Starting phenix.real_space_refine on Sat Mar 7 02:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170.map" model { file = "/net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqu_20170/03_2026/6oqu_20170_neut.cif" } resolution = 3.2 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 289 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: 8.24, per 1000 atoms: 0.22 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 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: 3.25 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: 208 helices and 28 sheets defined 61.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'W' and resid 6 through 21 removed outlier: 4.686A pdb=" N TYR W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 40 removed outlier: 3.813A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN W 40 " --> pdb=" O GLU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.688A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 72 through 83 removed outlier: 3.596A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.662A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 removed outlier: 4.518A pdb=" N GLU W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 169 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.672A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.648A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.601A pdb=" N ILE C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.632A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 removed outlier: 3.515A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.501A 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 Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 341 through 349 removed outlier: 4.009A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.748A pdb=" N ALA C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.813A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 4.335A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.645A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 removed outlier: 3.563A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.596A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 18 removed outlier: 4.053A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.673A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.611A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) 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 251 Proline residue: B 239 - end of helix removed outlier: 3.740A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.723A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 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: 3.872A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.645A 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 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.607A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.634A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.533A pdb=" N LYS B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 479 removed outlier: 3.672A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.574A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.629A pdb=" N GLU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.516A 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 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.632A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.585A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.526A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.514A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.522A 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 346 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.775A 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: 4.054A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.645A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.568A pdb=" N ILE A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.583A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.563A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.813A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS X 66 " --> pdb=" O THR X 62 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU X 71 " --> pdb=" O LYS X 67 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 144 No H-bonds generated for 'chain 'X' and resid 142 through 144' Processing helix chain 'X' and resid 145 through 155 removed outlier: 3.899A pdb=" N LYS X 151 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.610A pdb=" N ARG H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.879A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 4.144A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 107 Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.769A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.593A pdb=" N MET G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 203 removed outlier: 3.964A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP G 203 " --> pdb=" O HIS G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.600A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 156 through 169 removed outlier: 4.011A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.742A pdb=" N PHE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 197 No H-bonds generated for 'chain 'F' and resid 196 through 197' Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.673A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.886A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.220A 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: 3.729A 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 312 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 345 through 369 removed outlier: 7.294A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 383 through 400 removed outlier: 3.760A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.644A 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 420 through 432 removed outlier: 3.893A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 3.816A 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 456 removed outlier: 3.689A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 removed outlier: 4.218A pdb=" N VAL E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.657A pdb=" N GLU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 197 No H-bonds generated for 'chain 'E' and resid 196 through 197' 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: 3.518A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 258 removed outlier: 3.670A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.537A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.581A 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: 4.064A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.754A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.722A 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 451 removed outlier: 3.508A pdb=" N GLU E 451 " --> pdb=" O SER E 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 448 through 451' Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.643A pdb=" N THR D 83 " --> pdb=" O GLY D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 170 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 197 through 200 removed outlier: 4.174A pdb=" N ASP D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.588A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.689A pdb=" N ASP D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.726A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 378 removed outlier: 7.233A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 removed outlier: 3.847A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 removed outlier: 3.514A pdb=" N GLY D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.540A pdb=" N ALA D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.707A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR J 10 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.740A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 78 Processing helix chain 'L' and resid 4 through 42 removed outlier: 3.871A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 4.579A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.710A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.248A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.200A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 4.681A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.541A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET O 11 " --> pdb=" O ASP O 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.692A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 78 removed outlier: 3.546A pdb=" N ILE O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 42 removed outlier: 4.132A pdb=" N ALA P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 62 removed outlier: 3.706A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 78 Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.482A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 removed outlier: 4.095A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.793A pdb=" N ALA Q 67 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.764A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET R 11 " --> pdb=" O ASP R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.711A pdb=" N VAL R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 77 Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.528A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 60 removed outlier: 4.082A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 102 removed outlier: 3.936A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Y 94 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 139 removed outlier: 4.143A pdb=" N GLU Y 108 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 154 removed outlier: 3.502A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 15 removed outlier: 3.660A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.616A pdb=" N PHE a 48 " --> pdb=" O ASP a 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL a 50 " --> pdb=" O MET a 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 4.400A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (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 133 removed outlier: 3.636A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS a 132 " --> pdb=" O TYR a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 168 removed outlier: 3.803A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU a 160 " --> pdb=" O GLY a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 181 removed outlier: 4.005A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 3.680A 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: 4.380A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.029A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET a 215 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 232 No H-bonds generated for 'chain 'a' and resid 230 through 232' Processing helix chain 'a' and resid 233 through 269 removed outlier: 3.806A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.108A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.580A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.843A pdb=" N VAL I 56 " --> pdb=" O GLN I 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.578A pdb=" N MET I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL I 74 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 42 removed outlier: 4.437A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.714A pdb=" N THR S 51 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN S 52 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 76 Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.644A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 35 removed outlier: 13.508A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.252A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.571A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.454A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.614A 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 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.547A 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: 6.257A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 59 through 66 removed outlier: 3.672A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA E 28 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP E 27 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.566A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.566A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.602A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 14 through 16 removed outlier: 7.099A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.065A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA H 44 " --> pdb=" O GLU G 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.128A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.548A 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: 11.706A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.805A 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: 6.537A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.863A 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: 4.773A 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: 6.187A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER E 174 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL E 205 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE E 176 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY E 207 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY E 178 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.201A 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: 4.263A 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: 4.781A 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: 6.292A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 20 through 21 removed outlier: 4.483A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2215 hydrogen bonds defined for protein. 6429 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: 9.09 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6333 1.29 - 1.42: 8600 1.42 - 1.55: 22211 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.83e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.38e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 50611 4.78 - 9.57: 178 9.57 - 14.35: 2 14.35 - 19.14: 2 19.14 - 23.92: 4 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 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.91 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.85 19.98 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.58 17.25 1.00e+00 1.00e+00 2.97e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 22044 30.97 - 61.95: 657 61.95 - 92.92: 88 92.92 - 123.90: 2 123.90 - 154.87: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -145.64 23.04 0 2.50e+00 1.60e-01 8.49e+01 dihedral pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual 122.80 145.59 -22.79 0 2.50e+00 1.60e-01 8.31e+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 300.00 145.12 154.87 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 5897 0.197 - 0.394: 20 0.394 - 0.591: 2 0.591 - 0.789: 0 0.789 - 0.986: 1 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 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 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 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASP C 262 " pdb=" N ASP C 262 " pdb=" C ASP C 262 " pdb=" CB ASP C 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 14 " -0.022 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ALA I 14 " 0.080 2.00e-02 2.50e+03 pdb=" O ALA I 14 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL I 15 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.022 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C ALA D 264 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 5 " 0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C ASN L 5 " -0.072 2.00e-02 2.50e+03 pdb=" O ASN L 5 " 0.027 2.00e-02 2.50e+03 pdb=" N MET L 6 " 0.025 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 46 2.35 - 2.99: 21674 2.99 - 3.63: 53423 3.63 - 4.26: 84158 4.26 - 4.90: 143746 Nonbonded interactions: 303047 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.718 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.749 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.811 2.170 nonbonded pdb=" OG1 THR F 156 " pdb="MG MG F 501 " model vdw 1.833 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.848 2.170 ... (remaining 303042 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.670 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.113 37528 Z= 0.465 Angle : 0.927 23.924 50797 Z= 0.615 Chirality : 0.054 0.986 5920 Planarity : 0.005 0.055 6550 Dihedral : 15.072 154.874 13976 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 9.36 % Favored : 87.72 % Cbeta Deviations : 0.05 % 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: -2.70 (0.10), residues: 4807 helix: -1.84 (0.08), residues: 2579 sheet: -0.92 (0.19), residues: 564 loop : -1.67 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 36 TYR 0.031 0.002 TYR E 206 PHE 0.019 0.002 PHE E 410 TRP 0.018 0.002 TRP a 39 HIS 0.007 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00918 (37528) covalent geometry : angle 0.92701 (50797) hydrogen bonds : bond 0.16819 ( 2196) hydrogen bonds : angle 7.20111 ( 6429) *********************** 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 873 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 761 time to evaluate : 1.116 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 123 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8594 (mmmm) REVERT: W 143 ASP cc_start: 0.8772 (t0) cc_final: 0.8314 (t0) REVERT: C 76 MET cc_start: 0.9129 (mtm) cc_final: 0.8826 (mtm) REVERT: C 115 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8721 (pt) REVERT: C 236 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8852 (t80) REVERT: C 386 MET cc_start: 0.8847 (mmm) cc_final: 0.8278 (mmt) REVERT: C 501 LYS cc_start: 0.8895 (tttm) cc_final: 0.8614 (tttm) REVERT: B 14 GLN cc_start: 0.8253 (mm110) cc_final: 0.7859 (mm-40) REVERT: B 48 MET cc_start: 0.8855 (ptp) cc_final: 0.8448 (ptp) REVERT: B 386 MET cc_start: 0.8743 (mmm) cc_final: 0.8487 (mmt) REVERT: A 180 ILE cc_start: 0.8959 (pt) cc_final: 0.8700 (mm) REVERT: A 483 MET cc_start: 0.8407 (mmp) cc_final: 0.8188 (mmm) REVERT: A 511 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5652 (tp-100) REVERT: X 20 PHE cc_start: 0.6781 (m-80) cc_final: 0.6335 (m-80) REVERT: X 78 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7530 (tm-30) REVERT: X 146 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8467 (p) REVERT: X 150 ASP cc_start: 0.9105 (m-30) cc_final: 0.8878 (m-30) REVERT: H 51 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7694 (ttm110) REVERT: H 58 HIS cc_start: 0.7663 (m-70) cc_final: 0.7297 (m90) REVERT: G 57 HIS cc_start: 0.7308 (p-80) cc_final: 0.7002 (p-80) REVERT: G 116 MET cc_start: 0.9281 (mmm) cc_final: 0.8954 (mmm) REVERT: F 340 THR cc_start: 0.8653 (m) cc_final: 0.8430 (m) REVERT: E 97 MET cc_start: 0.8713 (mmt) cc_final: 0.8415 (mmm) REVERT: D 88 MET cc_start: 0.9105 (mtm) cc_final: 0.8899 (mtp) REVERT: D 301 ASP cc_start: 0.8293 (t0) cc_final: 0.7817 (t0) REVERT: D 322 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8435 (p) REVERT: J 55 ILE cc_start: 0.8362 (mm) cc_final: 0.8050 (mm) REVERT: L 63 ILE cc_start: 0.8522 (mm) cc_final: 0.8217 (mm) REVERT: L 68 VAL cc_start: 0.8930 (t) cc_final: 0.8574 (p) REVERT: L 73 TYR cc_start: 0.9004 (t80) cc_final: 0.8590 (t80) REVERT: M 6 MET cc_start: 0.6801 (mtt) cc_final: 0.6386 (mtm) REVERT: M 7 ASP cc_start: 0.7565 (m-30) cc_final: 0.7108 (p0) REVERT: N 16 MET cc_start: 0.7907 (mtp) cc_final: 0.7611 (tpp) REVERT: N 34 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7934 (mmtp) REVERT: O 7 ASP cc_start: 0.7021 (p0) cc_final: 0.6808 (p0) REVERT: O 8 LEU cc_start: 0.8431 (mt) cc_final: 0.7009 (tt) REVERT: O 28 ILE cc_start: 0.9238 (mt) cc_final: 0.9021 (mm) REVERT: O 42 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7842 (mp10) REVERT: P 11 MET cc_start: 0.8391 (tpp) cc_final: 0.7738 (mmm) REVERT: P 17 MET cc_start: 0.8188 (mtm) cc_final: 0.7644 (mtt) REVERT: P 57 MET cc_start: 0.8455 (tmm) cc_final: 0.8246 (tmm) REVERT: P 61 ASP cc_start: 0.8510 (m-30) cc_final: 0.8059 (m-30) REVERT: Q 16 MET cc_start: 0.8725 (ttm) cc_final: 0.8484 (ttm) REVERT: Q 35 PHE cc_start: 0.8651 (t80) cc_final: 0.8310 (t80) REVERT: Q 36 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8820 (tt) REVERT: R 34 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7451 (mmtm) REVERT: R 48 LEU cc_start: 0.8310 (tp) cc_final: 0.7797 (tt) REVERT: R 51 THR cc_start: 0.9311 (m) cc_final: 0.8688 (p) REVERT: R 52 GLN cc_start: 0.8950 (mm110) cc_final: 0.8336 (mm110) REVERT: R 76 PHE cc_start: 0.8026 (m-80) cc_final: 0.7778 (m-80) REVERT: Y 85 GLN cc_start: 0.8652 (tp40) cc_final: 0.8066 (tp40) REVERT: Y 150 ASP cc_start: 0.8979 (m-30) cc_final: 0.8673 (m-30) REVERT: a 6 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.4086 (tpt) REVERT: a 9 GLN cc_start: 0.8768 (mt0) cc_final: 0.8565 (pm20) REVERT: a 94 TYR cc_start: 0.6622 (t80) cc_final: 0.6364 (t80) REVERT: a 99 LYS cc_start: 0.7473 (mppt) cc_final: 0.7026 (ttpt) REVERT: a 219 GLU cc_start: 0.9113 (tt0) cc_final: 0.8812 (tt0) REVERT: a 237 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8922 (tt) REVERT: a 266 MET cc_start: 0.8834 (ttm) cc_final: 0.8627 (ptt) REVERT: I 10 TYR cc_start: 0.8509 (m-80) cc_final: 0.8263 (m-80) REVERT: I 17 MET cc_start: 0.8076 (ptp) cc_final: 0.7425 (ttp) REVERT: I 35 PHE cc_start: 0.8912 (t80) cc_final: 0.8493 (t80) REVERT: S 37 GLU cc_start: 0.8911 (tt0) cc_final: 0.8418 (tt0) REVERT: S 50 ARG cc_start: 0.8303 (ttm170) cc_final: 0.8033 (ttp-170) REVERT: S 61 ASP cc_start: 0.7632 (p0) cc_final: 0.7204 (t0) REVERT: S 73 TYR cc_start: 0.8762 (t80) cc_final: 0.8503 (t80) outliers start: 112 outliers final: 67 residues processed: 859 average time/residue: 0.2282 time to fit residues: 312.2589 Evaluate side-chains 663 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 588 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 115 ILE 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 374 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 17 ASN Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 GLN Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN W 94 GLN C 369 ASN B 26 HIS B 58 ASN B 186 GLN B 408 GLN A 65 ASN A 147 GLN A 408 GLN X 64 GLN X 145 ASN H 14 GLN G 59 ASN G 142 ASN G 274 GLN F 294 GLN F 353 HIS F 368 GLN F 437 HIS E 353 HIS E 441 GLN D 73 HIS D 170 HIS D 437 HIS J 52 GLN L 3 ASN L 5 ASN M 5 ASN N 3 ASN O 3 ASN R 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS S 3 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066595 restraints weight = 78211.672| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.07 r_work: 0.2756 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37528 Z= 0.148 Angle : 0.649 8.748 50797 Z= 0.337 Chirality : 0.045 0.316 5920 Planarity : 0.004 0.069 6550 Dihedral : 8.643 143.134 5462 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.26 % Allowed : 11.89 % Favored : 84.85 % 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: -0.66 (0.11), residues: 4807 helix: 0.04 (0.10), residues: 2646 sheet: -0.51 (0.21), residues: 522 loop : -0.99 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 98 TYR 0.024 0.001 TYR a 263 PHE 0.017 0.001 PHE a 174 TRP 0.012 0.001 TRP B 513 HIS 0.005 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00309 (37528) covalent geometry : angle 0.64921 (50797) hydrogen bonds : bond 0.05263 ( 2196) hydrogen bonds : angle 4.93571 ( 6429) *********************** 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 820 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 695 time to evaluate : 1.330 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 43 MET cc_start: 0.9317 (tpt) cc_final: 0.8968 (tpp) REVERT: W 135 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8539 (ttpp) REVERT: W 142 ILE cc_start: 0.8723 (mp) cc_final: 0.8479 (mm) REVERT: W 143 ASP cc_start: 0.8893 (t0) cc_final: 0.8477 (t0) REVERT: W 160 ASP cc_start: 0.8687 (t0) cc_final: 0.8487 (t0) REVERT: C 27 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8216 (p0) REVERT: C 236 TYR cc_start: 0.9494 (OUTLIER) cc_final: 0.9007 (t80) REVERT: B 97 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8975 (m) REVERT: B 180 ILE cc_start: 0.9310 (pt) cc_final: 0.9085 (mt) REVERT: B 415 ASP cc_start: 0.8459 (t0) cc_final: 0.7880 (t0) REVERT: B 419 LYS cc_start: 0.8367 (tptt) cc_final: 0.7935 (pttp) REVERT: B 429 GLU cc_start: 0.8774 (tp30) cc_final: 0.8553 (tp30) REVERT: A 418 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7769 (tpp-160) REVERT: A 501 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8898 (tptm) REVERT: X 15 VAL cc_start: 0.7936 (p) cc_final: 0.7682 (m) REVERT: X 49 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7243 (ttp80) REVERT: X 78 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7568 (tm-30) REVERT: X 96 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8739 (mm-40) REVERT: X 150 ASP cc_start: 0.9100 (m-30) cc_final: 0.8826 (m-30) REVERT: H 22 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8753 (pttt) REVERT: H 34 ILE cc_start: 0.9430 (mm) cc_final: 0.9216 (mm) REVERT: H 51 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8394 (ttp-110) REVERT: H 52 ILE cc_start: 0.9200 (mm) cc_final: 0.8929 (mt) REVERT: H 58 HIS cc_start: 0.7445 (m-70) cc_final: 0.7067 (m90) REVERT: H 65 SER cc_start: 0.9126 (m) cc_final: 0.8415 (t) REVERT: G 259 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8481 (mp0) REVERT: F 141 LYS cc_start: 0.9484 (tttt) cc_final: 0.9155 (ttpp) REVERT: E 14 ASP cc_start: 0.8568 (m-30) cc_final: 0.8303 (m-30) REVERT: E 209 MET cc_start: 0.8717 (mtm) cc_final: 0.8505 (mtm) REVERT: E 410 PHE cc_start: 0.8386 (m-80) cc_final: 0.8049 (m-80) REVERT: D 166 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9094 (mp) REVERT: D 301 ASP cc_start: 0.8581 (t0) cc_final: 0.8072 (t0) REVERT: J 37 GLU cc_start: 0.8614 (pp20) cc_final: 0.8091 (pp20) REVERT: L 8 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7442 (tm) REVERT: L 9 LEU cc_start: 0.8757 (mt) cc_final: 0.8554 (mt) REVERT: L 37 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8590 (tp30) REVERT: L 41 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8543 (mtm180) REVERT: L 70 LEU cc_start: 0.9206 (mt) cc_final: 0.8965 (mt) REVERT: L 73 TYR cc_start: 0.8986 (t80) cc_final: 0.8382 (t80) REVERT: M 37 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8333 (tt0) REVERT: M 50 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7802 (ttp80) REVERT: N 3 ASN cc_start: 0.5196 (OUTLIER) cc_final: 0.4226 (t0) REVERT: N 75 MET cc_start: 0.8057 (ttt) cc_final: 0.7746 (ttt) REVERT: O 16 MET cc_start: 0.8193 (ttp) cc_final: 0.7179 (mmm) REVERT: O 30 ILE cc_start: 0.8429 (mt) cc_final: 0.8213 (mp) REVERT: O 41 ARG cc_start: 0.8596 (ttm170) cc_final: 0.7862 (ttm-80) REVERT: O 42 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7157 (mp10) REVERT: O 63 ILE cc_start: 0.8187 (mm) cc_final: 0.7960 (mt) REVERT: P 11 MET cc_start: 0.8278 (tpp) cc_final: 0.7651 (mmm) REVERT: P 17 MET cc_start: 0.8197 (mtm) cc_final: 0.7947 (mtt) REVERT: P 42 GLN cc_start: 0.8431 (mm110) cc_final: 0.8005 (mm110) REVERT: P 48 LEU cc_start: 0.9105 (tp) cc_final: 0.8814 (tp) REVERT: P 50 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.8067 (ttm110) REVERT: P 52 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8583 (mm-40) REVERT: P 54 PHE cc_start: 0.8797 (m-80) cc_final: 0.8421 (m-80) REVERT: P 61 ASP cc_start: 0.8746 (m-30) cc_final: 0.8379 (m-30) REVERT: P 64 PRO cc_start: 0.9174 (Cg_exo) cc_final: 0.8917 (Cg_endo) REVERT: Q 11 MET cc_start: 0.8545 (tpp) cc_final: 0.8336 (tpp) REVERT: Q 16 MET cc_start: 0.8774 (ttm) cc_final: 0.8534 (ttm) REVERT: Q 35 PHE cc_start: 0.8697 (t80) cc_final: 0.8003 (t80) REVERT: Q 42 GLN cc_start: 0.8741 (mt0) cc_final: 0.8449 (mp10) REVERT: Q 51 THR cc_start: 0.9012 (m) cc_final: 0.8719 (p) REVERT: R 48 LEU cc_start: 0.8382 (tp) cc_final: 0.8017 (tt) REVERT: R 51 THR cc_start: 0.9435 (m) cc_final: 0.9045 (p) REVERT: R 52 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8589 (mm110) REVERT: R 61 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8223 (t70) REVERT: R 70 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8013 (tp) REVERT: R 75 MET cc_start: 0.8851 (ttt) cc_final: 0.7889 (tpp) REVERT: Y 2 ASN cc_start: 0.5318 (t0) cc_final: 0.4924 (m-40) REVERT: Y 53 ASP cc_start: 0.6138 (t0) cc_final: 0.5827 (t0) REVERT: Y 80 ASN cc_start: 0.8195 (m-40) cc_final: 0.7446 (m110) REVERT: Y 82 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: Y 150 ASP cc_start: 0.9073 (m-30) cc_final: 0.8686 (m-30) REVERT: a 6 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4668 (pmm) REVERT: a 11 TYR cc_start: 0.8325 (t80) cc_final: 0.8053 (t80) REVERT: a 76 GLN cc_start: 0.6804 (tt0) cc_final: 0.6436 (pt0) REVERT: a 99 LYS cc_start: 0.7395 (mppt) cc_final: 0.6872 (ttpt) REVERT: a 209 LEU cc_start: 0.8841 (mm) cc_final: 0.8583 (mt) REVERT: a 237 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8904 (tt) REVERT: a 257 MET cc_start: 0.9065 (ttp) cc_final: 0.8829 (tmm) REVERT: I 16 MET cc_start: 0.8427 (tpp) cc_final: 0.8098 (mmm) REVERT: I 17 MET cc_start: 0.8082 (ptp) cc_final: 0.7457 (ttp) REVERT: I 65 MET cc_start: 0.8367 (mmm) cc_final: 0.7787 (mmp) REVERT: S 37 GLU cc_start: 0.9184 (tt0) cc_final: 0.8744 (tt0) REVERT: S 57 MET cc_start: 0.9071 (tmm) cc_final: 0.8869 (tmm) outliers start: 125 outliers final: 57 residues processed: 784 average time/residue: 0.2135 time to fit residues: 271.4887 Evaluate side-chains 667 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 599 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 32 VAL 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 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 80 GLU Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 