 (tmm) REVERT: J 53 PHE cc_start: 0.8824 (t80) cc_final: 0.8441 (t80) REVERT: L 11 MET cc_start: 0.6843 (tpt) cc_final: 0.6420 (tpt) REVERT: L 16 MET cc_start: 0.8322 (mmm) cc_final: 0.8118 (mmm) REVERT: L 37 GLU cc_start: 0.7548 (pp20) cc_final: 0.7200 (mm-30) REVERT: L 76 PHE cc_start: 0.7067 (m-80) cc_final: 0.6448 (m-80) REVERT: M 75 MET cc_start: 0.7826 (ttt) cc_final: 0.7395 (tmm) REVERT: N 41 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7881 (mtp85) REVERT: N 52 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7760 (mp10) REVERT: O 10 TYR cc_start: 0.7081 (m-80) cc_final: 0.6580 (m-10) REVERT: O 11 MET cc_start: 0.6848 (mmm) cc_final: 0.6052 (mmm) REVERT: O 16 MET cc_start: 0.7745 (mtm) cc_final: 0.6968 (mpp) REVERT: O 17 MET cc_start: 0.7613 (ttm) cc_final: 0.7089 (tpp) REVERT: O 34 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8335 (mmmm) REVERT: O 75 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7314 (tpt) REVERT: P 41 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8093 (ttp-110) REVERT: P 42 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7924 (mp10) REVERT: P 55 ILE cc_start: 0.8771 (mm) cc_final: 0.8525 (mt) REVERT: P 73 TYR cc_start: 0.7548 (t80) cc_final: 0.5950 (m-80) REVERT: Q 6 MET cc_start: 0.2241 (mpp) cc_final: 0.1656 (ttt) REVERT: Q 8 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.5838 (tt) REVERT: Q 35 PHE cc_start: 0.8790 (t80) cc_final: 0.8402 (t80) REVERT: R 10 TYR cc_start: 0.8169 (m-80) cc_final: 0.7443 (m-80) REVERT: R 16 MET cc_start: 0.8503 (mtp) cc_final: 0.8158 (ttm) REVERT: R 65 MET cc_start: 0.8868 (mmm) cc_final: 0.8638 (mmm) REVERT: Y 1 MET cc_start: 0.4301 (ptt) cc_final: 0.3986 (tpt) REVERT: Y 16 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7049 (mt) REVERT: Y 64 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: Y 67 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8122 (tmtt) REVERT: Y 82 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8534 (tpp-160) REVERT: a 65 LYS cc_start: 0.5679 (tttt) cc_final: 0.5370 (pptt) REVERT: a 201 LEU cc_start: 0.8417 (tp) cc_final: 0.7889 (mm) REVERT: a 264 LEU cc_start: 0.8986 (mt) cc_final: 0.8622 (pp) REVERT: I 42 GLN cc_start: 0.7968 (mm110) cc_final: 0.7397 (tp40) REVERT: I 50 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8186 (mtm110) REVERT: I 54 PHE cc_start: 0.8569 (m-80) cc_final: 0.8054 (m-80) REVERT: I 57 MET cc_start: 0.6912 (ptt) cc_final: 0.6408 (ptt) REVERT: I 65 MET cc_start: 0.7059 (ptm) cc_final: 0.6789 (ptm) REVERT: S 17 MET cc_start: 0.7078 (tpt) cc_final: 0.6832 (mmm) REVERT: S 57 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7995 (tpt) outliers start: 100 outliers final: 64 residues processed: 625 average time/residue: 0.2197 time to fit residues: 224.6327 Evaluate side-chains 599 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 523 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 57 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 179 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 349 optimal weight: 0.0870 chunk 219 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 317 optimal weight: 0.0970 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 82 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 57 HIS D 243 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072538 restraints weight = 80102.211| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.97 