Starting phenix.real_space_refine on Sat Mar 7 02:27:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqr_20167/03_2026/6oqr_20167.map" } resolution = 3.1 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 23471 2.51 5 N 6314 2.21 5 O 6965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 296 residue(s): 0.03s 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: 36951 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: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3851 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 492} 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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "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: 7.69, per 1000 atoms: 0.21 Number of scatterers: 36951 At special positions: 0 Unit cell: (178.035, 214.721, 135.954, 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 6965 8.00 N 6314 7.00 C 23471 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: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 29 sheets defined 62.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'W' and resid 3 through 21 removed outlier: 3.888A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.677A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 removed outlier: 3.647A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 70 through 83 removed outlier: 3.580A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.565A 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: 4.018A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'W' and resid 162 through 174 removed outlier: 4.103A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.872A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.589A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.782A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.563A pdb=" N ILE C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.902A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.646A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.656A pdb=" N ALA C 285 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.551A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.954A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.777A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 4.377A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.509A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.091A pdb=" N ASP C 458 " --> pdb=" O TYR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.556A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.548A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.562A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.571A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (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 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.504A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.568A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (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: 3.853A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.582A 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 340 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.641A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.956A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.960A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.691A pdb=" N HIS B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.643A pdb=" N VAL B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.801A pdb=" N ASP B 458 " --> pdb=" O TYR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 removed outlier: 3.841A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.893A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 509 removed outlier: 3.507A pdb=" N LEU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.795A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.839A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.667A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.566A pdb=" N SER A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.526A pdb=" N ILE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.774A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.517A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.569A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.677A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.658A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.873A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.880A 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 509 removed outlier: 3.692A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 25 removed outlier: 4.018A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 4.046A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU X 97 " --> pdb=" O GLU X 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (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 Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.732A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.522A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.659A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.862A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 3.964A 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 108 removed outlier: 3.553A pdb=" N LEU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.643A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.714A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 196 through 203 removed outlier: 3.730A pdb=" N LYS G 199 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 281 removed outlier: 3.909A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (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 168 removed outlier: 3.874A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 195 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: 3.652A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.032A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.294A 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: 3.711A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.607A pdb=" N LEU F 315 " --> pdb=" O PHE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 370 Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 379 through 382 removed outlier: 3.561A pdb=" N LEU F 382 " --> pdb=" O MET F 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 379 through 382' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 433 removed outlier: 3.725A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.683A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.625A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.625A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 197 through 202 removed outlier: 3.759A pdb=" N ASP E 200 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 202 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.501A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.565A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.808A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 305 through 313 removed outlier: 3.772A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.506A pdb=" N ALA E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 3.756A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.567A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 451 through 458 removed outlier: 3.848A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 170 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 5.054A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.583A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.854A 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: 3.792A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 378 removed outlier: 7.670A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.607A 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 431 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.653A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.675A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR J 10 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA J 14 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA J 20 " --> pdb=" O MET J 16 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.112A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 Processing helix chain 'L' and resid 4 through 42 removed outlier: 3.501A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.690A pdb=" N GLY L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP L 61 " --> pdb=" O MET L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.908A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR L 73 " --> pdb=" O GLY L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 5.021A pdb=" N LEU M 9 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR M 10 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 3.788A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.464A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU N 19 " --> pdb=" O VAL N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.636A pdb=" N GLN N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.864A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 63 removed outlier: 3.645A pdb=" N GLN O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY O 58 " --> pdb=" O PHE O 54 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.618A pdb=" N ALA O 67 " --> pdb=" O ILE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 42 removed outlier: 3.779A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 78 removed outlier: 4.925A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 4.053A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU P 72 " --> pdb=" O VAL P 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.208A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.948A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.692A pdb=" N VAL Q 74 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET Q 75 " --> pdb=" O GLY Q 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.526A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 