344 optimal weight: 4.9990 chunk 431 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 147 GLN B 399 GLN A 20 ASN H 14 GLN G 229 GLN G 274 GLN D 243 ASN L 3 ASN N 3 ASN O 3 ASN Y 10 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065152 restraints weight = 78351.844| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.05 r_work: 0.2716 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 37528 Z= 0.232 Angle : 0.658 9.186 50797 Z= 0.336 Chirality : 0.046 0.245 5920 Planarity : 0.004 0.051 6550 Dihedral : 7.894 135.752 5392 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.14 % Allowed : 12.83 % Favored : 83.03 % 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: 0.51 (0.10), residues: 2652 sheet: -0.44 (0.22), residues: 518 loop : -0.86 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.017 0.002 TYR B 400 PHE 0.030 0.002 PHE E 189 TRP 0.013 0.001 TRP a 235 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00550 (37528) covalent geometry : angle 0.65750 (50797) hydrogen bonds : bond 0.05205 ( 2196) hydrogen bonds : angle 4.77478 ( 6429) *********************** 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 779 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 620 time to evaluate : 1.340 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 43 MET cc_start: 0.9391 (tpt) cc_final: 0.8943 (tpp) REVERT: W 135 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8573 (ttpp) REVERT: W 143 ASP cc_start: 0.8776 (t0) cc_final: 0.8323 (t0) REVERT: C 27 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8448 (p0) REVERT: C 48 MET cc_start: 0.9139 (mtm) cc_final: 0.8791 (mtt) REVERT: C 236 TYR cc_start: 0.9570 (OUTLIER) cc_final: 0.9039 (t80) REVERT: B 97 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9015 (m) REVERT: B 180 ILE cc_start: 0.9356 (pt) cc_final: 0.9080 (mt) REVERT: A 356 GLU cc_start: 0.8290 (tp30) cc_final: 0.8067 (tp30) REVERT: A 418 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7844 (tpp-160) REVERT: X 2 ASN cc_start: 0.6703 (t0) cc_final: 0.6362 (t0) REVERT: X 15 VAL cc_start: 0.8053 (p) cc_final: 0.7756 (m) REVERT: X 78 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7621 (tm-30) REVERT: X 96 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8708 (mm-40) REVERT: X 150 ASP cc_start: 0.9102 (m-30) cc_final: 0.8835 (m-30) REVERT: H 22 LYS cc_start: 0.9054 (ptpt) cc_final: 0.8797 (pttt) REVERT: H 51 ARG cc_start: 0.8695 (mtp180) cc_final: 0.8438 (ttp-170) REVERT: H 58 HIS cc_start: 0.7543 (m-70) cc_final: 0.7139 (m90) REVERT: H 65 SER cc_start: 0.9132 (m) cc_final: 0.8748 (t) REVERT: G 259 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8637 (mp0) REVERT: F 141 LYS cc_start: 0.9509 (tttt) cc_final: 0.9198 (ttpp) REVERT: E 14 ASP cc_start: 0.8708 (m-30) cc_final: 0.8488 (m-30) REVERT: E 410 PHE cc_start: 0.8426 (m-80) cc_final: 0.8110 (m-80) REVERT: D 166 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9135 (mp) REVERT: D 301 ASP cc_start: 0.8586 (t0) cc_final: 0.8136 (t0) REVERT: J 37 GLU cc_start: 0.8595 (pp20) cc_final: 0.8159 (pp20) REVERT: L 3 ASN cc_start: 0.4158 (OUTLIER) cc_final: 0.3589 (p0) REVERT: L 11 MET cc_start: 0.8942 (mmm) cc_final: 0.8674 (mmm) REVERT: L 73 TYR cc_start: 0.8985 (t80) cc_final: 0.8484 (t80) REVERT: M 6 MET cc_start: 0.6052 (mtm) cc_final: 0.5575 (mtm) REVERT: M 37 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8427 (tt0) REVERT: N 9 LEU cc_start: 0.8119 (mm) cc_final: 0.7742 (mp) REVERT: O 8 LEU cc_start: 0.8149 (mt) cc_final: 0.7003 (mp) REVERT: O 41 ARG cc_start: 0.8605 (ttm170) cc_final: 0.7996 (ttm170) REVERT: O 42 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7069 (mp10) REVERT: O 63 ILE cc_start: 0.8430 (mm) cc_final: 0.8153 (mm) REVERT: P 11 MET cc_start: 0.8474 (tpp) cc_final: 0.7749 (mmm) REVERT: P 17 MET cc_start: 0.8346 (mtm) cc_final: 0.7969 (mtt) REVERT: P 42 GLN cc_start: 0.8430 (mm110) cc_final: 0.7984 (mm110) REVERT: P 52 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8852 (mp10) REVERT: P 54 PHE cc_start: 0.8728 (m-80) cc_final: 0.8157 (m-80) REVERT: P 61 ASP cc_start: 0.8626 (m-30) cc_final: 0.8216 (m-30) REVERT: Q 35 PHE cc_start: 0.8706 (t80) cc_final: 0.8065 (t80) REVERT: Q 51 THR cc_start: 0.9078 (m) cc_final: 0.8773 (p) REVERT: R 75 MET cc_start: 0.8849 (ttt) cc_final: 0.7955 (tpp) REVERT: Y 2 ASN cc_start: 0.6109 (t0) cc_final: 0.4964 (m-40) REVERT: Y 80 ASN cc_start: 0.8297 (m-40) cc_final: 0.7639 (m110) REVERT: Y 82 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.8004 (tpp-160) REVERT: Y 150 ASP cc_start: 0.9068 (m-30) cc_final: 0.8735 (m-30) REVERT: a 6 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4668 (pmm) REVERT: a 9 GLN cc_start: 0.8454 (mt0) cc_final: 0.8224 (pm20) REVERT: a 11 TYR cc_start: 0.8447 (t80) cc_final: 0.8134 (t80) REVERT: a 91 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8702 (mtmm) REVERT: a 99 LYS cc_start: 0.7422 (mppt) cc_final: 0.6894 (ttpt) REVERT: a 167 LYS cc_start: 0.7666 (tttt) cc_final: 0.7459 (tttt) REVERT: a 202 SER cc_start: 0.9285 (t) cc_final: 0.9005 (p) REVERT: a 209 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8507 (mt) REVERT: a 237 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8871 (tt) REVERT: S 37 GLU cc_start: 0.9228 (tt0) cc_final: 0.8762 (tt0) REVERT: S 42 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7956 (mt0) outliers start: 159 outliers final: 95 residues processed: 736 average time/residue: 0.2097 time to fit residues: 252.9041 Evaluate side-chains 689 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 585 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 39 ILE 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 262 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 81 LYS 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 224 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 80 GLU Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 267 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 331 optimal weight: 0.6980 chunk 214 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 394 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 379 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN A 511 GLN X 37 GLN G 234 ASN G 274 GLN D 243 ASN L 3 ASN P 3 ASN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067854 restraints weight = 78232.668| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.07 r_work: 0.2771 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37528 Z= 0.124 Angle : 0.583 7.879 50797 Z= 0.297 Chirality : 0.043 0.200 5920 Planarity : 0.004 0.046 6550 Dihedral : 7.388 127.598 5389 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.00 % Allowed : 14.42 % Favored : 82.59 % 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: 0.28 (0.12), residues: 4807 helix: 0.90 (0.10), residues: 2644 sheet: -0.31 (0.22), residues: 529 loop : -0.69 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 50 TYR 0.016 0.001 TYR a 94 PHE 0.025 0.001 PHE E 189 TRP 0.014 0.001 TRP a 235 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00266 (37528) covalent geometry : angle 0.58297 (50797) hydrogen bonds : bond 0.04448 ( 2196) hydrogen bonds : angle 4.46934 ( 6429) *********************** 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 740 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 625 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8561 (ttpp) REVERT: W 143 ASP cc_start: 0.8687 (t0) cc_final: 0.8312 (t0) REVERT: W 146 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.6860 (p) REVERT: C 27 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8457 (p0) REVERT: C 48 MET cc_start: 0.9109 (mtm) cc_final: 0.8763 (mtt) REVERT: C 236 TYR cc_start: 0.9549 (OUTLIER) cc_final: 0.8881 (t80) REVERT: B 97 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8979 (m) REVERT: B 463 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8459 (ttpt) REVERT: A 172 GLN cc_start: 0.9063 (tt0) cc_final: 0.8756 (mt0) REVERT: A 418 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7819 (tpp-160) REVERT: A 463 LYS cc_start: 0.6291 (tttt) cc_final: 0.6071 (tttp) REVERT: X 15 VAL cc_start: 0.8053 (p) cc_final: 0.7773 (m) REVERT: X 49 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7059 (ttp80) REVERT: X 78 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7612 (tm-30) REVERT: X 96 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8716 (mm-40) REVERT: X 150 ASP cc_start: 0.9052 (m-30) cc_final: 0.8761 (m-30) REVERT: H 22 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8714 (pttt) REVERT: H 26 THR cc_start: 0.9207 (t) cc_final: 0.8815 (p) REVERT: H 51 ARG cc_start: 0.8736 (mtp180) cc_final: 0.8422 (ttp-110) REVERT: H 58 HIS cc_start: 0.7444 (m-70) cc_final: 0.6973 (m90) REVERT: H 65 SER cc_start: 0.9095 (m) cc_final: 0.8425 (t) REVERT: G 259 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8608 (mp0) REVERT: F 141 LYS cc_start: 0.9453 (tttt) cc_final: 0.9177 (ttpp) REVERT: E 14 ASP cc_start: 0.8620 (m-30) cc_final: 0.8371 (m-30) REVERT: E 410 PHE cc_start: 0.8312 (m-80) cc_final: 0.8002 (m-10) REVERT: D 301 ASP cc_start: 0.8617 (t0) cc_final: 0.8182 (t0) REVERT: J 37 GLU cc_start: 0.8553 (pp20) cc_final: 0.8056 (pp20) REVERT: L 3 ASN cc_start: 0.3034 (OUTLIER) cc_final: 0.2646 (p0) REVERT: L 73 TYR cc_start: 0.8945 (t80) cc_final: 0.8526 (t80) REVERT: M 7 ASP cc_start: 0.7554 (m-30) cc_final: 0.7202 (m-30) REVERT: M 10 TYR cc_start: 0.8260 (m-80) cc_final: 0.7899 (m-80) REVERT: M 37 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8458 (tt0) REVERT: N 9 LEU cc_start: 0.8171 (mm) cc_final: 0.7846 (mp) REVERT: N 42 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7405 (mt0) REVERT: O 7 ASP cc_start: 0.5689 (p0) cc_final: 0.5298 (p0) REVERT: O 8 LEU cc_start: 0.8185 (mt) cc_final: 0.7081 (mp) REVERT: O 16 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7112 (mmm) REVERT: O 41 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8144 (ttm-80) REVERT: O 42 GLN cc_start: 0.7781 (mm-40) cc_final: 0.6862 (mp10) REVERT: O 63 ILE cc_start: 0.8425 (mm) cc_final: 