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37528 Z= 0.113 Angle : 0.575 11.386 50797 Z= 0.292 Chirality : 0.042 0.262 5920 Planarity : 0.004 0.057 6550 Dihedral : 6.676 165.457 5358 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.19 % Allowed : 18.14 % Favored : 79.67 % 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: 0.96 (0.12), residues: 4807 helix: 1.39 (0.10), residues: 2649 sheet: 0.23 (0.22), residues: 524 loop : -0.35 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 401 TYR 0.035 0.001 TYR L 10 PHE 0.033 0.001 PHE L 53 TRP 0.030 0.001 TRP G 203 HIS 0.011 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00244 (37528) covalent geometry : angle 0.57491 (50797) hydrogen bonds : bond 0.03775 ( 2154) hydrogen bonds : angle 4.28084 ( 6267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 539 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9165 (tptt) cc_final: 0.8877 (tptt) REVERT: W 143 ASP cc_start: 0.8237 (t0) cc_final: 0.7988 (t0) REVERT: W 156 ASP cc_start: 0.7990 (p0) cc_final: 0.7479 (p0) REVERT: C 236 TYR cc_start: 0.9320 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 483 MET cc_start: 0.8939 (mmm) cc_final: 0.8486 (mtm) REVERT: C 484 GLN cc_start: 0.8890 (tp40) cc_final: 0.8294 (tp-100) REVERT: B 448 LEU cc_start: 0.8235 (mm) cc_final: 0.7949 (mm) REVERT: A 172 GLN cc_start: 0.8992 (tt0) cc_final: 0.8680 (tp40) REVERT: A 386 MET cc_start: 0.9141 (mmm) cc_final: 0.8785 (mmt) REVERT: X 36 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7753 (mtt180) REVERT: X 42 ASP cc_start: 0.6829 (m-30) cc_final: 0.6462 (m-30) REVERT: H 23 ILE cc_start: 0.9104 (pt) cc_final: 0.8831 (mm) REVERT: H 50 ILE cc_start: 0.9043 (mm) cc_final: 0.8555 (tt) REVERT: H 127 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8014 (tp40) REVERT: H 129 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: H 132 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: H 133 LEU cc_start: 0.8873 (mt) cc_final: 0.8622 (mt) REVERT: H 138 MET cc_start: 0.7179 (ttm) cc_final: 0.6636 (ttp) REVERT: G 31 MET cc_start: 0.8937 (ttp) cc_final: 0.8547 (ttp) REVERT: G 155 MET cc_start: 0.9229 (mmm) cc_final: 0.9012 (mmp) REVERT: G 199 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7343 (mmmt) REVERT: F 224 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9170 (tt) REVERT: E 368 GLN cc_start: 0.8755 (tp40) cc_final: 0.8080 (tp-100) REVERT: D 166 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8626 (mp) REVERT: D 374 ILE cc_start: 0.9431 (mt) cc_final: 0.9230 (mt) REVERT: D 445 MET cc_start: 0.9014 (mmt) cc_final: 0.8791 (mmm) REVERT: J 17 MET cc_start: 0.7919 (mtm) cc_final: 0.7539 (tmm) REVERT: J 53 PHE cc_start: 0.8848 (t80) cc_final: 0.8416 (t80) REVERT: J 57 MET cc_start: 0.8419 (tmm) cc_final: 0.8032 (tmm) REVERT: L 11 MET cc_start: 0.7018 (tpt) cc_final: 0.6604 (mmm) REVERT: L 37 GLU cc_start: 0.7435 (pp20) cc_final: 0.7179 (mm-30) REVERT: L 41 ARG cc_start: 0.6634 (mmp-170) cc_final: 0.6411 (mmp-170) REVERT: L 75 MET cc_start: 0.7237 (tpt) cc_final: 0.6502 (tpp) REVERT: L 76 PHE cc_start: 0.7048 (m-80) cc_final: 0.6295 (m-80) REVERT: M 75 MET cc_start: 0.7830 (ttt) cc_final: 0.7399 (tmm) REVERT: N 52 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7784 (mp10) REVERT: O 10 TYR cc_start: 0.7031 (m-80) cc_final: 0.6545 (m-10) REVERT: O 11 MET cc_start: 0.6894 (mmm) cc_final: 0.6146 (mmm) REVERT: O 16 MET cc_start: 0.7715 (mtm) cc_final: 0.7205 (mpp) REVERT: O 17 MET cc_start: 0.7585 (ttm) cc_final: 0.6961 (tpp) REVERT: O 75 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7234 (tpt) REVERT: P 10 TYR cc_start: 0.6863 (m-80) cc_final: 0.6652 (m-80) REVERT: P 41 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8089 (ttp-110) REVERT: P 42 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7841 (mp10) REVERT: P 55 ILE cc_start: 0.8828 (mm) cc_final: 0.8593 (mt) REVERT: P 73 TYR cc_start: 0.7537 (t80) cc_final: 0.5813 (m-80) REVERT: Q 6 MET cc_start: 0.2268 (mpp) cc_final: 0.1670 (ttt) REVERT: Q 8 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.5976 (tt) REVERT: Q 35 PHE cc_start: 0.8760 (t80) cc_final: 0.8400 (t80) REVERT: Q 41 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6382 (mtm110) REVERT: Q 54 PHE cc_start: 0.7846 (m-80) cc_final: 0.7571 (m-80) REVERT: R 10 TYR cc_start: 0.8259 (m-80) cc_final: 0.7410 (m-80) REVERT: R 16 MET cc_start: 0.8530 (mtp) cc_final: 0.8144 (ttm) REVERT: R 57 MET cc_start: 0.8912 (ttp) cc_final: 0.8690 (ttp) REVERT: R 65 MET cc_start: 0.8837 (mmm) cc_final: 0.8608 (mmm) REVERT: Y 1 MET cc_start: 0.4298 (ptt) cc_final: 0.4083 (tpt) REVERT: Y 16 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7107 (mt) REVERT: Y 64 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8398 (pp30) REVERT: Y 67 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8121 (tmtt) REVERT: Y 82 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8485 (tpp-160) REVERT: a 6 MET cc_start: 0.4619 (mmp) cc_final: 0.4243 (mmp) REVERT: a 65 LYS cc_start: 0.5659 (tttt) cc_final: 0.5387 (pptt) REVERT: a 115 MET cc_start: 0.6803 (ptp) cc_final: 0.6468 (ptp) REVERT: a 185 HIS cc_start: 0.0788 (OUTLIER) cc_final: -0.0097 (m-70) REVERT: a 201 LEU cc_start: 0.8319 (tp) cc_final: 0.7789 (mm) REVERT: a 264 LEU cc_start: 0.9021 (mt) cc_final: 0.8647 (pp) REVERT: I 50 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8170 (mtm110) REVERT: I 54 PHE cc_start: 0.8505 (m-80) cc_final: 0.8076 (m-80) REVERT: I 57 MET cc_start: 0.7129 (ptt) cc_final: 0.6515 (ptt) REVERT: S 65 MET cc_start: 0.7491 (mtp) cc_final: 0.7229 (mtp) outliers start: 84 outliers final: 61 residues processed: 593 average time/residue: 0.2216 time to fit residues: 214.5870 Evaluate side-chains 592 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 520 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 317 optimal weight: 0.0770 chunk 283 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 289 optimal weight: 0.7980 chunk 281 optimal weight: 0.9990 chunk 258 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 432 optimal weight: 8.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 HIS ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 57 HIS ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072682 restraints weight = 79796.284| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.99 r_work: 0.2934 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37528 Z= 0.114 Angle : 0.587 11.898 50797 Z= 0.296 Chirality : 0.042 0.256 5920 Planarity : 0.004 0.057 6550 Dihedral : 6.605 164.969 5357 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.11 % Allowed : 18.33 % Favored : 79.56 % 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: 1.01 (0.12), residues: 4807 helix: 1.41 (0.10), residues: 2648 sheet: 0.25 (0.22), residues: 519 loop : -0.30 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 