4.031A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL R 60 " --> pdb=" O VAL R 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP R 61 " --> pdb=" O MET R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 77 Processing helix chain 'Y' and resid 3 through 25 removed outlier: 3.833A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 3 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Y 16 " --> pdb=" O ILE Y 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS Y 21 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 140 removed outlier: 3.862A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Y 124 " --> pdb=" O LEU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 removed outlier: 3.926A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 15 removed outlier: 3.693A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 65 removed outlier: 3.718A pdb=" N LEU a 52 " --> pdb=" O PHE a 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU a 57 " --> pdb=" O GLY a 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER a 62 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS a 65 " --> pdb=" O ARG a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.951A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.748A pdb=" N LEU a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.829A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (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: 4.554A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.968A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY a 227 " --> pdb=" O ILE a 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU a 228 " --> pdb=" O LEU a 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 233 Processing helix chain 'a' and resid 234 through 269 Proline residue: a 240 - end of helix removed outlier: 4.451A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.855A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 4.021A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'S' and resid 6 through 42 removed outlier: 3.918A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 4.889A pdb=" N ILE S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL S 56 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP S 61 " --> pdb=" O MET S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing sheet with id=AA1, first strand: chain 'W' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'W' and resid 139 through 142 removed outlier: 6.484A pdb=" N VAL W 110 " --> pdb=" O LYS W 141 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU B 66 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 35 removed outlier: 13.387A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 67 removed outlier: 4.139A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 67 removed outlier: 6.570A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 45 removed outlier: 4.813A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS A 42 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 66 removed outlier: 7.105A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.580A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 331 removed outlier: 8.059A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.446A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'A' and resid 107 through 109 Processing sheet with id=AB7, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.563A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 31 through 34 removed outlier: 6.212A pdb=" N VAL H 8 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER H 17 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU H 6 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU H 19 " --> pdb=" O TYR H 4 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR H 4 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 14 through 27 removed outlier: 7.258A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY H 27 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.653A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR G 168 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU G 187 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL G 170 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER G 185 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN G 172 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR G 183 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 174 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL G 181 " --> pdb=" O PHE G 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.729A 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: 6.459A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.722A 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 78 Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.409A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.409A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.197A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.589A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.235A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.550A pdb=" N ILE a 41 " --> pdb=" O LEU a 21 " (cutoff:3.500A) 2231 hydrogen bonds defined for protein. 6444 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: 8.53 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6329 1.28 - 1.42: 8549 1.42 - 1.55: 22243 1.55 - 1.68: 25 1.68 - 1.81: 360 Bond restraints: 37506 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C PRO C 342 " pdb=" O PRO C 342 " ideal model delta sigma weight residual 1.238 1.153 0.085 1.24e-02 6.50e+03 4.68e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.36e+01 ... (remaining 37501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 50598 4.76 - 9.51: 158 9.51 - 14.27: 4 14.27 - 19.03: 2 19.03 - 23.79: 4 Bond angle restraints: 50766 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+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 5.30e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.61 22.26 1.00e+00 1.00e+00 4.95e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.86 19.97 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 136.83 118.52 18.31 1.00e+00 1.00e+00 3.35e+02 ... (remaining 50761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 21932 28.35 - 56.71: 732 56.71 - 85.06: 103 85.06 - 113.42: 13 113.42 - 141.77: 5 Dihedral angle restraints: 22785 sinusoidal: 9007 harmonic: 13778 Sorted by residual: 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 300.00 158.22 141.77 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 80.10 -140.09 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 170.76 129.24 1 2.00e+01 2.50e-03 3.92e+01 ... (remaining 22782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5338 0.083 - 0.166: 548 0.166 - 0.249: 24 0.249 - 0.332: 5 0.332 - 0.415: 3 Chirality restraints: 5918 Sorted by residual: 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 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA SER a 202 " pdb=" N SER a 202 " pdb=" C SER a 202 " pdb=" CB SER a 202 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASP L 7 " pdb=" N ASP L 7 " pdb=" C ASP L 7 " pdb=" CB ASP L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 5915 not shown) Planarity restraints: 6547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ALA D 264 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 414 " -0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASP B 414 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP B 414 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B 415 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 338 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER C 338 " -0.062 2.00e-02 2.50e+03 pdb=" O SER C 338 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA C 339 " 0.022 2.00e-02 2.50e+03 ... (remaining 6544 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 51 2.38 - 3.01: 23278 3.01 - 3.64: 53198 3.64 - 4.27: 84005 4.27 - 4.90: 143173 Nonbonded interactions: 303705 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.753 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.851 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.851 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.892 2.170 ... (remaining 303700 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 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 33.040 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 37506 Z= 0.469 Angle : 0.900 23.786 50766 Z= 0.586 Chirality : 0.051 0.415 5918 Planarity : 0.005 0.055 6547 Dihedral : 14.878 141.774 13971 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.50 % Allowed : 8.09 % Favored : 89.41 % Cbeta Deviations : 0.07 % 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: -2.47 (0.10), residues: 4805 helix: -1.67 (0.09), residues: 2555 sheet: -1.11 (0.19), residues: 545 loop : -1.43 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 164 TYR 0.022 0.002 TYR F 297 PHE 0.020 0.002 PHE a 158 TRP 0.017 0.002 TRP a 39 HIS 0.013 0.002 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00954 (37506) covalent geometry : angle 0.90004 (50766) hydrogen bonds : bond 0.17195 ( 2198) hydrogen bonds : angle 7.21864 ( 6444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 773 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 119 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8094 (tm-30) REVERT: W 156 ASP cc_start: 0.7916 (p0) cc_final: 0.7196 (p0) REVERT: C 161 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8592 (mtt180) REVERT: C 236 TYR cc_start: 0.9424 (OUTLIER) cc_final: 0.8756 (t80) REVERT: C 386 MET cc_start: 0.9000 (mmm) cc_final: 0.8550 (mmt) REVERT: C 412 ASP cc_start: 0.8058 (t0) cc_final: 0.7838 (t0) REVERT: B 2 GLN cc_start: 0.8004 (pm20) cc_final: 0.7516 (pm20) REVERT: B 422 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: A 86 MET cc_start: 0.8609 (mtt) cc_final: 0.8385 (mtt) REVERT: A 376 ARG cc_start: 0.8379 (mmt90) cc_final: 0.8159 (mmp80) REVERT: A 401 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8347 (ttm-80) REVERT: X 17 PHE cc_start: 0.7855 (m-10) cc_final: 0.7466 (m-10) REVERT: X 42 ASP cc_start: 0.8426 (m-30) cc_final: 0.8223 (m-30) REVERT: X 64 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8308 (mm-40) REVERT: H 49 MET cc_start: 0.8858 (mmt) cc_final: 0.8440 (mmm) REVERT: H 72 GLN cc_start: 0.8081 (mt0) cc_final: 0.7689 (mt0) REVERT: H 111 ASP cc_start: 0.8761 (t0) cc_final: 0.8403 (t0) REVERT: G 102 MET cc_start: 0.8953 (ttp) cc_final: 0.8729 (mtp) REVERT: G 201 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (mttm) REVERT: F 281 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9251 (ptm160) REVERT: E 88 MET cc_start: 0.9099 (mtm) cc_final: 0.8758 (mtp) REVERT: E 371 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8592 (ttpp) REVERT: D 275 MET cc_start: 0.9212 (tpp) cc_final: 0.8883 (tpp) REVERT: D 381 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8110 (mm-30) REVERT: J 42 GLN cc_start: 0.8732 (mt0) cc_final: 0.8438 (mp10) REVERT: J 57 MET cc_start: 0.9149 (tmm) cc_final: 0.8924 (tmm) REVERT: J 63 ILE cc_start: 0.8253 (mm) cc_final: 0.8000 (mm) REVERT: J 75 MET cc_start: 0.8616 (ttp) cc_final: 0.7888 (tmm) REVERT: L 10 TYR cc_start: 0.8058 (m-80) cc_final: 0.7756 (m-80) REVERT: M 6 MET cc_start: 0.7997 (mtt) cc_final: 0.7197 (tpp) REVERT: M 17 MET cc_start: 0.8349 (mtm) cc_final: 0.7922 (tpp) REVERT: M 42 GLN cc_start: 0.8971 (pt0) cc_final: 0.8488 (pp30) REVERT: O 42 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8102 (mp10) REVERT: O 50 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7808 (ttp-170) REVERT: O 51 THR cc_start: 0.8853 (m) cc_final: 0.8591 (m) REVERT: O 57 MET cc_start: 0.8337 (tmm) cc_final: 0.8034 (ptm) REVERT: P 16 MET cc_start: 0.7980 (mtt) cc_final: 0.7759 (mtp) REVERT: P 17 MET cc_start: 0.8356 (mtm) cc_final: 0.8091 (mtt) REVERT: P 42 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8083 (mm-40) REVERT: P 50 ARG cc_start: 0.8208 (ptt180) cc_final: 0.7695 (ttp-110) REVERT: P 54 PHE cc_start: 0.8664 (m-80) cc_final: 0.8270 (m-80) REVERT: Q 57 MET cc_start: 0.8317 (tmm) cc_final: 0.8036 (tmm) REVERT: R 6 MET cc_start: 0.7099 (mmt) cc_final: 0.6558 (mtm) REVERT: R 16 MET cc_start: 0.8172 (mtp) cc_final: 0.7909 (mtp) REVERT: R 34 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8519 (mmtp) REVERT: R 55 ILE cc_start: 0.8710 (mm) cc_final: 0.8448 (mm) REVERT: R 57 MET cc_start: 0.8877 (ttp) cc_final: 0.8443 (tmm) REVERT: R 59 LEU cc_start: 0.9012 (mt) cc_final: 0.8583 (tt) REVERT: R 72 LEU cc_start: 0.8827 (mt) cc_final: 0.8602 (mt) REVERT: Y 42 ASP cc_start: 0.8425 (m-30) cc_final: 0.8225 (m-30) REVERT: Y 64 GLN cc_start: 0.8603 (mp10) cc_final: 0.7969 (mp10) REVERT: Y 80 ASN cc_start: 0.8547 (m-40) cc_final: 0.7810 (t0) REVERT: Y 83 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7745 (ttp80) REVERT: Y 96 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8304 (tm-30) REVERT: Y 133 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: a 10 ASP cc_start: 0.8173 (t0) cc_final: 0.7894 (t0) REVERT: a 33 ASN cc_start: 0.4075 (OUTLIER) cc_final: 0.3807 (p0) REVERT: a 54 LEU cc_start: 0.7601 (mp) cc_final: 0.6893 (tt) REVERT: a 66 LYS cc_start: 0.5681 (mtpt) cc_final: 0.5181 (tttt) REVERT: a 115 MET cc_start: 0.7715 (mtm) cc_final: 0.7490 (mtt) REVERT: a 131 GLU cc_start: 0.8010 (tt0) cc_final: 0.7608 (tp30) REVERT: a 139 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7134 (tp) REVERT: a 153 MET cc_start: 0.8439 (mtp) cc_final: 0.8199 (mtt) REVERT: a 181 GLN cc_start: 0.8533 (mt0) cc_final: 0.8275 (mt0) REVERT: a 241 TRP cc_start: 0.8315 (t-100) cc_final: 0.7998 (t-100) REVERT: I 37 GLU cc_start: 0.7509 (tp30) cc_final: 0.7285 (tp30) REVERT: I 42 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7402 (mp10) REVERT: I 73 TYR cc_start: 0.7194 (t80) cc_final: 0.6815 (t80) REVERT: S 6 MET cc_start: 0.7257 (mmt) cc_final: 0.6889 (mmp) REVERT: S 34 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8254 (mmtm) REVERT: S 65 MET cc_start: 0.8952 (mmt) cc_final: 0.8642 (mtm) outliers start: 96 outliers final: 52 residues processed: 851 average time/residue: 0.2253 time to fit residues: 305.8273 Evaluate side-chains 666 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 606 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 ARG 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 C residue 458 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN C 511 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 HIS A 20 ASN A 65 ASN A 344 ASN H 14 GLN G 142 ASN G 180 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 353 HIS F 437 HIS J 3 ASN J 42 GLN M 5 ASN N 3 ASN O 3 ASN P 52 GLN Q 3 ASN Q 5 ASN Q 42 GLN Q 52 GLN R 52 GLN a 32 GLN a 76 GLN a 132 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN S 5 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064403 restraints weight = 75865.867| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.07 r_work: 0.2723 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37506 Z= 0.153 Angle : 0.639 8.173 50766 Z= 0.334 Chirality : 0.044 0.253 5918 Planarity : 0.004 0.047 6547 Dihedral : 8.835 144.949 5439 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 12.44 % Favored : 85.29 % 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: -0.44 (0.12), residues: 4805 helix: 0.19 (0.10), residues: 2609 sheet: -0.70 (0.20), residues: 555 loop : -0.69 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 115 TYR 0.020 0.001 TYR Q 10 PHE 0.019 0.001 PHE N 53 TRP 0.015 0.001 TRP a 231 HIS 0.009 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00327 (37506) covalent geometry : angle 0.63883 (50766) hydrogen bonds : bond 0.05473 ( 2198) hydrogen bonds : angle 4.90877 ( 6444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 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: 87 poor density : 692 time to evaluate : 1.312 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: W 12 LYS cc_start: 0.9371 (ttmm) cc_final: 0.9129 (tppt) REVERT: W 156 ASP cc_start: 0.8295 (p0) cc_final: 0.7602 (p0) REVERT: C 236 TYR cc_start: 0.9547 (OUTLIER) cc_final: 0.8961 (t80) REVERT: C 386 MET cc_start: 0.9430 (mmm) cc_final: 0.9145 (mmm) REVERT: C 412 ASP cc_start: 0.8412 (t0) cc_final: 0.8153 (t0) REVERT: B 422 ASP cc_start: 0.7428 (m-30) cc_final: 0.7133 (m-30) REVERT: B 425 GLN cc_start: 0.7588 (tt0) cc_final: 0.7371 (mt0) REVERT: A 343 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9319 (p) REVERT: A 484 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 488 GLN cc_start: 0.8565 (mt0) cc_final: 0.8053 (mt0) REVERT: X 17 PHE cc_start: 0.7846 (m-10) cc_final: 0.7542 (m-10) REVERT: X 82 ARG cc_start: 0.8814 (tpp-160) cc_final: 0.8514 (tpp-160) REVERT: X 112 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: H 49 MET cc_start: 0.9314 (mmt) cc_final: 0.8921 (mmm) REVERT: F 226 MET cc_start: 0.9020 (mtt) cc_final: 0.8736 (mtt) REVERT: F 424 ILE cc_start: 0.8915 (pt) cc_final: 0.8707 (mt) REVERT: E 88 MET cc_start: 0.9166 (mtm) cc_final: 0.8895 (mtp) REVERT: E 366 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8167 (tpt90) REVERT: E 371 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8503 (ttpp) REVERT: E 459 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8256 (tp) REVERT: D 381 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8382 (mm-30) REVERT: J 17 MET cc_start: 0.8375 (mtm) cc_final: 0.7687 (mmm) REVERT: J 42 GLN cc_start: 0.8704 (mt0) cc_final: 0.8466 (mp10) REVERT: J 52 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8394 (mm-40) REVERT: J 57 MET cc_start: 0.8994 (tmm) cc_final: 0.8672 (tmm) REVERT: J 75 MET cc_start: 0.8629 (ttp) cc_final: 0.7993 (tmm) REVERT: L 37 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8351 (mt-10) REVERT: L 41 ARG cc_start: 0.9122 (ttm110) cc_final: 0.8523 (ttm-80) REVERT: L 57 MET cc_start: 0.9346 (tmm) cc_final: 0.9052 (tmm) REVERT: L 61 ASP cc_start: 0.8789 (m-30) cc_final: 0.8539 (m-30) REVERT: M 17 MET cc_start: 0.8556 (mtm) cc_final: 0.8252 (mmm) REVERT: M 42 GLN cc_start: 0.8766 (pt0) cc_final: 0.8370 (pp30) REVERT: M 61 ASP cc_start: 0.8740 (m-30) cc_final: 0.8187 (t0) REVERT: M 65 MET cc_start: 0.9230 (mmm) cc_final: 0.8530 (mmm) REVERT: N 75 MET cc_start: 0.8417 (ttm) cc_final: 0.7950 (mmp) REVERT: O 42 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7646 (mp10) REVERT: O 57 MET cc_start: 0.8598 (tmm) cc_final: 0.8322 (ppp) REVERT: P 41 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: P 42 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7585 (mp10) REVERT: P 45 LEU cc_start: 0.8829 (mt) cc_final: 0.8622 (mt) REVERT: P 50 ARG cc_start: 0.7991 (ptt180) cc_final: 0.7325 (ttm110) REVERT: P 53 PHE cc_start: 0.8996 (t80) cc_final: 0.8792 (t80) REVERT: P 54 PHE cc_start: 0.8731 (m-80) cc_final: 0.8133 (m-80) REVERT: Q 5 ASN cc_start: 0.4648 (OUTLIER) cc_final: 0.4405 (m-40) REVERT: Q 17 MET cc_start: 0.8178 (mtp) cc_final: 0.7869 (mmp) REVERT: Q 28 ILE cc_start: 0.8832 (mt) cc_final: 0.8387 (pt) REVERT: Q 31 LEU cc_start: 0.7875 (tp) cc_final: 0.7661 (tp) REVERT: Q 50 ARG cc_start: 0.9265 (ptm160) cc_final: 0.8774 (ptm160) REVERT: Q 57 MET cc_start: 0.8434 (tmm) cc_final: 0.8181 (tmm) REVERT: Q 75 MET cc_start: 0.8908 (mmt) cc_final: 0.8619 (mmm) REVERT: R 6 MET cc_start: 0.7287 (mmt) cc_final: 0.6863 (mtm) REVERT: R 16 MET cc_start: 0.8420 (mtp) cc_final: 0.8212 (mtp) REVERT: R 51 THR cc_start: 0.8890 (m) cc_final: 0.8607 (p) REVERT: R 55 ILE cc_start: 0.8745 (mm) cc_final: 0.8366 (mm) REVERT: R 57 MET cc_start: 0.8851 (ttp) cc_final: 0.8560 (tmm) REVERT: R 59 LEU cc_start: 0.9151 (mt) cc_final: 0.8782 (tt) REVERT: Y 1 MET cc_start: 0.3889 (ptt) cc_final: 0.3208 (mmm) REVERT: Y 51 HIS cc_start: 0.7800 (t70) cc_final: 0.7555 (t-90) REVERT: Y 96 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8557 (tm-30) REVERT: Y 117 ARG cc_start: 0.9062 (ttt-90) cc_final: 0.8829 (ttp80) REVERT: Y 133 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8722 (tm-30) REVERT: a 6 MET cc_start: 0.4972 (tmm) cc_final: 0.3465 (ptm) REVERT: a 11 TYR cc_start: 0.7557 (t80) cc_final: 0.7247 (t80) REVERT: a 54 LEU cc_start: 0.7555 (mp) cc_final: 0.6875 (tt) REVERT: a 56 PHE cc_start: 0.7276 (t80) cc_final: 0.7052 (t80) REVERT: a 66 LYS cc_start: 0.5753 (mtpt) cc_final: 0.5408 (tttt) REVERT: a 115 MET cc_start: 0.7548 (mtm) cc_final: 0.7239 (mtt) REVERT: a 131 GLU cc_start: 0.8022 (tt0) cc_final: 0.7747 (tp30) REVERT: a 153 MET cc_start: 0.8462 (mtp) cc_final: 0.8235 (mtt) REVERT: a 169 LYS cc_start: 0.6555 (mmtp) cc_final: 0.6286 (mmtp) REVERT: a 259 LEU cc_start: 0.9722 (tp) cc_final: 0.9516 (tp) REVERT: I 73 TYR cc_start: 0.7173 (t80) cc_final: 0.6622 (t80) REVERT: S 6 MET cc_start: 0.7411 (mmt) cc_final: 0.6886 (mmp) REVERT: S 7 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5955 (m-30) REVERT: S 34 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8624 (mmtm) REVERT: S 52 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8622 (tp40) REVERT: S 65 MET cc_start: 0.8967 (mmt) cc_final: 0.8703 (mtt) outliers start: 87 outliers final: 40 residues processed: 754 average time/residue: 0.2132 time to fit residues: 261.3964 Evaluate side-chains 646 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 599 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 430 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 458 optimal weight: 6.9990 chunk 346 optimal weight: 0.0020 chunk 269 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 147 GLN B 399 GLN A 147 GLN A 488 GLN H 14 GLN H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS P 52 GLN Q 3 ASN Q 42 GLN R 52 GLN ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.063689 restraints weight = 75692.445| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.05 r_work: 0.2708 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37506 Z= 0.185 Angle : 0.609 8.884 50766 Z= 0.315 Chirality : 0.044 0.237 5918 Planarity : 0.004 0.051 6547 Dihedral : 7.867 124.522 5375 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.74 % Allowed : 13.98 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4805 helix: 0.72 (0.10), residues: 2616 sheet: -0.63 (0.20), residues: 557 loop : -0.50 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 50 TYR 0.014 0.001 TYR C 236 PHE 0.027 0.001 PHE I 35 TRP 0.014 0.001 TRP a 235 HIS 0.005 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00428 (37506) covalent geometry : angle 0.60912 (50766) hydrogen bonds : bond 0.05118 ( 2198) hydrogen bonds : angle 4.64388 ( 6444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 632 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 141 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8483 (mmmm) REVERT: W 156 ASP cc_start: 0.8227 (p0) cc_final: 0.7786 (p0) REVERT: C 236 TYR cc_start: 0.9543 (OUTLIER) cc_final: 0.8991 (t80) REVERT: C 386 MET cc_start: 0.9406 (mmm) cc_final: 0.9120 (mmm) REVERT: C 412 ASP cc_start: 0.8450 (t0) cc_final: 0.8163 (t0) REVERT: B 402 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 422 ASP cc_start: 0.7382 (m-30) cc_final: 0.7042 (m-30) REVERT: A 343 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9306 (p) REVERT: X 17 PHE cc_start: 0.8053 (m-10) cc_final: 0.7744 (m-10) REVERT: X 82 ARG cc_start: 0.8820 (tpp-160) cc_final: 0.8587 (tpp-160) REVERT: X 104 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8841 (pp30) REVERT: H 49 MET cc_start: 0.9302 (mmt) cc_final: 0.8919 (mmm) REVERT: E 88 MET cc_start: 0.9207 (mtm) cc_final: 0.8947 (mtp) REVERT: E 366 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8157 (tpt90) REVERT: E 371 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8463 (ttpp) REVERT: D 381 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8354 (mm-30) REVERT: J 17 MET cc_start: 0.8402 (mtm) cc_final: 0.7913 (mmt) REVERT: J 42 GLN cc_start: 0.8698 (mt0) cc_final: 0.8347 (mp10) REVERT: J 57 MET cc_start: 0.8993 (tmm) cc_final: 0.8712 (tmm) REVERT: J 75 MET cc_start: 0.8668 (ttp) cc_final: 0.7997 (tmm) REVERT: L 17 MET cc_start: 0.8548 (mpp) cc_final: 0.8272 (mmp) REVERT: L 57 MET cc_start: 0.9329 (tmm) cc_final: 0.8916 (tmm) REVERT: L 61 ASP cc_start: 0.8760 (m-30) cc_final: 0.8116 (m-30) REVERT: M 42 GLN cc_start: 0.8806 (pt0) cc_final: 0.8378 (pp30) REVERT: M 46 ILE cc_start: 0.9124 (mt) cc_final: 0.8890 (mt) REVERT: M 61 ASP cc_start: 0.8993 (m-30) cc_final: 0.8472 (t0) REVERT: M 65 MET cc_start: 0.9285 (mmm) cc_final: 0.8648 (mmm) REVERT: N 11 MET cc_start: 0.8011 (mmm) cc_final: 0.7776 (mmm) REVERT: N 75 MET cc_start: 0.8385 (ttm) cc_final: 0.8116 (mmp) REVERT: O 31 LEU cc_start: 0.8685 (mt) cc_final: 0.8431 (mp) REVERT: O 42 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7569 (mp10) REVERT: O 50 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8280 (ttm170) REVERT: P 41 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7508 (ttm-80) REVERT: P 42 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7684 (mp10) REVERT: P 50 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7339 (ttm110) REVERT: P 53 PHE cc_start: 0.8982 (t80) cc_final: 0.8733 (t80) REVERT: P 54 PHE cc_start: 0.8762 (m-80) cc_final: 0.8173 (m-80) REVERT: P 73 TYR cc_start: 0.7043 (t80) cc_final: 0.6552 (t80) REVERT: P 76 PHE cc_start: 0.7578 (m-80) cc_final: 0.7373 (m-80) REVERT: Q 3 ASN cc_start: 0.4944 (OUTLIER) cc_final: 0.4501 (m-40) REVERT: Q 31 LEU cc_start: 0.8007 (tp) cc_final: 0.7764 (tp) REVERT: Q 57 MET cc_start: 0.8567 (tmm) cc_final: 0.8252 (tmm) REVERT: Q 75 MET cc_start: 0.8904 (mmt) cc_final: 0.8574 (mmm) REVERT: R 6 MET cc_start: 0.7582 (mmt) cc_final: 0.7070 (mtm) REVERT: R 51 THR cc_start: 0.8911 (m) cc_final: 0.8676 (p) REVERT: R 55 ILE cc_start: 0.8817 (mm) cc_final: 0.8494 (mm) REVERT: R 57 MET cc_start: 0.8870 (ttp) cc_final: 0.8403 (tmm) REVERT: Y 1 MET cc_start: 0.4002 (ptt) cc_final: 0.3138 (mmm) REVERT: Y 51 HIS cc_start: 0.7826 (t70) cc_final: 0.7490 (t-90) REVERT: Y 64 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8656 (mm-40) REVERT: Y 96 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8557 (tm-30) REVERT: Y 117 ARG cc_start: 0.9076 (ttt-90) cc_final: 0.8871 (ttp80) REVERT: Y 133 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8749 (tm-30) REVERT: a 6 MET cc_start: 0.5211 (tmm) cc_final: 0.3260 (ptm) REVERT: a 10 ASP cc_start: 0.7821 (t0) cc_final: 0.7312 (t0) REVERT: a 54 LEU cc_start: 0.7548 (mp) cc_final: 0.6855 (tt) REVERT: a 56 PHE cc_start: 0.7160 (t80) cc_final: 0.6910 (t80) REVERT: a 91 LYS cc_start: 0.9285 (tppt) cc_final: 0.9071 (mmmm) REVERT: a 99 LYS cc_start: 0.8205 (mttm) cc_final: 0.8005 (pptt) REVERT: a 131 GLU cc_start: 0.8107 (tt0) cc_final: 0.7834 (tp30) REVERT: a 153 MET cc_start: 0.8460 (mtp) cc_final: 0.8201 (mtt) REVERT: I 34 LYS cc_start: 0.9349 (mttm) cc_final: 0.9129 (mttp) REVERT: I 73 TYR cc_start: 0.7122 (t80) cc_final: 0.6520 (t80) REVERT: S 6 MET cc_start: 0.7400 (mmt) cc_final: 0.6835 (mmp) REVERT: S 7 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.5812 (m-30) REVERT: S 34 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8756 (mmtm) REVERT: S 65 MET cc_start: 0.8993 (mmt) cc_final: 0.8673 (mtm) outliers start: 105 outliers final: 64 residues processed: 701 average time/residue: 0.2130 time to fit residues: 242.8714 Evaluate side-chains 678 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 609 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 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 95 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 3 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 356 optimal weight: 0.4980 chunk 134 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 448 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN P 52 GLN Q 5 ASN Q 42 GLN R 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064824 restraints weight = 75723.577| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.07 r_work: 0.2738 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37506 Z= 0.141 Angle : 0.583 9.924 50766 Z= 0.298 Chirality : 0.043 0.232 5918 Planarity : 0.004 0.053 6547 Dihedral : 7.483 117.577 5368 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 15.28 % Favored : 82.16 % 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: 0.50 (0.12), residues: 4805 helix: 1.06 (0.10), residues: 2613 sheet: -0.51 (0.21), residues: 546 loop : -0.39 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 50 TYR 0.012 0.001 TYR S 73 PHE 0.032 0.001 PHE Y 14 TRP 0.017 0.001 TRP a 235 HIS 0.004 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00317 (37506) covalent geometry : angle 0.58268 (50766) hydrogen bonds : bond 0.04615 ( 2198) hydrogen bonds : angle 4.46956 ( 6444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 640 time to evaluate : 1.289 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 141 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8520 (mmmm) REVERT: W 156 ASP cc_start: 0.8227 (p0) cc_final: 0.7618 (p0) REVERT: C 402 GLU cc_start: 0.9012 (tp30) cc_final: 0.8691 (tp30) REVERT: B 402 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 422 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: A 343 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9302 (p) REVERT: X 17 PHE cc_start: 0.8078 (m-10) cc_final: 0.7789 (m-10) REVERT: X 82 ARG cc_start: 0.8803 (tpp-160) cc_final: 0.8589 (tpp-160) REVERT: X 104 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8829 (pp30) REVERT: H 49 MET cc_start: 0.9307 (mmt) cc_final: 0.8957 (mmm) REVERT: G 157 GLN cc_start: 0.8663 (tt0) cc_final: 0.8372 (tt0) REVERT: F 159 MET cc_start: 0.9349 (ttp) cc_final: 0.9141 (ttm) REVERT: F 342 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8695 (tpp-160) REVERT: F 385 GLU cc_start: 0.8722 (pm20) cc_final: 0.8386 (pm20) REVERT: E 88 MET cc_start: 0.9191 (mtm) cc_final: 0.8960 (mtp) REVERT: E 371 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8363 (ttpp) REVERT: D 381 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8370 (mm-30) REVERT: J 17 MET cc_start: 0.8349 (mtm) cc_final: 0.7899 (mmt) REVERT: J 42 GLN cc_start: 0.8658 (mt0) cc_final: 0.8350 (mp10) REVERT: J 57 MET cc_start: 0.8943 (tmm) cc_final: 0.8622 (tmm) REVERT: J 75 MET cc_start: 0.8616 (ttp) cc_final: 0.8093 (tmm) REVERT: L 17 MET cc_start: 0.8565 (mpp) cc_final: 0.8148 (mmp) REVERT: L 37 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8271 (mt-10) REVERT: L 57 MET cc_start: 0.9216 (tmm) cc_final: 0.8924 (tmm) REVERT: L 61 ASP cc_start: 0.8745 (m-30) cc_final: 0.8059 (m-30) REVERT: M 42 GLN cc_start: 0.8645 (pt0) cc_final: 0.8248 (pp30) REVERT: M 50 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8294 (ptp-110) REVERT: M 61 ASP cc_start: 0.8943 (m-30) cc_final: 0.8357 (t0) REVERT: M 65 MET cc_start: 0.9253 (mmm) cc_final: 0.8725 (mmm) REVERT: N 11 MET cc_start: 0.7878 (mmm) cc_final: 0.7658 (mmm) REVERT: N 75 MET cc_start: 0.8340 (ttm) cc_final: 0.8068 (mmp) REVERT: O 8 LEU cc_start: 0.7366 (mt) cc_final: 0.7106 (tt) REVERT: O 59 LEU cc_start: 0.8258 (mt) cc_final: 0.8000 (mt) REVERT: P 17 MET cc_start: 0.6766 (mtt) cc_final: 0.5221 (ptt) REVERT: P 31 LEU cc_start: 0.8192 (tp) cc_final: 0.7761 (tp) REVERT: P 41 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: P 42 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7841 (mp10) REVERT: P 50 ARG cc_start: 0.8019 (ptt180) cc_final: 0.7368 (ttm110) REVERT: P 54 PHE cc_start: 0.8646 (m-80) cc_final: 0.8283 (m-80) REVERT: P 73 TYR cc_start: 0.6845 (t80) cc_final: 0.6232 (t80) REVERT: P 76 PHE cc_start: 0.7521 (m-80) cc_final: 0.7314 (m-80) REVERT: Q 5 ASN cc_start: 0.5096 (OUTLIER) cc_final: 0.4875 (m-40) REVERT: Q 57 MET cc_start: 0.8602 (tmm) cc_final: 0.8287 (tmm) REVERT: R 6 MET cc_start: 0.7564 (mmt) cc_final: 0.6999 (mtm) REVERT: R 11 MET cc_start: 0.8766 (tpp) cc_final: 0.8518 (tpp) REVERT: R 57 MET cc_start: 0.8798 (ttp) cc_final: 0.8428 (tmm) REVERT: Y 1 MET cc_start: 0.3954 (ptt) cc_final: 0.3151 (mmm) REVERT: Y 64 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8577 (mm-40) REVERT: a 6 MET cc_start: 0.5468 (tmm) cc_final: 0.3725 (ptm) REVERT: a 54 LEU cc_start: 0.7561 (mp) cc_final: 0.6879 (tt) REVERT: a 56 PHE cc_start: 0.6998 (t80) cc_final: 0.6710 (t80) REVERT: a 91 LYS cc_start: 0.9282 (tppt) cc_final: 0.9066 (mmmm) REVERT: a 99 LYS cc_start: 0.8228 (mttm) cc_final: 0.7862 (ptpp) REVERT: a 131 GLU cc_start: 0.8090 (tt0) cc_final: 0.7831 (tp30) REVERT: a 153 MET cc_start: 0.8459 (mtp) cc_final: 0.8195 (mtt) REVERT: I 73 TYR cc_start: 0.6906 (t80) cc_final: 0.6421 (t80) REVERT: S 6 MET cc_start: 0.7404 (mmt) cc_final: 0.6786 (mmp) REVERT: S 7 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.5787 (m-30) REVERT: S 34 LYS cc_start: 0.9004 (mmtm) cc_final: 0.8769 (mmtm) REVERT: S 42 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8204 (mm-40) REVERT: S 57 MET cc_start: 0.8566 (tmm) cc_final: 0.8302 (tmm) REVERT: S 65 MET cc_start: 0.9000 (mmt) cc_final: 0.8671 (mtm) outliers start: 98 outliers final: 69 residues processed: 705 average time/residue: 0.2139 time to fit residues: 245.0660 Evaluate side-chains 686 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 613 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP 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 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 258 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 465 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 428 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN W 120 GLN H 14 GLN H 24 GLN H 55 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 57 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN Q 5 ASN Q 42 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065472 restraints weight = 75325.820| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.06 r_work: 0.2743 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37506 Z= 0.134 Angle : 0.579 11.000 50766 Z= 0.293 Chirality : 0.043 0.218 5918 Planarity : 0.004 0.051 6547 Dihedral : 7.226 114.712 5364 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.63 % Allowed : 15.86 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4805 helix: 1.25 (0.10), residues: 2619 sheet: -0.48 (0.21), residues: 538 loop : -0.36 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 50 TYR 0.014 0.001 TYR Q 73 PHE 0.032 0.001 PHE Y 14 TRP 0.018 0.001 TRP a 235 HIS 0.009 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00302 (37506) covalent geometry : angle 0.57909 (50766) hydrogen bonds : bond 0.04424 ( 2198) hydrogen bonds : angle 4.38565 ( 6444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 622 time to evaluate : 1.295 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 123 LYS cc_start: 0.8806 (mttt) cc_final: 0.8604 (mttp) REVERT: W 141 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8580 (mmmm) REVERT: W 156 ASP cc_start: 0.8237 (p0) cc_final: 0.7650 (p0) REVERT: C 402 GLU cc_start: 0.9005 (tp30) cc_final: 0.8668 (tp30) REVERT: B 402 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 343 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9293 (p) REVERT: X 17 PHE cc_start: 0.8068 (m-10) cc_final: 0.7787 (m-10) REVERT: X 29 LEU cc_start: 0.7945 (mt) cc_final: 0.7724 (mt) REVERT: X 104 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8811 (pp30) REVERT: H 49 MET cc_start: 0.9282 (mmt) cc_final: 0.8956 (mmm) REVERT: H 111 ASP cc_start: 0.8573 (t0) cc_final: 0.8323 (t0) REVERT: G 157 GLN cc_start: 0.8678 (tt0) cc_final: 0.8374 (tt0) REVERT: G 168 TYR cc_start: 0.9179 (m-80) cc_final: 0.8900 (m-80) REVERT: F 342 ARG cc_start: 0.8894 (tpp-160) cc_final: 0.8689 (tpp-160) REVERT: F 385 GLU cc_start: 0.8668 (pm20) cc_final: 0.8353 (pm20) REVERT: E 88 MET cc_start: 0.9182 (mtm) cc_final: 0.8966 (mtp) REVERT: E 366 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7934 (tpt90) REVERT: E 371 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8355 (ttpp) REVERT: D 381 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8383 (mm-30) REVERT: J 17 MET cc_start: 0.8338 (mtm) cc_final: 0.7948 (mmt) REVERT: J 42 GLN cc_start: 0.8625 (mt0) cc_final: 0.8299 (mp10) REVERT: J 57 MET cc_start: 0.8970 (tmm) cc_final: 0.8506 (tmm) REVERT: J 75 MET cc_start: 0.8569 (ttp) cc_final: 0.8127 (tmm) REVERT: L 57 MET cc_start: 0.9159 (tmm) cc_final: 0.8914 (tmm) REVERT: L 61 ASP cc_start: 0.8692 (m-30) cc_final: 0.7972 (m-30) REVERT: L 73 TYR cc_start: 0.7834 (t80) cc_final: 0.7627 (t80) REVERT: M 17 MET cc_start: 0.8438 (mtt) cc_final: 0.8218 (mmm) REVERT: M 42 GLN cc_start: 0.8636 (pt0) cc_final: 0.8268 (pp30) REVERT: M 61 ASP cc_start: 0.8977 (m-30) cc_final: 0.8393 (t0) REVERT: M 65 MET cc_start: 0.9278 (mmm) cc_final: 0.8742 (mmm) REVERT: M 75 MET cc_start: 0.8659 (tpp) cc_final: 0.8442 (tpp) REVERT: N 16 MET cc_start: 0.7539 (mmm) cc_final: 0.7262 (mmm) REVERT: P 10 TYR cc_start: 0.7426 (m-80) cc_final: 0.7221 (m-80) REVERT: P 31 LEU cc_start: 0.8138 (tp) cc_final: 0.7714 (tp) REVERT: P 42 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7779 (mp10) REVERT: P 50 ARG cc_start: 0.7775 (ptt180) cc_final: 0.7284 (ttm110) REVERT: P 73 TYR cc_start: 0.6695 (t80) cc_final: 0.6299 (t80) REVERT: Q 6 MET cc_start: 0.6298 (ptp) cc_final: 0.5952 (tmm) REVERT: Q 57 MET cc_start: 0.8612 (tmm) cc_final: 0.8297 (tmm) REVERT: R 6 MET cc_start: 0.7443 (mmt) cc_final: 0.6910 (mtm) REVERT: R 55 ILE cc_start: 0.8846 (mm) cc_final: 0.8540 (mm) REVERT: R 57 MET cc_start: 0.8823 (ttp) cc_final: 0.8428 (tmm) REVERT: Y 1 MET cc_start: 0.3931 (ptt) cc_final: 0.3055 (mmm) REVERT: Y 64 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8594 (mm-40) REVERT: a 6 MET cc_start: 0.5332 (tmm) cc_final: 0.3523 (ptm) REVERT: a 54 LEU cc_start: 0.7559 (mp) cc_final: 0.6873 (tt) REVERT: a 56 PHE cc_start: 0.6906 (t80) cc_final: 0.6574 (t80) REVERT: a 91 LYS cc_start: 0.9324 (tppt) cc_final: 0.9111 (mmmm) REVERT: a 99 LYS cc_start: 0.8238 (mttm) cc_final: 0.7886 (ptpp) REVERT: a 115 MET cc_start: 0.7412 (mtm) cc_final: 0.7067 (mtt) REVERT: a 131 GLU cc_start: 0.8107 (tt0) cc_final: 0.7847 (tp30) REVERT: a 215 MET cc_start: 0.8744 (mmm) cc_final: 0.8218 (mmm) REVERT: I 11 MET cc_start: 0.8620 (tpt) cc_final: 0.8350 (tpp) REVERT: I 73 TYR cc_start: 0.6939 (t80) cc_final: 0.6420 (t80) REVERT: S 6 MET cc_start: 0.7297 (mmt) cc_final: 0.6651 (mmp) REVERT: S 7 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: S 22 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9154 (mp) REVERT: S 34 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8159 (mmmt) REVERT: S 37 GLU cc_start: 0.8649 (tt0) cc_final: 0.7766 (tt0) REVERT: S 65 MET cc_start: 0.9008 (mmt) cc_final: 0.8632 (mtm) outliers start: 101 outliers final: 67 residues processed: 689 average time/residue: 0.2141 time to fit residues: 240.5111 Evaluate side-chains 674 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 604 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP 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 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 55 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 22 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 310 optimal weight: 0.3980 chunk 444 optimal weight: 0.4980 chunk 424 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 456 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS X 4 ASN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN H 55 GLN H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN J 52 GLN Q 5 ASN Q 42 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.066439 restraints weight = 75349.982| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.06 r_work: 0.2766 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37506 Z= 0.120 Angle : 0.575 11.537 50766 Z= 0.288 Chirality : 0.042 0.213 5918 Planarity : 0.004 0.051 6547 Dihedral : 6.744 112.115 5357 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.24 % Allowed : 16.85 % Favored : 80.91 % 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: 0.91 (0.12), residues: 4805 helix: 1.45 (0.10), residues: 2609 sheet: -0.38 (0.21), residues: 543 loop : -0.30 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 50 TYR 0.015 0.001 TYR Q 73 PHE 0.028 0.001 PHE Y 14 TRP 0.022 0.001 TRP a 235 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00262 (37506) covalent geometry : angle 0.57492 (50766) hydrogen bonds : bond 0.04183 ( 2198) hydrogen bonds : angle 