0.8207 (mt) REVERT: P 11 MET cc_start: 0.8632 (tpp) cc_final: 0.7899 (mmm) REVERT: P 42 GLN cc_start: 0.8364 (mm110) cc_final: 0.7943 (mm-40) REVERT: P 52 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8768 (mp10) REVERT: P 54 PHE cc_start: 0.8634 (m-80) cc_final: 0.8330 (m-80) REVERT: P 61 ASP cc_start: 0.8998 (m-30) cc_final: 0.8575 (p0) REVERT: Q 35 PHE cc_start: 0.8664 (t80) cc_final: 0.7966 (t80) REVERT: Q 51 THR cc_start: 0.8957 (m) cc_final: 0.8709 (p) REVERT: R 11 MET cc_start: 0.8784 (tpp) cc_final: 0.8504 (tpp) REVERT: R 75 MET cc_start: 0.8804 (ttt) cc_final: 0.8040 (tpp) REVERT: Y 2 ASN cc_start: 0.6065 (t0) cc_final: 0.5060 (m-40) REVERT: Y 80 ASN cc_start: 0.8326 (m-40) cc_final: 0.7683 (m110) REVERT: Y 82 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7998 (tpp-160) REVERT: Y 150 ASP cc_start: 0.9034 (m-30) cc_final: 0.8624 (m-30) REVERT: a 6 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4449 (pmm) REVERT: a 11 TYR cc_start: 0.8457 (t80) cc_final: 0.8130 (t80) REVERT: a 41 ILE cc_start: 0.8417 (mm) cc_final: 0.8214 (tp) REVERT: a 76 GLN cc_start: 0.6665 (pt0) cc_final: 0.6450 (pp30) REVERT: a 99 LYS cc_start: 0.7298 (mppt) cc_final: 0.6862 (ttpt) REVERT: a 202 SER cc_start: 0.9228 (t) cc_final: 0.8999 (p) REVERT: a 209 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8538 (mt) REVERT: I 16 MET cc_start: 0.8493 (tpp) cc_final: 0.7969 (mmm) REVERT: I 41 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7859 (tpp80) REVERT: S 42 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7910 (mt0) outliers start: 115 outliers final: 64 residues processed: 711 average time/residue: 0.2145 time to fit residues: 249.7243 Evaluate side-chains 668 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 595 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 32 VAL 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 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 404 optimal weight: 20.0000 chunk 445 optimal weight: 0.9980 chunk 374 optimal weight: 0.7980 chunk 443 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 320 optimal weight: 0.5980 chunk 263 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN G 234 ASN G 274 GLN D 243 ASN M 52 GLN R 52 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.067887 restraints weight = 78073.485| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.06 r_work: 0.2784 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37528 Z= 0.120 Angle : 0.570 8.327 50797 Z= 0.288 Chirality : 0.042 0.198 5920 Planarity : 0.004 0.046 6550 Dihedral : 7.016 125.481 5382 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.50 % Allowed : 15.48 % Favored : 82.01 % 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: 0.59 (0.12), residues: 4807 helix: 1.15 (0.10), residues: 2638 sheet: -0.15 (0.22), residues: 526 loop : -0.56 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 50 TYR 0.018 0.001 TYR a 263 PHE 0.029 0.001 PHE P 54 TRP 0.009 0.001 TRP B 513 HIS 0.002 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00263 (37528) covalent geometry : angle 0.56951 (50797) hydrogen bonds : bond 0.04211 ( 2196) hydrogen bonds : angle 4.33977 ( 6429) *********************** 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 711 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 615 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9359 (tpt) cc_final: 0.9148 (tpt) REVERT: W 135 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8523 (ttpp) REVERT: W 143 ASP cc_start: 0.8684 (t0) cc_final: 0.8318 (t0) REVERT: W 146 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6795 (p) REVERT: C 27 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (p0) REVERT: C 48 MET cc_start: 0.9113 (mtm) cc_final: 0.8767 (mtt) REVERT: C 236 TYR cc_start: 0.9547 (OUTLIER) cc_final: 0.8808 (t80) REVERT: B 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8974 (m) REVERT: A 172 GLN cc_start: 0.9046 (tt0) cc_final: 0.8785 (mt0) REVERT: A 418 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7861 (tpp-160) REVERT: A 463 LYS cc_start: 0.6136 (tttt) cc_final: 0.5888 (tttm) REVERT: X 15 VAL cc_start: 0.8073 (p) cc_final: 0.7804 (m) REVERT: X 78 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7597 (tm-30) REVERT: X 83 ARG cc_start: 0.7511 (ttt90) cc_final: 0.7159 (ttt90) REVERT: X 150 ASP cc_start: 0.9086 (m-30) cc_final: 0.8817 (m-30) REVERT: H 22 LYS cc_start: 0.8994 (ptpt) cc_final: 0.8752 (pttt) REVERT: H 26 THR cc_start: 0.9229 (t) cc_final: 0.8844 (p) REVERT: H 51 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8444 (ttm110) REVERT: H 58 HIS cc_start: 0.7432 (m-70) cc_final: 0.6924 (m90) REVERT: H 65 SER cc_start: 0.9080 (m) cc_final: 0.8365 (t) REVERT: F 89 ASN cc_start: 0.8928 (t0) cc_final: 0.8619 (t0) REVERT: E 14 ASP cc_start: 0.8635 (m-30) cc_final: 0.8426 (m-30) REVERT: E 410 PHE cc_start: 0.8308 (m-80) cc_final: 0.7979 (m-10) REVERT: D 301 ASP cc_start: 0.8533 (t0) cc_final: 0.8185 (t0) REVERT: J 11 MET cc_start: 0.8633 (mmt) cc_final: 0.8375 (tpp) REVERT: J 17 MET cc_start: 0.8365 (mmm) cc_final: 0.8140 (mmt) REVERT: J 37 GLU cc_start: 0.8510 (pp20) cc_final: 0.8031 (pp20) REVERT: L 11 MET cc_start: 0.8797 (mmm) cc_final: 0.8502 (mmm) REVERT: L 34 LYS cc_start: 0.9333 (mmmm) cc_final: 0.8839 (mmmm) REVERT: L 72 LEU cc_start: 0.8868 (mm) cc_final: 0.8583 (mm) REVERT: L 73 TYR cc_start: 0.8801 (t80) cc_final: 0.8506 (t80) REVERT: M 7 ASP cc_start: 0.7400 (m-30) cc_final: 0.6710 (m-30) REVERT: M 10 TYR cc_start: 0.8469 (m-80) cc_final: 0.7922 (m-80) REVERT: M 37 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8478 (tt0) REVERT: N 9 LEU cc_start: 0.8201 (mm) cc_final: 0.7919 (mp) REVERT: N 42 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7505 (mt0) REVERT: O 7 ASP cc_start: 0.5615 (p0) cc_final: 0.5359 (p0) REVERT: O 8 LEU cc_start: 0.8188 (mt) cc_final: 0.7181 (mp) REVERT: O 10 TYR cc_start: 0.9041 (m-80) cc_final: 0.8579 (m-80) REVERT: O 16 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7205 (mmm) REVERT: O 41 ARG cc_start: 0.8556 (ttm170) cc_final: 0.8166 (ttm-80) REVERT: O 42 GLN cc_start: 0.7727 (mm-40) cc_final: 0.6697 (mp10) REVERT: O 63 ILE cc_start: 0.8571 (mm) cc_final: 0.8358 (mt) REVERT: P 11 MET cc_start: 0.8563 (tpp) cc_final: 0.7697 (mmm) REVERT: P 42 GLN cc_start: 0.8362 (mm110) cc_final: 0.7959 (mm-40) REVERT: P 50 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8041 (mtm110) REVERT: P 54 PHE cc_start: 0.8593 (m-10) cc_final: 0.8234 (m-80) REVERT: P 61 ASP cc_start: 0.8830 (m-30) cc_final: 0.8290 (m-30) REVERT: Q 7 ASP cc_start: 0.8027 (t0) cc_final: 0.6422 (p0) REVERT: Q 35 PHE cc_start: 0.8693 (t80) cc_final: 0.8063 (t80) REVERT: R 11 MET cc_start: 0.8820 (tpp) cc_final: 0.8543 (tpp) REVERT: Y 2 ASN cc_start: 0.6028 (t0) cc_final: 0.5062 (m-40) REVERT: Y 16 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8076 (mt) REVERT: Y 80 ASN cc_start: 0.8353 (m-40) cc_final: 0.7696 (m110) REVERT: Y 150 ASP cc_start: 0.9030 (m-30) cc_final: 0.8771 (m-30) REVERT: a 6 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4315 (pmm) REVERT: a 11 TYR cc_start: 0.8478 (t80) cc_final: 0.8169 (t80) REVERT: a 41 ILE cc_start: 0.8406 (mm) cc_final: 0.8197 (tp) REVERT: a 99 LYS cc_start: 0.7442 (mppt) cc_final: 0.6969 (ttpt) REVERT: a 193 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (pp) REVERT: a 209 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8550 (mt) REVERT: I 16 MET cc_start: 0.8677 (tpp) cc_final: 0.8185 (mmm) REVERT: I 17 MET cc_start: 0.8194 (mtm) cc_final: 0.7953 (ptp) REVERT: I 41 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7866 (tpp80) REVERT: S 42 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7882 (mt0) outliers start: 96 outliers final: 67 residues processed: 684 average time/residue: 0.2135 time to fit residues: 237.8829 Evaluate side-chains 670 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 593 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL 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 83 THR Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 326 optimal weight: 0.7980 chunk 395 optimal weight: 6.9990 chunk 425 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 416 optimal weight: 1.9990 chunk 422 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 456 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN G 274 GLN D 243 ASN ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Y 37 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.067329 restraints weight = 78465.649| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.07 r_work: 0.2771 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37528 Z= 0.141 Angle : 0.576 10.854 50797 Z= 0.291 Chirality : 0.043 0.189 5920 Planarity : 0.004 0.047 6550 Dihedral : 6.779 127.336 5374 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.00 % Allowed : 15.25 % Favored : 81.75 % 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: 0.74 (0.12), residues: 4807 helix: 1.30 (0.10), residues: 2639 sheet: -0.09 (0.22), residues: 526 loop : -0.54 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 49 TYR 0.022 0.001 TYR a 94 PHE 0.027 0.001 PHE P 54 TRP 0.010 0.001 TRP B 513 HIS 0.003 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00325 (37528) covalent geometry : angle 0.57625 (50797) hydrogen bonds : bond 0.04221 ( 2196) hydrogen bonds : angle 4.29361 ( 6429) *********************** 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 728 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 613 time to evaluate : 1.258 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 43 MET cc_start: 0.9356 (tpt) cc_final: 0.9122 (tpt) REVERT: W 135 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8491 (ttpp) REVERT: W 143 ASP cc_start: 0.8673 (t0) cc_final: 0.8295 (t0) REVERT: W 146 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.7036 (p) REVERT: W 160 ASP cc_start: 0.8717 (t0) cc_final: 0.8516 (t0) REVERT: C 236 TYR cc_start: 0.9568 (OUTLIER) cc_final: 0.8734 (t80) REVERT: B 97 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8968 (m) REVERT: B 157 