50 TYR 0.033 0.001 TYR P 10 PHE 0.031 0.001 PHE L 35 TRP 0.029 0.001 TRP G 203 HIS 0.015 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00248 (37528) covalent geometry : angle 0.58674 (50797) hydrogen bonds : bond 0.03742 ( 2154) hydrogen bonds : angle 4.27276 ( 6267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 539 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9173 (tptt) cc_final: 0.8878 (tptt) REVERT: W 143 ASP cc_start: 0.8163 (t0) cc_final: 0.7906 (t0) REVERT: W 156 ASP cc_start: 0.7982 (p0) cc_final: 0.7474 (p0) REVERT: C 236 TYR cc_start: 0.9326 (OUTLIER) cc_final: 0.7800 (t80) REVERT: C 483 MET cc_start: 0.8884 (mmm) cc_final: 0.8480 (mtm) REVERT: C 484 GLN cc_start: 0.8964 (tp40) cc_final: 0.8336 (tp40) REVERT: B 448 LEU cc_start: 0.8223 (mm) cc_final: 0.7941 (mm) REVERT: A 172 GLN cc_start: 0.8988 (tt0) cc_final: 0.8684 (tp40) REVERT: X 36 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7676 (mtm-85) REVERT: X 42 ASP cc_start: 0.6756 (m-30) cc_final: 0.6392 (m-30) REVERT: H 15 MET cc_start: 0.8718 (mtm) cc_final: 0.8477 (mtm) REVERT: H 23 ILE cc_start: 0.9100 (pt) cc_final: 0.8821 (mm) REVERT: H 81 ASP cc_start: 0.8357 (p0) cc_final: 0.8078 (p0) REVERT: H 127 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: H 129 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: H 132 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: H 133 LEU cc_start: 0.8900 (mt) cc_final: 0.8678 (mt) REVERT: H 138 MET cc_start: 0.7486 (ttm) cc_final: 0.6884 (ttp) REVERT: G 31 MET cc_start: 0.8937 (ttp) cc_final: 0.8552 (ttp) REVERT: G 68 GLU cc_start: 0.8225 (pt0) cc_final: 0.7759 (pp20) REVERT: G 155 MET cc_start: 0.9233 (mmm) cc_final: 0.9021 (mmp) REVERT: G 199 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7318 (mmmt) REVERT: G 246 MET cc_start: 0.9381 (mmp) cc_final: 0.9071 (mmp) REVERT: F 224 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9160 (tt) REVERT: E 368 GLN cc_start: 0.8763 (tp40) cc_final: 0.8087 (tp-100) REVERT: D 166 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8614 (mp) REVERT: D 374 ILE cc_start: 0.9419 (mt) cc_final: 0.9216 (mt) REVERT: D 445 MET cc_start: 0.8999 (mmt) cc_final: 0.8775 (mmm) REVERT: J 53 PHE cc_start: 0.8822 (t80) cc_final: 0.8390 (t80) REVERT: J 57 MET cc_start: 0.8388 (tmm) cc_final: 0.8022 (tmm) REVERT: J 65 MET cc_start: 0.8129 (mmp) cc_final: 0.7860 (mmp) REVERT: L 10 TYR cc_start: 0.6807 (m-80) cc_final: 0.6544 (m-80) REVERT: L 11 MET cc_start: 0.6978 (tpt) cc_final: 0.6592 (mmm) REVERT: L 37 GLU cc_start: 0.7480 (pp20) cc_final: 0.7213 (mm-30) REVERT: L 41 ARG cc_start: 0.6627 (mmp-170) cc_final: 0.6402 (mmp-170) REVERT: L 75 MET cc_start: 0.7043 (tpt) cc_final: 0.6285 (tpp) REVERT: L 76 PHE cc_start: 0.6896 (m-80) cc_final: 0.6120 (m-80) REVERT: M 75 MET cc_start: 0.7838 (ttt) cc_final: 0.7389 (tmm) REVERT: N 10 TYR cc_start: 0.7160 (m-80) cc_final: 0.6942 (m-80) REVERT: N 11 MET cc_start: 0.7861 (tpt) cc_final: 0.7593 (tpp) REVERT: N 52 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7804 (mp10) REVERT: O 10 TYR cc_start: 0.7017 (m-80) cc_final: 0.6536 (m-10) REVERT: O 11 MET cc_start: 0.6896 (mmm) cc_final: 0.6135 (mmm) REVERT: O 16 MET cc_start: 0.7793 (mtm) cc_final: 0.6865 (mpp) REVERT: O 17 MET cc_start: 0.7484 (ttm) cc_final: 0.6994 (tpp) REVERT: O 75 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7214 (tpt) REVERT: P 10 TYR cc_start: 0.6906 (m-80) cc_final: 0.6663 (m-80) REVERT: P 41 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8105 (ttp-110) REVERT: P 42 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7868 (mp10) REVERT: P 55 ILE cc_start: 0.8825 (mm) cc_final: 0.8586 (mt) REVERT: P 73 TYR cc_start: 0.7511 (t80) cc_final: 0.5755 (m-80) REVERT: Q 8 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.5976 (tt) REVERT: Q 35 PHE cc_start: 0.8751 (t80) cc_final: 0.8396 (t80) REVERT: Q 41 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6386 (mtm110) REVERT: Q 54 PHE cc_start: 0.7840 (m-80) cc_final: 0.7556 (m-80) REVERT: Q 66 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7090 (tp) REVERT: R 6 MET cc_start: 0.6475 (mmp) cc_final: 0.5948 (mtt) REVERT: R 10 TYR cc_start: 0.8257 (m-80) cc_final: 0.7470 (m-80) REVERT: R 16 MET cc_start: 0.8535 (mtp) cc_final: 0.8160 (ttm) REVERT: R 57 MET cc_start: 0.8915 (ttp) cc_final: 0.8699 (ttp) REVERT: R 65 MET cc_start: 0.8830 (mmm) cc_final: 0.8599 (mmm) REVERT: Y 16 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7097 (mt) REVERT: Y 64 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (pp30) REVERT: Y 67 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8116 (tmtt) REVERT: Y 82 ARG cc_start: 0.8773 (tpp-160) cc_final: 0.8529 (tpp-160) REVERT: a 6 MET cc_start: 0.4575 (mmp) cc_final: 0.4205 (mmp) REVERT: a 65 LYS cc_start: 0.5673 (tttt) cc_final: 0.5432 (pptt) REVERT: a 115 MET cc_start: 0.6722 (ptp) cc_final: 0.6456 (ptp) REVERT: a 201 LEU cc_start: 0.8298 (tp) cc_final: 0.7781 (mm) REVERT: a 264 LEU cc_start: 0.8989 (mt) cc_final: 0.8598 (pp) REVERT: I 50 ARG cc_start: 0.8919 (mtm110) cc_final: 0.8175 (mtm110) REVERT: I 54 PHE cc_start: 0.8552 (m-80) cc_final: 0.8121 (m-80) REVERT: I 57 MET cc_start: 0.7285 (ptt) cc_final: 0.6597 (ptt) REVERT: S 65 MET cc_start: 0.7496 (mtp) cc_final: 0.7285 (mtp) outliers start: 81 outliers final: 64 residues processed: 594 average time/residue: 0.2200 time to fit residues: 213.7619 Evaluate side-chains 601 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 526 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 402 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 188 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 422 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 237 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 57 HIS D 243 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072276 restraints weight = 79776.683| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.14 r_work: 0.2911 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37528 Z= 0.131 Angle : 0.599 11.867 50797 Z= 0.302 Chirality : 0.042 0.258 5920 Planarity : 0.004 0.058 6550 Dihedral : 6.618 165.730 5357 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.22 % Allowed : 18.25 % Favored : 79.54 % 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: 4807 helix: 1.40 (0.10), residues: 2653 sheet: 0.25 (0.22), residues: 519 loop : -0.29 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 50 TYR 0.032 0.001 TYR P 10 PHE 0.032 0.001 PHE L 35 TRP 0.028 0.001 TRP G 203 HIS 0.022 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00299 (37528) covalent geometry : angle 0.59883 (50797) hydrogen bonds : bond 0.03827 ( 2154) hydrogen bonds : angle 4.30892 ( 6267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10709.35 seconds wall clock time: 182 minutes 50.71 seconds (10970.71 seconds total)