4.30848 ( 6444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 622 time to evaluate : 1.332 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 141 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8645 (mmmm) REVERT: W 156 ASP cc_start: 0.8250 (p0) cc_final: 0.7677 (p0) REVERT: C 402 GLU cc_start: 0.8979 (tp30) cc_final: 0.8616 (tp30) REVERT: B 402 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 422 ASP cc_start: 0.7012 (m-30) cc_final: 0.6786 (m-30) REVERT: A 343 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9300 (p) REVERT: X 104 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8805 (pp30) REVERT: H 49 MET cc_start: 0.9263 (mmt) cc_final: 0.8929 (mmm) REVERT: G 155 MET cc_start: 0.9203 (mmp) cc_final: 0.8960 (mmm) REVERT: G 157 GLN cc_start: 0.8621 (tt0) cc_final: 0.8329 (tt0) REVERT: G 168 TYR cc_start: 0.9146 (m-80) cc_final: 0.8887 (m-80) REVERT: F 373 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9032 (mt) REVERT: F 385 GLU cc_start: 0.8640 (pm20) cc_final: 0.8332 (pm20) REVERT: E 0 MET cc_start: 0.6038 (pmm) cc_final: 0.5806 (ttp) REVERT: E 88 MET cc_start: 0.9169 (mtm) cc_final: 0.8953 (mtp) REVERT: E 371 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8311 (ttpp) REVERT: D 381 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8335 (mm-30) REVERT: J 17 MET cc_start: 0.8298 (mtm) cc_final: 0.7938 (mmt) REVERT: J 57 MET cc_start: 0.8890 (tmm) cc_final: 0.8359 (tmm) REVERT: J 75 MET cc_start: 0.8509 (ttp) cc_final: 0.8073 (tmm) REVERT: L 17 MET cc_start: 0.8398 (mmp) cc_final: 0.8186 (mmm) REVERT: L 61 ASP cc_start: 0.8622 (m-30) cc_final: 0.8273 (p0) REVERT: M 42 GLN cc_start: 0.8605 (pt0) cc_final: 0.8261 (pp30) REVERT: M 61 ASP cc_start: 0.8995 (m-30) cc_final: 0.8225 (t0) REVERT: M 65 MET cc_start: 0.9296 (mmm) cc_final: 0.8434 (mmm) REVERT: N 11 MET cc_start: 0.7945 (mmm) cc_final: 0.7307 (tpp) REVERT: N 16 MET cc_start: 0.7392 (mmm) cc_final: 0.7123 (tpp) REVERT: O 66 ILE cc_start: 0.8094 (pt) cc_final: 0.7868 (pt) REVERT: P 10 TYR cc_start: 0.7439 (m-80) cc_final: 0.7235 (m-80) REVERT: P 31 LEU cc_start: 0.8167 (tp) cc_final: 0.7853 (tp) REVERT: P 42 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7734 (mp10) REVERT: P 50 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7151 (ttm110) REVERT: P 73 TYR cc_start: 0.6631 (t80) cc_final: 0.6038 (t80) REVERT: P 76 PHE cc_start: 0.7100 (m-80) cc_final: 0.6722 (m-80) REVERT: Q 6 MET cc_start: 0.6237 (ptp) cc_final: 0.5922 (tmm) REVERT: Q 7 ASP cc_start: 0.8388 (t70) cc_final: 0.8015 (t0) REVERT: Q 17 MET cc_start: 0.8123 (mmm) cc_final: 0.7662 (mpp) REVERT: Q 57 MET cc_start: 0.8625 (tmm) cc_final: 0.8286 (tmm) REVERT: R 6 MET cc_start: 0.7373 (mmt) cc_final: 0.6854 (mtm) REVERT: R 55 ILE cc_start: 0.8802 (mm) cc_final: 0.8483 (mm) REVERT: R 57 MET cc_start: 0.8819 (ttp) cc_final: 0.8475 (tmm) REVERT: Y 1 MET cc_start: 0.3925 (ptt) cc_final: 0.3168 (mmm) REVERT: Y 49 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7695 (ptp-170) REVERT: Y 64 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8610 (mm-40) REVERT: a 6 MET cc_start: 0.5369 (tmm) cc_final: 0.3605 (ptm) REVERT: a 15 HIS cc_start: 0.7831 (m90) cc_final: 0.7388 (m-70) REVERT: a 54 LEU cc_start: 0.7601 (mp) cc_final: 0.7093 (tt) REVERT: a 91 LYS cc_start: 0.9367 (tppt) cc_final: 0.9104 (mmmm) REVERT: a 99 LYS cc_start: 0.8253 (mttm) cc_final: 0.7890 (ptpp) REVERT: a 131 GLU cc_start: 0.8090 (tt0) cc_final: 0.7852 (tp30) REVERT: a 244 PHE cc_start: 0.8072 (t80) cc_final: 0.7865 (t80) REVERT: I 11 MET cc_start: 0.8672 (tpt) cc_final: 0.8440 (tpp) REVERT: I 73 TYR cc_start: 0.6831 (t80) cc_final: 0.6370 (t80) REVERT: S 6 MET cc_start: 0.7320 (mmt) cc_final: 0.6821 (mmp) REVERT: S 16 MET cc_start: 0.9045 (mmt) cc_final: 0.8533 (mmt) REVERT: S 22 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9174 (mp) REVERT: S 34 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8172 (mmmt) REVERT: S 37 GLU cc_start: 0.8609 (tt0) cc_final: 0.7753 (tt0) REVERT: S 57 MET cc_start: 0.8619 (tmm) cc_final: 0.8352 (tmm) REVERT: S 65 MET cc_start: 0.8984 (mmt) cc_final: 0.8616 (mtm) outliers start: 86 outliers final: 63 residues processed: 679 average time/residue: 0.2118 time to fit residues: 235.6401 Evaluate side-chains 666 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 600 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP 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 83 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain S residue 22 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 464 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 338 optimal weight: 0.6980 chunk 408 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN W 120 GLN H 14 GLN H 55 GLN G 57 HIS G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN F 35 ASN ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN P 52 GLN Q 5 ASN a 14 HIS a 181 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.063074 restraints weight = 76226.389| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.06 r_work: 0.2695 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 37506 Z= 0.263 Angle : 0.653 11.176 50766 Z= 0.332 Chirality : 0.046 0.197 5918 Planarity : 0.004 0.051 6547 Dihedral : 6.934 125.301 5354 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.69 % Allowed : 17.11 % Favored : 80.20 % 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: 0.73 (0.12), residues: 4805 helix: 1.32 (0.10), residues: 2605 sheet: -0.50 (0.21), residues: 539 loop : -0.38 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 50 TYR 0.018 0.002 TYR a 263 PHE 0.046 0.002 PHE X 17 TRP 0.021 0.002 TRP a 241 HIS 0.009 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00632 (37506) covalent geometry : angle 0.65332 (50766) hydrogen bonds : bond 0.04812 ( 2198) hydrogen bonds : angle 4.50109 ( 6444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 594 time to evaluate : 1.333 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 141 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8668 (mmmm) REVERT: W 156 ASP cc_start: 0.8216 (p0) cc_final: 0.7670 (p0) REVERT: C 386 MET cc_start: 0.9375 (mmm) cc_final: 0.9174 (mmt) REVERT: C 402 GLU cc_start: 0.9002 (tp30) cc_final: 0.8659 (tp30) REVERT: B 402 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 343 THR cc_start: 0.9623 (OUTLIER) cc_final: 0.9301 (p) REVERT: A 463 LYS cc_start: 0.5172 (tmtt) cc_final: 0.4736 (tmtt) REVERT: X 17 PHE cc_start: 0.7774 (m-80) cc_final: 0.7412 (m-80) REVERT: X 104 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8852 (pp30) REVERT: X 112 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: H 49 MET cc_start: 0.9278 (mmt) cc_final: 0.8931 (mmm) REVERT: H 111 ASP cc_start: 0.8685 (t0) cc_final: 0.8410 (t0) REVERT: H 129 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8053 (ttp-170) REVERT: G 155 MET cc_start: 0.9226 (mmp) cc_final: 0.8988 (mmm) REVERT: G 168 TYR cc_start: 0.9208 (m-80) cc_final: 0.8912 (m-80) REVERT: F 385 GLU cc_start: 0.8766 (pm20) cc_final: 0.8396 (pm20) REVERT: E 88 MET cc_start: 0.9280 (mtm) cc_final: 0.9014 (mtp) REVERT: E 323 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.8398 (ttm-80) REVERT: E 371 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8333 (ttpp) REVERT: D 381 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8363 (mm-30) REVERT: J 17 MET cc_start: 0.8268 (mtm) cc_final: 0.7951 (mmt) REVERT: J 41 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8388 (mtm-85) REVERT: J 57 MET cc_start: 0.8978 (tmm) cc_final: 0.8485 (tmm) REVERT: J 75 MET cc_start: 0.8561 (ttp) cc_final: 0.8033 (tmm) REVERT: L 61 ASP cc_start: 0.8680 (m-30) cc_final: 0.8301 (p0) REVERT: M 41 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8421 (tpp80) REVERT: M 42 GLN cc_start: 0.8744 (pt0) cc_final: 0.8335 (pp30) REVERT: M 61 ASP cc_start: 0.9112 (m-30) cc_final: 0.8318 (t0) REVERT: M 65 MET cc_start: 0.9286 (mmm) cc_final: 0.8543 (mmm) REVERT: M 75 MET cc_start: 0.8430 (tpp) cc_final: 0.8087 (tpp) REVERT: N 16 MET cc_start: 0.7339 (mmm) cc_final: 0.6910 (tpp) REVERT: N 42 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7272 (mt0) REVERT: O 16 MET cc_start: 0.7027 (mmm) cc_final: 0.6676 (mmm) REVERT: O 66 ILE cc_start: 0.8082 (pt) cc_final: 0.7822 (pt) REVERT: P 31 LEU cc_start: 0.8154 (tp) cc_final: 0.7843 (tp) REVERT: P 42 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7657 (mp10) REVERT: P 50 ARG cc_start: 0.7761 (ptt180) cc_final: 0.7196 (ttm110) REVERT: P 76 PHE cc_start: 0.7105 (m-80) cc_final: 0.6707 (m-80) REVERT: Q 5 ASN cc_start: 0.4755 (OUTLIER) cc_final: 0.4496 (m-40) REVERT: Q 6 MET cc_start: 0.6225 (ptp) cc_final: 0.5929 (tmm) REVERT: Q 7 ASP cc_start: 0.8466 (t70) cc_final: 0.8144 (t0) REVERT: Q 31 LEU cc_start: 0.8131 (tp) cc_final: 0.7902 (tt) REVERT: Q 57 MET cc_start: 0.8630 (tmm) cc_final: 0.8278 (tmm) REVERT: R 6 MET cc_start: 0.7402 (mmt) cc_final: 0.6874 (mtm) REVERT: R 11 MET cc_start: 0.8727 (tpp) cc_final: 0.8505 (tpp) REVERT: R 55 ILE cc_start: 0.8886 (mm) cc_final: 0.8607 (mm) REVERT: R 57 MET cc_start: 0.8817 (ttp) cc_final: 0.8309 (tmm) REVERT: Y 1 MET cc_start: 0.4145 (ptt) cc_final: 0.2908 (mmm) REVERT: Y 64 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8599 (mm-40) REVERT: a 6 MET cc_start: 0.5798 (tmm) cc_final: 0.4421 (ptt) REVERT: a 54 LEU cc_start: 0.7632 (mp) cc_final: 0.7016 (tt) REVERT: a 91 LYS cc_start: 0.9367 (tppt) cc_final: 0.9100 (mmmm) REVERT: a 99 LYS cc_start: 0.8245 (mttm) cc_final: 0.7842 (ptpp) REVERT: a 131 GLU cc_start: 0.8122 (tt0) cc_final: 0.7849 (tp30) REVERT: I 35 PHE cc_start: 0.8866 (t80) cc_final: 0.8317 (t80) REVERT: I 50 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8625 (mtm110) REVERT: I 73 TYR cc_start: 0.6750 (t80) cc_final: 0.6283 (t80) REVERT: I 74 VAL cc_start: 0.8486 (t) cc_final: 0.8135 (p) REVERT: S 6 MET cc_start: 0.7297 (mmt) cc_final: 0.6728 (mmp) REVERT: S 7 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5842 (m-30) REVERT: S 16 MET cc_start: 0.9026 (mmt) cc_final: 0.8597 (mmt) REVERT: S 34 