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9254 (mm) REVERT: B 463 LYS cc_start: 0.9011 (mmtp) cc_final: 0.8512 (ttpt) REVERT: A 172 GLN cc_start: 0.9062 (tt0) cc_final: 0.8783 (mt0) REVERT: A 418 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7849 (tpp-160) REVERT: A 463 LYS cc_start: 0.6002 (tttt) cc_final: 0.5660 (tttm) REVERT: X 3 LEU cc_start: 0.7844 (mt) cc_final: 0.7643 (tp) REVERT: X 15 VAL cc_start: 0.8060 (p) cc_final: 0.7797 (m) REVERT: X 78 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7586 (tm-30) REVERT: X 150 ASP cc_start: 0.9074 (m-30) cc_final: 0.8809 (m-30) REVERT: H 22 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8727 (pttt) REVERT: H 26 THR cc_start: 0.9193 (t) cc_final: 0.8858 (p) REVERT: H 51 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8452 (ttm110) REVERT: H 58 HIS cc_start: 0.7367 (m-70) cc_final: 0.6828 (m90) REVERT: H 65 SER cc_start: 0.9087 (m) cc_final: 0.8367 (t) REVERT: F 89 ASN cc_start: 0.8909 (t0) cc_final: 0.8693 (t0) REVERT: E 410 PHE cc_start: 0.8325 (m-80) cc_final: 0.7989 (m-10) REVERT: D 301 ASP cc_start: 0.8561 (t0) cc_final: 0.8221 (t0) REVERT: J 37 GLU cc_start: 0.8541 (pp20) cc_final: 0.8139 (pp20) REVERT: L 34 LYS cc_start: 0.9315 (mmmm) cc_final: 0.8758 (mmmm) REVERT: M 7 ASP cc_start: 0.7421 (m-30) cc_final: 0.6709 (m-30) REVERT: M 10 TYR cc_start: 0.8486 (m-80) cc_final: 0.7967 (m-80) REVERT: M 37 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8478 (tt0) REVERT: N 9 LEU cc_start: 0.8245 (mm) cc_final: 0.7943 (mp) REVERT: N 16 MET cc_start: 0.7865 (tpp) cc_final: 0.7591 (mmm) REVERT: N 42 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7565 (mt0) REVERT: O 7 ASP cc_start: 0.5491 (p0) cc_final: 0.5255 (p0) REVERT: O 8 LEU cc_start: 0.8132 (mt) cc_final: 0.7125 (mp) REVERT: O 41 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8180 (ttm-80) REVERT: O 42 GLN cc_start: 0.7735 (mm-40) cc_final: 0.6728 (mp10) REVERT: O 59 LEU cc_start: 0.8861 (tt) cc_final: 0.8648 (pt) REVERT: O 63 ILE cc_start: 0.8548 (mm) cc_final: 0.8336 (mt) REVERT: P 11 MET cc_start: 0.8592 (tpp) cc_final: 0.7699 (mmm) REVERT: P 42 GLN cc_start: 0.8405 (mm110) cc_final: 0.7995 (mm-40) REVERT: P 52 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8935 (mm110) REVERT: P 61 ASP cc_start: 0.8792 (m-30) cc_final: 0.8303 (m-30) REVERT: Q 35 PHE cc_start: 0.8679 (t80) cc_final: 0.8140 (t80) REVERT: R 11 MET cc_start: 0.8804 (tpp) cc_final: 0.8540 (tpp) REVERT: R 75 MET cc_start: 0.8707 (tpt) cc_final: 0.8115 (tpp) REVERT: Y 2 ASN cc_start: 0.5949 (t0) cc_final: 0.5089 (m-40) REVERT: Y 16 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8085 (mt) REVERT: Y 49 ARG cc_start: 0.7514 (mmp80) cc_final: 0.7266 (mmp80) REVERT: Y 80 ASN cc_start: 0.8338 (m-40) cc_final: 0.7699 (m110) REVERT: Y 150 ASP cc_start: 0.9115 (m-30) cc_final: 0.8774 (m-30) REVERT: a 6 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.4239 (pmm) REVERT: a 11 TYR cc_start: 0.8531 (t80) cc_final: 0.8208 (t80) REVERT: a 41 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (tp) REVERT: a 99 LYS cc_start: 0.7401 (mppt) cc_final: 0.6853 (ttpt) REVERT: a 203 LYS cc_start: 0.8936 (mttp) cc_final: 0.8727 (mttp) REVERT: a 209 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8559 (mt) REVERT: I 16 MET cc_start: 0.8741 (tpp) cc_final: 0.8244 (mmm) REVERT: S 42 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7675 (mt0) outliers start: 115 outliers final: 81 residues processed: 698 average time/residue: 0.2166 time to fit residues: 247.5736 Evaluate side-chains 681 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 591 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS 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 157 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 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 83 THR Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 141 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 435 optimal weight: 7.9990 chunk 376 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 342 optimal weight: 0.7980 chunk 293 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 389 optimal weight: 4.9990 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN W 94 GLN G 274 GLN D 243 ASN L 3 ASN R 52 GLN Y 37 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN a 252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.066747 restraints weight = 78347.270| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.07 r_work: 0.2763 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37528 Z= 0.159 Angle : 0.594 10.843 50797 Z= 0.298 Chirality : 0.043 0.355 5920 Planarity : 0.004 0.054 6550 Dihedral : 6.709 129.622 5371 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.31 % Allowed : 16.06 % Favored : 80.63 % 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: 0.80 (0.12), residues: 4807 helix: 1.35 (0.10), residues: 2642 sheet: -0.05 (0.22), residues: 523 loop : -0.53 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 83 TYR 0.018 0.001 TYR B 236 PHE 0.014 0.001 PHE Y 14 TRP 0.010 0.001 TRP B 513 HIS 0.003 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00374 (37528) covalent geometry : angle 0.59409 (50797) hydrogen bonds : bond 0.04268 ( 2196) hydrogen bonds : angle 4.32946 ( 6429) *********************** 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 727 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 600 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9335 (tpt) cc_final: 0.9101 (tpt) REVERT: W 135 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8525 (ttpp) REVERT: W 143 ASP cc_start: 0.8657 (t0) cc_final: 0.8270 (t0) REVERT: W 146 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7135 (p) REVERT: C 236 TYR cc_start: 0.9573 (OUTLIER) cc_final: 0.8728 (t80) REVERT: C 386 MET cc_start: 0.9148 (mmt) cc_final: 0.8868 (mmt) REVERT: B 97 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8989 (m) REVERT: B 157 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B 403 LEU cc_start: 0.6317 (tt) cc_final: 0.5082 (mt) REVERT: B 463 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8525 (ttpt) REVERT: A 172 GLN cc_start: 0.9066 (tt0) cc_final: 0.8796 (mt0) REVERT: A 418 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7898 (tpp-160) REVERT: A 463 LYS cc_start: 0.6129 (tttt) cc_final: 0.5910 (tttp) REVERT: X 15 VAL cc_start: 0.8102 (p) cc_final: 0.7844 (m) REVERT: X 78 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7521 (tm-30) REVERT: X 150 ASP cc_start: 0.9090 (m-30) cc_final: 0.8828 (m-30) REVERT: H 22 LYS cc_start: 0.9006 (ptpt) cc_final: 0.8754 (pttt) REVERT: H 26 THR cc_start: 0.9221 (t) cc_final: 0.8940 (p) REVERT: H 51 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8449 (ttm110) REVERT: H 58 HIS cc_start: 0.7371 (m-70) cc_final: 0.6878 (m90) REVERT: H 65 SER cc_start: 0.9103 (m) cc_final: 0.8551 (t) REVERT: F 89 ASN cc_start: 0.8916 (t0) cc_final: 0.8692 (t0) REVERT: E 410 PHE cc_start: 0.8276 (m-80) cc_final: 0.8002 (m-80) REVERT: D 301 ASP cc_start: 0.8611 (t0) cc_final: 0.8293 (t0) REVERT: J 37 GLU cc_start: 0.8548 (pp20) cc_final: 0.8221 (pp20) REVERT: L 73 TYR cc_start: 0.9005 (t80) cc_final: 0.8585 (t80) REVERT: M 10 TYR cc_start: 0.8490 (m-80) cc_final: 0.7901 (m-80) REVERT: M 37 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8476 (tt0) REVERT: N 9 LEU cc_start: 0.8220 (mm) cc_final: 0.7914 (mp) REVERT: N 16 MET cc_start: 0.7923 (tpp) cc_final: 0.7661 (mmm) REVERT: N 42 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7688 (mt0) REVERT: N 65 MET cc_start: 0.8879 (mmp) cc_final: 0.8558 (mmp) REVERT: O 7 ASP cc_start: 0.5460 (p0) cc_final: 0.5191 (p0) REVERT: O 8 LEU cc_start: 0.8209 (mt) cc_final: 0.7176 (mp) REVERT: O 41 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8197 (ttm-80) REVERT: O 42 GLN cc_start: 0.7858 (mm-40) cc_final: 0.6807 (mp10) REVERT: O 63 ILE cc_start: 0.8651 (mm) cc_final: 0.8424 (mm) REVERT: P 11 MET cc_start: 0.8581 (tpp) cc_final: 0.7808 (mmm) REVERT: P 42 GLN cc_start: 0.8424 (mm110) cc_final: 0.8009 (mm-40) REVERT: P 46 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8744 (mm) REVERT: P 54 PHE cc_start: 0.8540 (m-80) cc_final: 0.8337 (m-80) REVERT: P 57 MET cc_start: 0.8313 (tmm) cc_final: 0.7931 (ppp) REVERT: P 61 ASP cc_start: 0.8923 (m-30) cc_final: 0.8498 (p0) REVERT: Q 35 PHE cc_start: 0.8681 (t80) cc_final: 0.8169 (t80) REVERT: R 61 ASP cc_start: 0.7512 (t0) cc_final: 0.7200 (t70) REVERT: R 75 MET cc_start: 0.8677 (tpt) cc_final: 0.7885 (tpp) REVERT: Y 2 ASN cc_start: 0.5935 (t0) cc_final: 0.5186 (m-40) REVERT: Y 16 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8165 (mt) REVERT: Y 30 MET cc_start: 0.7801 (mmm) cc_final: 0.7490 (mmt) REVERT: Y 80 ASN cc_start: 0.8371 (m-40) cc_final: 0.7746 (m110) REVERT: Y 150 ASP cc_start: 0.9083 (m-30) cc_final: 0.8744 (m-30) REVERT: a 6 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4320 (pmm) REVERT: a 11 TYR cc_start: 0.8423 (t80) cc_final: 0.8085 (t80) REVERT: a 20 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6484 (mm-40) REVERT: a 99 LYS cc_start: 0.7404 (mppt) cc_final: 0.6783 (ttpt) REVERT: a 193 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (pp) REVERT: a 209 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (mt) REVERT: I 16 MET cc_start: 0.8645 (tpp) cc_final: 0.8265 (mmm) REVERT: I 41 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7341 (tpp80) outliers start: 127 outliers final: 88 residues processed: 693 average time/residue: 0.2207 time to fit residues: 249.5055 Evaluate side-chains 688 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 591 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 120 GLN Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS 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 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 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 83 THR Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 317 optimal weight: 0.4980 chunk 434 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 351 optimal weight: 0.7980 chunk 330 optimal weight: 7.9990 chunk 249 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN D 243 ASN L 3 ASN O 52 GLN R 52 GLN Y 37 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.068428 restraints weight = 77813.972| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.07 r_work: 0.2793 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37528 Z= 0.118 Angle : 0.596 19.484 50797 Z= 0.296 Chirality : 0.043 0.300 5920 Planarity : 0.004 0.057 6550 Dihedral : 6.473 126.787 5371 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.40 % Allowed : 16.97 % Favored : 80.63 % 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: 0.95 (0.12), residues: 4807 helix: 1.47 (0.10), residues: 2641 sheet: 0.00 (0.22), residues: 526 loop : -0.44 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 36 TYR 0.024 0.001 TYR a 94 PHE 0.023 0.001 PHE B 467 TRP 0.008 0.001 TRP a 111 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00256 (37528) covalent geometry : angle 0.59558 (50797) hydrogen bonds : bond 0.03992 ( 2196) hydrogen bonds : angle 4.26152 ( 6429) *********************** 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 703 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 611 time to evaluate : 1.464 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: W 43 MET cc_start: 0.9330 (tpt) cc_final: 0.9091 (tpt) REVERT: W 135 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8442 (ttpp) REVERT: W 143 ASP cc_start: 0.8678 (t0) cc_final: 0.8299 (t0) REVERT: W 146 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6954 (p) REVERT: C 236 TYR cc_start: 0.9569 (OUTLIER) cc_final: 0.8638 (t80) REVERT: C 386 MET cc_start: 0.9107 (mmt) cc_final: 0.8902 (mmt) REVERT: B 97 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8980 (m) REVERT: B 157 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9230 (mm) REVERT: B 403 LEU cc_start: 0.6321 (tt) cc_final: 0.5086 (mt) REVERT: A 52 MET cc_start: 0.8568 (mtt) cc_final: 0.8290 (mtt) REVERT: A 172 GLN cc_start: 0.9078 (tt0) cc_final: 0.8855 (mt0) REVERT: A 418 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7882 (tpp-160) REVERT: X 15 VAL cc_start: 0.8091 (p) cc_final: 0.7845 (m) REVERT: X 78 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7600 (tm-30) REVERT: X 83 ARG cc_start: 0.7573 (ttt90) cc_final: 0.6976 (ttt90) REVERT: X 150 ASP cc_start: 0.9111 (m-30) cc_final: 0.8828 (m-30) REVERT: H 22 LYS cc_start: 0.8984 (ptpt) cc_final: 0.8735 (pttt) REVERT: H 26 THR cc_start: 0.9209 (t) cc_final: 0.8883 (p) REVERT: H 51 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8452 (ttm110) REVERT: H 58 HIS cc_start: 0.7328 (m-70) cc_final: 0.6828 (m90) REVERT: H 65 SER cc_start: 0.9052 (m) cc_final: 0.8354 (t) REVERT: F 35 ASN cc_start: 0.8805 (p0) cc_final: 0.8554 (p0) REVERT: E 410 PHE cc_start: 0.8212 (m-80) cc_final: 0.7882 (m-80) REVERT: D 301 ASP cc_start: 0.8488 (t0) cc_final: 0.8173 (t0) REVERT: J 37 GLU cc_start: 0.8490 (pp20) cc_final: 0.8173 (pp20) REVERT: L 73 TYR cc_start: 0.8948 (t80) cc_final: 0.8612 (t80) REVERT: M 7 ASP cc_start: 0.7017 (m-30) cc_final: 0.6626 (m-30) REVERT: M 10 TYR cc_start: 0.8443 (m-80) cc_final: 0.7901 (m-80) REVERT: M 37 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8529 (tt0) REVERT: M 41 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7967 (mtt90) REVERT: N 9 LEU cc_start: 0.8136 (mm) cc_final: 0.7848 (mp) REVERT: N 11 MET cc_start: 0.7053 (tpt) cc_final: 0.6670 (tpt) REVERT: N 42 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7640 (mt0) REVERT: N 65 MET cc_start: 0.8877 (mmp) cc_final: 0.8577 (mmp) REVERT: N 73 TYR cc_start: 0.8179 (t80) cc_final: 0.7978 (t80) REVERT: O 6 MET cc_start: 0.6172 (mmt) cc_final: 0.5959 (mmt) REVERT: O 8 LEU cc_start: 0.8187 (mt) cc_final: 0.7188 (mp) REVERT: O 9 LEU cc_start: 0.7860 (mp) cc_final: 0.7309 (mt) REVERT: O 41 ARG cc_start: 0.8540 (ttm170) cc_final: 0.8161 (ttm-80) REVERT: O 42 GLN cc_start: 0.7761 (mm-40) cc_final: 0.6757 (mp10) REVERT: O 63 ILE cc_start: 0.8618 (mm) cc_final: 0.8405 (mm) REVERT: P 11 MET cc_start: 0.8563 (tpp) cc_final: 0.7721 (mmm) REVERT: P 42 GLN cc_start: 0.8525 (mm110) cc_final: 0.8107 (mm-40) REVERT: P 52 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8747 (mp10) REVERT: P 54 PHE cc_start: 0.8518 (m-80) cc_final: 0.8302 (m-80) REVERT: P 61 ASP cc_start: 0.8921 (m-30) cc_final: 0.8439 (p0) REVERT: Q 35 PHE cc_start: 0.8654 (t80) cc_final: 0.8160 (t80) REVERT: R 75 MET cc_start: 0.8666 (tpt) cc_final: 0.7815 (tpp) REVERT: Y 2 ASN cc_start: 0.5790 (t0) cc_final: 0.5031 (m-40) REVERT: Y 16 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8181 (mt) REVERT: Y 19 LEU cc_start: 0.8493 (mt) cc_final: 0.8248 (tp) REVERT: Y 30 MET cc_start: 0.7761 (mmm) cc_final: 0.7476 (mmp) REVERT: Y 80 ASN cc_start: 0.8364 (m-40) cc_final: 0.7794 (m110) REVERT: Y 150 ASP cc_start: 0.9065 (m-30) cc_final: 0.8720 (m-30) REVERT: a 6 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.4350 (pmm) REVERT: a 11 TYR cc_start: 0.8446 (t80) cc_final: 0.8096 (t80) REVERT: a 20 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6484 (mm-40) REVERT: a 76 GLN cc_start: 0.7418 (tm-30) cc_final: 0.6732 (pp30) REVERT: a 99 LYS cc_start: 0.7391 (mppt) cc_final: 0.6783 (ttpt) REVERT: a 193 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8076 (pp) REVERT: a 203 LYS cc_start: 0.8885 (mttp) cc_final: 0.8682 (mttp) REVERT: a 209 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8574 (mt) REVERT: I 16 MET cc_start: 0.8668 (tpp) cc_final: 0.8320 (mmm) REVERT: I 52 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8915 (mm-40) REVERT: S 6 MET cc_start: 0.8469 (ppp) cc_final: 0.7770 (pmm) REVERT: S 42 GLN cc_start: 0.8234 (mt0) cc_final: 0.7726 (mt0) outliers start: 92 outliers final: 65 residues processed: 679 average time/residue: 0.2203 time to fit residues: 243.2790 Evaluate side-chains 665 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 592 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 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 C residue 323 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain G residue 110 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 83 THR Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 179 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 352 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 317 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN A 358 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN D 243 ASN O 52 GLN R 52 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.068298 restraints weight = 78242.895| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.04 r_work: 0.2796 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 37528 Z= 0.130 Angle : 0.613 16.772 50797 Z= 0.304 Chirality : 0.043 0.265 5920 Planarity : 0.004 0.055 6550 Dihedral : 6.333 126.442 5368 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.48 % Allowed : 16.92 % Favored : 80.60 % 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: 1.02 (0.12), residues: 4807 helix: 1.53 (0.10), residues: 2638 sheet: 0.03 (0.22), residues: 526 loop : -0.42 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 50 TYR 0.028 0.001 TYR a 94 PHE 0.024 0.001 PHE L 53 TRP 0.007 0.001 TRP a 111 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00300 (37528) covalent geometry : angle 0.61254 (50797) hydrogen bonds : bond 0.04079 ( 2196) hydrogen bonds : angle 4.27256 ( 6429) *********************** 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 705 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 610 time to evaluate : 1.188 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 43 MET cc_start: 0.9296 (tpt) cc_final: 0.8964 (tpp) REVERT: W 135 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8483 (ttpp) REVERT: W 143 ASP cc_start: 0.8674 (t0) cc_final: 0.8317 (t0) REVERT: W 146 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7043 (p) REVERT: C 48 MET cc_start: 0.9097 (mtm) cc_final: 0.8794 (mtt) REVERT: C 236 TYR cc_start: 0.9551 (OUTLIER) cc_final: 0.8587 (t80) REVERT: B 67 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8798 (mt-10) REVERT: B 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8987 (m) REVERT: B 157 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9205 (mm) REVERT: B 403 LEU cc_start: 0.6223 (tt) cc_final: 0.4977 (mt) REVERT: A 52 MET cc_start: 0.8572 (mtt) cc_final: 0.8323 (mtt) REVERT: A 418 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7907 (tpp-160) REVERT: A 463 LYS cc_start: 0.5808 (tmtt) cc_final: 0.5023 (tmtt) REVERT: X 15 VAL cc_start: 0.8114 (p) cc_final: 0.7909 (m) REVERT: X 78 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7537 (tm-30) REVERT: X 82 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7329 (mmm160) REVERT: X 83 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7035 (ttt90) REVERT: X 150 ASP cc_start: 0.9076 (m-30) cc_final: 0.8804 (m-30) REVERT: H 22 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8762 (pttt) REVERT: H 26 THR cc_start: 0.9239 (t) cc_final: 0.8936 (p) REVERT: H 51 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8475 (ttm110) REVERT: H 58 HIS cc_start: 0.7335 (m-70) cc_final: 0.6828 (m90) REVERT: H 65 SER cc_start: 0.9040 (m) cc_final: 0.8415 (t) REVERT: F 35 ASN cc_start: 0.8774 (p0) cc_final: 0.8523 (p0) REVERT: E 410 PHE cc_start: 0.8177 (m-80) cc_final: 0.7858 (m-80) REVERT: D 301 ASP cc_start: 0.8497 (t0) cc_final: 0.8209 (t0) REVERT: D 322 SER cc_start: 0.8798 (t) cc_final: 0.8560 (m) REVERT: J 37 GLU cc_start: 0.8508 (pp20) cc_final: 0.8183 (pp20) REVERT: M 7 ASP cc_start: 0.7176 (m-30) cc_final: 0.6523 (m-30) REVERT: M 10 TYR cc_start: 0.8469 (m-80) cc_final: 0.7869 (m-80) REVERT: M 17 MET cc_start: 0.7885 (ptm) cc_final: 0.7656 (ptt) REVERT: M 37 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8569 (tt0) REVERT: M 41 ARG cc_start: 0.8313 (mtm110) cc_final: 0.8036 (mtt90) REVERT: M 75 MET cc_start: 0.8015 (mmm) cc_final: 0.7771 (mmp) REVERT: N 9 LEU cc_start: 0.8164 (mm) cc_final: 0.7883 (mp) REVERT: N 11 MET cc_start: 0.7249 (tpt) cc_final: 0.6907 (tpt) REVERT: N 16 MET cc_start: 0.7918 (mmm) cc_final: 0.7704 (mmm) REVERT: N 42 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7742 (mt0) REVERT: N 65 MET cc_start: 0.8833 (mmp) cc_final: 0.8538 (mmp) REVERT: N 75 MET cc_start: 0.7735 (tmm) cc_final: 0.7472 (tmm) REVERT: O 6 MET cc_start: 0.6567 (mmt) cc_final: 0.6332 (mmp) REVERT: O 8 LEU cc_start: 0.8002 (mt) cc_final: 0.7111 (mp) REVERT: O 9 LEU cc_start: 0.7918 (mp) cc_final: 0.7254 (mt) REVERT: O 41 ARG cc_start: 0.8557 (ttm170) cc_final: 0.8183 (ttm-80) REVERT: O 42 GLN cc_start: 0.7852 (mm-40) cc_final: 0.6846 (mp10) REVERT: P 11 MET cc_start: 0.8603 (tpp) cc_final: 0.7777 (mmm) REVERT: P 42 GLN cc_start: 0.8533 (mm110) cc_final: 0.8072 (mm110) REVERT: Q 35 PHE cc_start: 0.8654 (t80) cc_final: 0.8232 (t80) REVERT: Q 57 MET cc_start: 0.8962 (tpp) cc_final: 0.8544 (tpt) REVERT: Y 2 ASN cc_start: 0.5820 (t0) cc_final: 0.5094 (m-40) REVERT: Y 19 LEU cc_start: 0.8479 (mt) cc_final: 0.8239 (tp) REVERT: Y 30 MET cc_start: 0.7756 (mmm) cc_final: 0.7528 (mmp) REVERT: Y 80 ASN cc_start: 0.8438 (m-40) cc_final: 0.7841 (m110) REVERT: Y 150 ASP cc_start: 0.9022 (m-30) cc_final: 0.8698 (m-30) REVERT: a 6 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4317 (pmm) REVERT: a 11 TYR cc_start: 0.8423 (t80) cc_final: 0.8073 (t80) REVERT: a 20 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6525 (mm-40) REVERT: a 99 LYS cc_start: 0.7319 (mppt) cc_final: 0.6760 (ttpt) REVERT: a 193 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8041 (pp) REVERT: a 209 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8570 (mt) REVERT: I 16 MET cc_start: 0.8708 (tpp) cc_final: 0.8335 (mmm) REVERT: I 52 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8837 (mm-40) REVERT: I 54 PHE cc_start: 0.9044 (m-80) cc_final: 0.8783 (m-80) REVERT: I 70 LEU cc_start: 0.8627 (mt) cc_final: 0.8226 (tp) REVERT: S 6 MET cc_start: 0.8459 (ppp) cc_final: 0.7808 (pmm) outliers start: 95 outliers final: 72 residues processed: 679 average time/residue: 0.2237 time to fit residues: 246.6029 Evaluate side-chains 673 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 594 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 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 C residue 323 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 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 83 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 317 optimal weight: 0.9980 chunk 283 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 258 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 253 optimal weight: 0.3980 chunk 432 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN F 89 ASN D 243 ASN Y 64 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068000 restraints weight = 77884.908| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.03 r_work: 0.2783 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 37528 Z= 0.140 Angle : 0.623 17.223 50797 Z= 0.308 Chirality : 0.043 0.261 5920 Planarity : 0.004 0.065 6550 Dihedral : 6.291 126.310 5366 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.32 % Allowed : 17.26 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 4807 helix: 1.53 (0.10), residues: 2640 sheet: 0.08 (0.22), residues: 519 loop : -0.41 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG I 50 TYR 0.031 0.001 TYR a 94 PHE 0.032 0.001 PHE a 109 TRP 0.008 0.001 TRP G 203 HIS 0.003 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00327 (37528) covalent geometry : angle 0.62286 (50797) hydrogen bonds : bond 0.04046 ( 2196) hydrogen bonds : angle 4.30109 ( 6429) ********************** 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 691 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 602 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9317 (tpt) cc_final: 0.9051 (tpt) REVERT: W 135 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8469 (ttpp) REVERT: W 143 ASP cc_start: 0.8697 (t0) cc_final: 0.8304 (t0) REVERT: W 146 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 48 MET cc_start: 0.9110 (mtm) cc_final: 0.8788 (mtt) REVERT: C 236 TYR cc_start: 0.9571 (OUTLIER) cc_final: 0.8594 (t80) REVERT: B 67 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8797 (mt-10) REVERT: B 97 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8990 (m) REVERT: B 157 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9198 (mm) REVERT: B 403 LEU cc_start: 0.6222 (tt) cc_final: 0.4989 (mt) REVERT: A 52 MET cc_start: 0.8604 (mtt) cc_final: 0.8344 (mtt) REVERT: A 418 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7873 (tpp-160) REVERT: A 463 LYS cc_start: 0.5935 (tmtt) cc_final: 0.5089 (tmtt) REVERT: X 15 VAL cc_start: 0.8167 (p) cc_final: 0.7942 (m) REVERT: X 78 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7525 (tm-30) REVERT: X 82 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7310 (mmm160) REVERT: X 83 ARG cc_start: 0.7593 (ttt90) cc_final: 0.7000 (ttt90) REVERT: X 150 ASP cc_start: 0.9067 (m-30) cc_final: 0.8792 (m-30) REVERT: H 22 LYS cc_start: 0.8985 (ptpt) cc_final: 0.8725 (pttt) REVERT: H 26 THR cc_start: 0.9251 (t) cc_final: 0.8956 (p) REVERT: H 51 ARG cc_start: 0.8772 (mtp180) cc_final: 0.8458 (ttm110) REVERT: H 58 HIS cc_start: 0.7296 (m-70) cc_final: 0.6848 (m90) REVERT: H 65 SER cc_start: 0.9050 (m) cc_final: 0.8399 (t) REVERT: F 35 ASN cc_start: 0.8799 (p0) cc_final: 0.8548 (p0) REVERT: E 410 PHE cc_start: 0.8251 (m-80) cc_final: 0.7885 (m-80) REVERT: D 301 ASP cc_start: 0.8595 (t0) cc_final: 0.8292 (t0) REVERT: D 322 SER cc_start: 0.8771 (t) cc_final: 0.8520 (m) REVERT: J 37 GLU cc_start: 0.8518 (pp20) cc_final: 0.8163 (pp20) REVERT: J 75 MET cc_start: 0.8885 (ttt) cc_final: 0.8668 (tmm) REVERT: M 7 ASP cc_start: 0.7190 (m-30) cc_final: 0.6582 (m-30) REVERT: M 10 TYR cc_start: 0.8478 (m-80) cc_final: 0.7851 (m-80) REVERT: M 37 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8527 (tt0) REVERT: M 75 MET cc_start: 0.8044 (mmm) cc_final: 0.7803 (mmp) REVERT: N 11 MET cc_start: 0.7015 (tpt) cc_final: 0.6700 (tpt) REVERT: N 42 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7705 (mt0) REVERT: N 75 MET cc_start: 0.7853 (tmm) cc_final: 0.7538 (tmm) REVERT: O 6 MET cc_start: 0.6707 (mmt) cc_final: 0.6331 (mmt) REVERT: O 8 LEU cc_start: 0.8035 (mt) cc_final: 0.7047 (mp) REVERT: O 9 LEU cc_start: 0.7814 (mp) cc_final: 0.7323 (mt) REVERT: O 41 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8224 (ttm-80) REVERT: O 42 GLN cc_start: 0.7835 (mm-40) cc_final: 0.6798 (mp10) REVERT: P 11 MET cc_start: 0.8533 (tpp) cc_final: 0.7757 (mmm) REVERT: P 42 GLN cc_start: 0.8605 (mm110) cc_final: 0.8141 (mm110) REVERT: P 52 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8738 (mp10) REVERT: P 61 ASP cc_start: 0.8838 (m-30) cc_final: 0.8459 (p0) REVERT: Q 35 PHE cc_start: 0.8683 (t80) cc_final: 0.8251 (t80) REVERT: R 50 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8245 (ptp-110) REVERT: R 75 MET cc_start: 0.8596 (tpt) cc_final: 0.7668 (tpp) REVERT: Y 2 ASN cc_start: 0.5922 (t0) cc_final: 0.5221 (m-40) REVERT: Y 19 LEU cc_start: 0.8481 (mt) cc_final: 0.8253 (tp) REVERT: Y 30 MET cc_start: 0.7726 (mmm) cc_final: 0.7517 (mmt) REVERT: Y 80 ASN cc_start: 0.8351 (m-40) cc_final: 0.7703 (m110) REVERT: Y 150 ASP cc_start: 0.9083 (m-30) cc_final: 0.8749 (m-30) REVERT: a 6 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.4340 (pmm) REVERT: a 11 TYR cc_start: 0.8460 (t80) cc_final: 0.8130 (t80) REVERT: a 20 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6435 (mm-40) REVERT: a 76 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5470 (tm-30) REVERT: a 99 LYS cc_start: 0.7263 (mppt) cc_final: 0.6687 (ttpt) REVERT: a 193 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8012 (pp) REVERT: a 209 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8568 (mt) REVERT: I 16 MET cc_start: 0.8678 (tpp) cc_final: 0.8338 (mmm) REVERT: I 17 MET cc_start: 0.8192 (mtm) cc_final: 0.7980 (mtm) REVERT: I 37 GLU cc_start: 0.8222 (tp30) cc_final: 0.7913 (tp30) REVERT: I 41 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7222 (tpp80) REVERT: I 52 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8832 (mm-40) REVERT: I 54 PHE cc_start: 0.9068 (m-80) cc_final: 0.8858 (m-80) REVERT: I 70 LEU cc_start: 0.8656 (mt) cc_final: 0.8179 (tp) REVERT: S 6 MET cc_start: 0.8487 (ppp) cc_final: 0.7875 (pmm) outliers start: 89 outliers final: 73 residues processed: 669 average time/residue: 0.2226 time to fit residues: 243.1941 Evaluate side-chains 672 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 592 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 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 83 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 402 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 422 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN D 243 ASN R 52 GLN ** Y 64 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 = 0.3441 r_free = 0.3441 target = 0.097144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068481 restraints weight = 78049.118| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.11 r_work: 0.2782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 37528 Z= 0.174 Angle : 0.708 59.193 50797 Z= 0.377 Chirality : 0.044 0.798 5920 Planarity : 0.004 0.065 6550 Dihedral : 6.300 126.288 5366 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.02 % Rotamer: Outliers : 2.24 % Allowed : 17.44 % Favored : 80.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.04 (0.12), residues: 4807 helix: 1.54 (0.10), residues: 2640 sheet: 0.08 (0.22), residues: 519 loop : -0.41 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 50 TYR 0.028 0.001 TYR a 94 PHE 0.030 0.001 PHE E 189 TRP 0.008 0.001 TRP B 513 HIS 0.003 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00398 (37528) covalent geometry : angle 0.70777 (50797) hydrogen bonds : bond 0.04054 ( 2196) hydrogen bonds : angle 4.31020 ( 6429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11507.50 seconds wall clock time: 196 minutes 12.12 seconds (11772.12 seconds total)