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8653 (mmtm) REVERT: S 57 MET cc_start: 0.8705 (tmm) cc_final: 0.8435 (tmm) REVERT: S 65 MET cc_start: 0.9035 (mmt) cc_final: 0.8639 (mtm) outliers start: 103 outliers final: 74 residues processed: 664 average time/residue: 0.2113 time to fit residues: 229.7158 Evaluate side-chains 657 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 579 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 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 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 66 ILE 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 5 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 166 optimal weight: 0.7980 chunk 355 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 310 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 382 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN B 14 GLN H 5 HIS ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN P 52 GLN Q 5 ASN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.066141 restraints weight = 75158.340| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.06 r_work: 0.2764 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37506 Z= 0.123 Angle : 0.606 17.052 50766 Z= 0.301 Chirality : 0.043 0.202 5918 Planarity : 0.004 0.052 6547 Dihedral : 6.565 115.388 5353 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.96 % Allowed : 17.58 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 4805 helix: 1.53 (0.10), residues: 2602 sheet: -0.44 (0.21), residues: 545 loop : -0.31 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG X 36 TYR 0.016 0.001 TYR Q 73 PHE 0.037 0.001 PHE X 17 TRP 0.029 0.002 TRP a 39 HIS 0.009 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00266 (37506) covalent geometry : angle 0.60574 (50766) hydrogen bonds : bond 0.04196 ( 2198) hydrogen bonds : angle 4.33745 ( 6444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 603 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 141 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8654 (mmmm) REVERT: W 156 ASP cc_start: 0.8099 (p0) cc_final: 0.7607 (p0) REVERT: C 402 GLU cc_start: 0.8999 (tp30) cc_final: 0.8663 (tp30) REVERT: C 483 MET cc_start: 0.9172 (mmm) cc_final: 0.8874 (mmm) REVERT: B 402 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 343 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9320 (p) REVERT: A 463 LYS cc_start: 0.5287 (tmtt) cc_final: 0.4815 (tmtt) REVERT: X 17 PHE cc_start: 0.7803 (m-80) cc_final: 0.7579 (m-80) REVERT: X 104 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8837 (pp30) REVERT: X 112 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: H 49 MET cc_start: 0.9193 (mmt) cc_final: 0.8887 (mmm) REVERT: H 111 ASP cc_start: 0.8600 (t0) cc_final: 0.8359 (t0) REVERT: G 155 MET cc_start: 0.9204 (mmp) cc_final: 0.8940 (mmm) REVERT: G 157 GLN cc_start: 0.8649 (tt0) cc_final: 0.8359 (tt0) REVERT: G 168 TYR cc_start: 0.9122 (m-80) cc_final: 0.8866 (m-80) REVERT: F 385 GLU cc_start: 0.8592 (pm20) cc_final: 0.8358 (pm20) REVERT: E 88 MET cc_start: 0.9156 (mtm) cc_final: 0.8943 (mtp) REVERT: E 366 ARG cc_start: 0.8351 (mmm160) cc_final: 0.8107 (tpt90) REVERT: E 371 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8315 (ttpp) REVERT: D 381 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8305 (mm-30) REVERT: J 57 MET cc_start: 0.8922 (tmm) cc_final: 0.8378 (tmm) REVERT: J 75 MET cc_start: 0.8351 (ttp) cc_final: 0.8080 (tmm) REVERT: L 6 MET cc_start: 0.7365 (ppp) cc_final: 0.6797 (ppp) REVERT: L 41 ARG cc_start: 0.9062 (ttm110) cc_final: 0.7710 (ttp80) REVERT: L 61 ASP cc_start: 0.8787 (m-30) cc_final: 0.8561 (p0) REVERT: M 17 MET cc_start: 0.8572 (mmm) cc_final: 0.7908 (mtt) REVERT: M 42 GLN cc_start: 0.8583 (pt0) cc_final: 0.8289 (pp30) REVERT: M 61 ASP cc_start: 0.9013 (m-30) cc_final: 0.8164 (t0) REVERT: M 65 MET cc_start: 0.9297 (mmm) cc_final: 0.8481 (mmm) REVERT: M 75 MET cc_start: 0.8374 (tpp) cc_final: 0.8017 (tpp) REVERT: N 16 MET cc_start: 0.7062 (mmm) cc_final: 0.6810 (tpp) REVERT: N 17 MET cc_start: 0.8233 (tmm) cc_final: 0.7999 (tmm) REVERT: N 37 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: O 16 MET cc_start: 0.6890 (mmm) cc_final: 0.6583 (mmm) REVERT: O 41 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7453 (tpp-160) REVERT: P 31 LEU cc_start: 0.8079 (tp) cc_final: 0.7813 (tp) REVERT: P 42 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7630 (mp10) REVERT: P 50 ARG cc_start: 0.7710 (ptt180) cc_final: 0.7019 (ttp-110) REVERT: P 73 TYR cc_start: 0.6479 (t80) cc_final: 0.5718 (t80) REVERT: P 76 PHE cc_start: 0.7101 (m-80) cc_final: 0.6691 (m-80) REVERT: Q 6 MET cc_start: 0.6394 (ptp) cc_final: 0.6188 (tmm) REVERT: Q 7 ASP cc_start: 0.8423 (t70) cc_final: 0.8148 (t0) REVERT: Q 31 LEU cc_start: 0.8137 (tp) cc_final: 0.7906 (tt) REVERT: Q 37 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: Q 52 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8605 (mm-40) REVERT: Q 57 MET cc_start: 0.8702 (tmm) cc_final: 0.8359 (tmm) REVERT: R 6 MET cc_start: 0.7355 (mmt) cc_final: 0.6824 (mtm) REVERT: R 55 ILE cc_start: 0.8901 (mm) cc_final: 0.8587 (mm) REVERT: R 57 MET cc_start: 0.8720 (ttp) cc_final: 0.8420 (tmm) REVERT: R 65 MET cc_start: 0.9087 (mmp) cc_final: 0.8740 (mmm) REVERT: Y 1 MET cc_start: 0.4428 (ptt) cc_final: 0.3267 (mmm) REVERT: Y 64 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8649 (mm-40) REVERT: Y 83 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7872 (tmm-80) REVERT: a 6 MET cc_start: 0.5544 (tmm) cc_final: 0.4255 (ptt) REVERT: a 54 LEU cc_start: 0.7531 (mp) cc_final: 0.7038 (tt) REVERT: a 91 LYS cc_start: 0.9327 (tppt) cc_final: 0.9071 (mmmm) REVERT: a 99 LYS cc_start: 0.8247 (mttm) cc_final: 0.7870 (ptpp) REVERT: I 35 PHE cc_start: 0.8793 (t80) cc_final: 0.8536 (t80) REVERT: I 73 TYR cc_start: 0.6846 (t80) cc_final: 0.6372 (t80) REVERT: I 74 VAL cc_start: 0.8565 (t) cc_final: 0.8233 (p) REVERT: S 6 MET cc_start: 0.7278 (mmt) cc_final: 0.6583 (mmp) REVERT: S 16 MET cc_start: 0.8941 (mmt) cc_final: 0.8545 (mmt) REVERT: S 57 MET cc_start: 0.8707 (tmm) cc_final: 0.8444 (tmm) REVERT: S 65 MET cc_start: 0.8967 (mmt) cc_final: 0.8585 (mtm) outliers start: 75 outliers final: 54 residues processed: 656 average time/residue: 0.2132 time to fit residues: 227.4854 Evaluate side-chains 644 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 586 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain B residue 3 LEU 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 262 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP 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 83 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 248 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 435 optimal weight: 7.9990 chunk 457 optimal weight: 1.9990 chunk 408 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 259 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN P 52 GLN Q 5 ASN a 76 GLN ** a 252 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 = 0.3495 r_free = 0.3495 target = 0.099693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.065931 restraints weight = 75666.264| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.08 r_work: 0.2758 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37506 Z= 0.132 Angle : 0.607 17.981 50766 Z= 0.301 Chirality : 0.043 0.276 5918 Planarity : 0.004 0.052 6547 Dihedral : 6.377 116.964 5352 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.77 % Allowed : 18.05 % Favored : 80.18 % 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: 1.07 (0.12), residues: 4805 helix: 1.62 (0.10), residues: 2603 sheet: -0.35 (0.21), residues: 532 loop : -0.28 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 36 TYR 0.028 0.001 TYR a 263 PHE 0.035 0.001 PHE X 17 TRP 0.029 0.001 TRP a 39 HIS 0.010 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00301 (37506) covalent geometry : angle 0.60735 (50766) hydrogen bonds : bond 0.04175 ( 2198) hydrogen bonds : angle 4.31558 ( 6444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 603 time to evaluate : 1.168 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 67 GLN cc_start: 0.8822 (mt0) cc_final: 0.8594 (mt0) REVERT: W 141 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8653 (mmmm) REVERT: W 156 ASP cc_start: 0.8102 (p0) cc_final: 0.7594 (p0) REVERT: C 402 GLU cc_start: 0.8977 (tp30) cc_final: 0.8635 (tp30) REVERT: B 402 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 343 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9311 (p) REVERT: A 463 LYS cc_start: 0.5155 (tmtt) cc_final: 0.4614 (tmtt) REVERT: X 104 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8850 (pp30) REVERT: X 112 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8470 (tp30) REVERT: H 49 MET cc_start: 0.9225 (mmt) cc_final: 0.8889 (mmm) REVERT: H 111 ASP cc_start: 0.8638 (t0) cc_final: 0.8341 (t0) REVERT: H 129 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.7931 (ttp-170) REVERT: G 155 MET cc_start: 0.9208 (mmp) cc_final: 0.8921 (mmm) REVERT: G 157 GLN cc_start: 0.8627 (tt0) cc_final: 0.8342 (tt0) REVERT: G 168 TYR cc_start: 0.9143 (m-80) cc_final: 0.8887 (m-80) REVERT: F 385 GLU cc_start: 0.8666 (pm20) cc_final: 0.8403 (pm20) REVERT: E 88 MET cc_start: 0.9240 (mtm) cc_final: 0.9007 (mtp) REVERT: E 323 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8386 (ttm-80) REVERT: E 366 ARG cc_start: 0.8344 (mmm160) cc_final: 0.8069 (tpt90) REVERT: E 371 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8255 (ttpp) REVERT: D 381 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8367 (mm-30) REVERT: J 17 MET cc_start: 0.8516 (tpp) cc_final: 0.8047 (tpp) REVERT: J 57 MET cc_start: 0.8913 (tmm) cc_final: 0.8364 (tmm) REVERT: J 75 MET cc_start: 0.8378 (ttp) cc_final: 0.8084 (tmm) REVERT: L 6 MET cc_start: 0.7324 (ppp) cc_final: 0.6741 (ppp) REVERT: L 37 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8184 (mt-10) REVERT: L 41 ARG cc_start: 0.9000 (ttm110) cc_final: 0.7512 (ttp80) REVERT: L 52 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8548 (mm-40) REVERT: M 17 MET cc_start: 0.8700 (mmm) cc_final: 0.8004 (mtt) REVERT: M 42 GLN cc_start: 0.8678 (pt0) cc_final: 0.8280 (pp30) REVERT: M 61 ASP cc_start: 0.9068 (m-30) cc_final: 0.8105 (t0) REVERT: M 65 MET cc_start: 0.9308 (mmm) cc_final: 0.8444 (mmm) REVERT: M 75 MET cc_start: 0.8448 (tpp) cc_final: 0.8086 (tpp) REVERT: N 11 MET cc_start: 0.7760 (mmm) cc_final: 0.7236 (tpp) REVERT: N 17 MET cc_start: 0.8226 (tmm) cc_final: 0.7755 (tmm) REVERT: N 37 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: O 16 MET cc_start: 0.7097 (mmm) cc_final: 0.6739 (mmm) REVERT: O 41 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7483 (tpp-160) REVERT: P 31 LEU cc_start: 0.8034 (tp) cc_final: 0.7803 (tp) REVERT: P 42 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7542 (mp10) REVERT: P 50 ARG cc_start: 0.7680 (ptt180) cc_final: 0.7070 (ttm110) REVERT: P 73 TYR cc_start: 0.6342 (t80) cc_final: 0.5671 (t80) REVERT: P 76 PHE cc_start: 0.7079 (m-80) cc_final: 0.6660 (m-80) REVERT: Q 17 MET cc_start: 0.8087 (mmm) cc_final: 0.7608 (mpp) REVERT: Q 31 LEU cc_start: 0.8086 (tp) cc_final: 0.7852 (tt) REVERT: Q 37 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: Q 52 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8609 (mm-40) REVERT: Q 57 MET cc_start: 0.8687 (tmm) cc_final: 0.8388 (tmm) REVERT: R 6 MET cc_start: 0.7332 (mmt) cc_final: 0.6827 (mtm) REVERT: R 11 MET cc_start: 0.8726 (tpp) cc_final: 0.8510 (tpp) REVERT: R 55 ILE cc_start: 0.8861 (mm) cc_final: 0.8546 (mm) REVERT: R 57 MET cc_start: 0.8682 (ttp) cc_final: 0.8360 (tmm) REVERT: Y 1 MET cc_start: 0.4562 (ptt) cc_final: 0.3360 (mmm) REVERT: Y 64 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8644 (mm-40) REVERT: a 6 MET cc_start: 0.5604 (tmm) cc_final: 0.4196 (ptt) REVERT: a 91 LYS cc_start: 0.9322 (tppt) cc_final: 0.9074 (mmmm) REVERT: a 99 LYS cc_start: 0.8243 (mttm) cc_final: 0.7851 (ptpp) REVERT: I 35 PHE cc_start: 0.8759 (t80) cc_final: 0.8470 (t80) REVERT: I 73 TYR cc_start: 0.6781 (t80) cc_final: 0.6389 (t80) REVERT: I 74 VAL cc_start: 0.8547 (t) cc_final: 0.8225 (p) REVERT: S 6 MET cc_start: 0.7147 (mmt) cc_final: 0.6710 (mmp) REVERT: S 16 MET cc_start: 0.8987 (mmt) cc_final: 0.8297 (mmt) REVERT: S 65 MET cc_start: 0.8867 (mmt) cc_final: 0.8503 (mtm) outliers start: 68 outliers final: 54 residues processed: 650 average time/residue: 0.2121 time to fit residues: 224.8532 Evaluate side-chains 640 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 582 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain B residue 3 LEU 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 262 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP 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 83 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 273 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 357 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 450 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 114 optimal weight: 0.4980 chunk 337 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN W 119 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 252 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 = 0.3509 r_free = 0.3509 target = 0.100393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067174 restraints weight = 75835.843| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.15 r_work: 0.2781 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37506 Z= 0.121 Angle : 0.607 18.822 50766 Z= 0.301 Chirality : 0.043 0.274 5918 Planarity : 0.004 0.054 6547 Dihedral : 6.241 115.021 5352 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.62 % Allowed : 18.00 % Favored : 80.39 % 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: 1.16 (0.12), residues: 4805 helix: 1.69 (0.10), residues: 2598 sheet: -0.25 (0.21), residues: 527 loop : -0.25 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 50 TYR 0.027 0.001 TYR a 263 PHE 0.025 0.001 PHE J 53 TRP 0.028 0.001 TRP a 39 HIS 0.010 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00269 (37506) covalent geometry : angle 0.60745 (50766) hydrogen bonds : bond 0.04032 ( 2198) hydrogen bonds : angle 4.27511 ( 6444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 607 time to evaluate : 1.288 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 67 GLN cc_start: 0.8841 (mt0) cc_final: 0.8613 (mt0) REVERT: W 141 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8655 (mmmm) REVERT: W 156 ASP cc_start: 0.8203 (p0) cc_final: 0.7671 (p0) REVERT: C 402 GLU cc_start: 0.8979 (tp30) cc_final: 0.8642 (tp30) REVERT: C 412 ASP cc_start: 0.8349 (t0) cc_final: 0.8047 (t0) REVERT: B 402 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 343 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9320 (p) REVERT: A 463 LYS cc_start: 0.5119 (tmtt) cc_final: 0.4550 (tmtt) REVERT: X 104 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8853 (pp30) REVERT: X 112 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: H 49 MET cc_start: 0.9221 (mmt) cc_final: 0.8869 (mmm) REVERT: H 111 ASP cc_start: 0.8628 (t0) cc_final: 0.8324 (t0) REVERT: G 155 MET cc_start: 0.9188 (mmp) cc_final: 0.8894 (mmm) REVERT: G 157 GLN cc_start: 0.8640 (tt0) cc_final: 0.8329 (tt0) REVERT: G 168 TYR cc_start: 0.9089 (m-80) cc_final: 0.8817 (m-80) REVERT: F 385 GLU cc_start: 0.8641 (pm20) cc_final: 0.8388 (pm20) REVERT: E 0 MET cc_start: 0.6786 (pmm) cc_final: 0.6501 (ttp) REVERT: E 323 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8419 (ttm-80) REVERT: E 366 ARG cc_start: 0.8307 (mmm160) cc_final: 0.8043 (tpt90) REVERT: E 371 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8255 (ttpp) REVERT: E 376 ILE cc_start: 0.8538 (tt) cc_final: 0.8319 (tt) REVERT: D 381 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8358 (mm-30) REVERT: J 17 MET cc_start: 0.8432 (tpp) cc_final: 0.7885 (tpp) REVERT: J 57 MET cc_start: 0.8867 (tmm) cc_final: 0.8329 (tmm) REVERT: J 75 MET cc_start: 0.8358 (ttp) cc_final: 0.8148 (tmm) REVERT: L 6 MET cc_start: 0.7179 (ppp) cc_final: 0.6526 (ppp) REVERT: L 52 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8573 (mm-40) REVERT: L 61 ASP cc_start: 0.7972 (p0) cc_final: 0.7625 (p0) REVERT: M 17 MET cc_start: 0.8707 (mmm) cc_final: 0.7991 (mtt) REVERT: M 42 GLN cc_start: 0.8586 (pt0) cc_final: 0.8236 (pp30) REVERT: M 61 ASP cc_start: 0.9036 (m-30) cc_final: 0.8080 (t0) REVERT: M 65 MET cc_start: 0.9283 (mmm) cc_final: 0.8419 (mmm) REVERT: M 75 MET cc_start: 0.8452 (tpp) cc_final: 0.8033 (tpp) REVERT: N 11 MET cc_start: 0.7785 (mmm) cc_final: 0.7326 (tpp) REVERT: N 37 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: O 16 MET cc_start: 0.6930 (mmm) cc_final: 0.6594 (mmm) REVERT: O 41 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: P 31 LEU cc_start: 0.8049 (tp) cc_final: 0.7838 (tp) REVERT: P 42 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7601 (mp10) REVERT: P 50 ARG cc_start: 0.7661 (ptt180) cc_final: 0.6945 (ttp-110) REVERT: P 73 TYR cc_start: 0.6201 (t80) cc_final: 0.5475 (t80) REVERT: P 76 PHE cc_start: 0.7013 (m-80) cc_final: 0.6595 (m-80) REVERT: Q 31 LEU cc_start: 0.8010 (tp) cc_final: 0.7777 (tt) REVERT: Q 37 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: Q 52 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8637 (mm-40) REVERT: Q 57 MET cc_start: 0.8675 (tmm) cc_final: 0.8373 (tmm) REVERT: R 11 MET cc_start: 0.8705 (tpp) cc_final: 0.8491 (tpp) REVERT: R 16 MET cc_start: 0.8286 (mtp) cc_final: 0.7770 (ttp) REVERT: R 55 ILE cc_start: 0.8852 (mm) cc_final: 0.8539 (mm) REVERT: R 57 MET cc_start: 0.8650 (ttp) cc_final: 0.8321 (tmm) REVERT: R 75 MET cc_start: 0.8671 (tpp) cc_final: 0.8394 (tpt) REVERT: Y 1 MET cc_start: 0.4458 (ptt) cc_final: 0.3306 (mmm) REVERT: Y 22 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.4924 (mmp) REVERT: Y 83 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7792 (ptm-80) REVERT: a 6 MET cc_start: 0.5659 (tmm) cc_final: 0.4168 (ptt) REVERT: a 91 LYS cc_start: 0.9255 (tppt) cc_final: 0.9001 (mmmm) REVERT: a 99 LYS cc_start: 0.8123 (mttm) cc_final: 0.7761 (ptpp) REVERT: a 215 MET cc_start: 0.9208 (mmm) cc_final: 0.8799 (mmm) REVERT: I 35 PHE cc_start: 0.8784 (t80) cc_final: 0.8448 (t80) REVERT: I 73 TYR cc_start: 0.6842 (t80) cc_final: 0.6604 (t80) REVERT: I 74 VAL cc_start: 0.8588 (t) cc_final: 0.8315 (p) REVERT: S 6 MET cc_start: 0.7125 (mmt) cc_final: 0.6494 (mmp) REVERT: S 16 MET cc_start: 0.8946 (mmt) cc_final: 0.8330 (mmt) REVERT: S 65 MET cc_start: 0.8816 (mmt) cc_final: 0.8469 (mtm) outliers start: 62 outliers final: 49 residues processed: 648 average time/residue: 0.2055 time to fit residues: 218.6739 Evaluate side-chains 632 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 578 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 60 optimal weight: 1.9990 chunk 418 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 429 optimal weight: 6.9990 chunk 466 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 303 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 325 optimal weight: 0.0370 chunk 76 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN a 15 HIS ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067969 restraints weight = 75259.817| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.14 r_work: 0.2805 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37506 Z= 0.117 Angle : 0.612 19.547 50766 Z= 0.302 Chirality : 0.043 0.263 5918 Planarity : 0.004 0.059 6547 Dihedral : 6.126 114.645 5352 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.51 % Allowed : 18.49 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 4805 helix: 1.74 (0.10), residues: 2599 sheet: -0.17 (0.21), residues: 527 loop : -0.17 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 50 TYR 0.032 0.001 TYR a 263 PHE 0.021 0.001 PHE Q 35 TRP 0.028 0.001 TRP a 39 HIS 0.010 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00256 (37506) covalent geometry : angle 0.61210 (50766) hydrogen bonds : bond 0.03984 ( 2198) hydrogen bonds : angle 4.24197 ( 6444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12012.38 seconds wall clock time: 204 minutes 45.59 seconds (12285.59 seconds total)