Starting phenix.real_space_refine on Sat Mar 7 02:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wnq_21854/03_2026/6wnq_21854.map" } resolution = 3.4 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 23522 2.51 5 N 6325 2.21 5 O 6976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 283 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37024 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} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "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: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 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: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.09, per 1000 atoms: 0.22 Number of scatterers: 37024 At special positions: 0 Unit cell: (183.43, 214.721, 131.638, 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 6976 8.00 N 6325 7.00 C 23522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8830 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 27 sheets defined 61.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.847A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.765A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.884A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 82 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 104 removed outlier: 3.709A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 162 through 172 Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.539A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.751A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.737A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.724A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.131A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 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: 3.736A 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 Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.532A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.087A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 4.067A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 4.679A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.551A pdb=" N ALA C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.122A 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 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.836A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 190 removed outlier: 3.880A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 231 through 251 Proline residue: B 239 - end of helix removed outlier: 3.698A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.764A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.855A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.524A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.558A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.746A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.942A pdb=" N LYS B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 510 Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.713A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.520A 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 251 Proline residue: A 239 - end of helix removed outlier: 4.120A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.646A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.504A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.704A 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 339 through 347 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.037A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.919A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 4.221A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.535A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.620A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'X' and resid 5 through 25 Processing helix chain 'X' and resid 25 through 137 removed outlier: 3.720A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 155 removed outlier: 4.198A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.659A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.664A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.918A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 57 removed outlier: 3.804A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 107 Processing helix chain 'G' and resid 118 through 128 removed outlier: 3.636A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.629A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 198 through 203 removed outlier: 4.023A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 281 removed outlier: 3.580A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.518A 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 130 through 137 Processing helix chain 'F' and resid 156 through 168 removed outlier: 3.802A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.589A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) 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: 3.589A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.876A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.252A 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: 3.718A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 3.556A pdb=" N LEU F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 382 removed outlier: 3.606A 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 removed outlier: 3.710A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 removed outlier: 3.676A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.560A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.512A 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: 3.532A 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 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.534A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.603A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.977A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 4.184A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 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 443 Processing helix chain 'E' and resid 448 through 458 removed outlier: 4.264A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 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: 5.094A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 259 Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.697A 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 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 removed outlier: 4.379A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.909A 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 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 444 removed outlier: 4.001A pdb=" N PHE D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 444' Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.982A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 6 Processing helix chain 'I' and resid 7 through 42 removed outlier: 3.554A pdb=" N VAL I 15 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.535A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.030A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.161A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.073A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.545A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.749A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.254A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 77 Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.887A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.610A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.751A pdb=" N LEU O 8 " --> pdb=" O LEU O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 77 removed outlier: 3.600A pdb=" N ILE O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL O 56 " --> pdb=" O GLN O 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 5 through 42 removed outlier: 4.052A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 61 removed outlier: 4.483A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 77 Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.871A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.740A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.919A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 4 through 42 removed outlier: 4.660A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.565A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'Y' and resid 2 through 25 Processing helix chain 'Y' and resid 25 through 117 removed outlier: 3.651A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 140 Processing helix chain 'Y' and resid 141 through 156 Processing helix chain 'a' and resid 7 through 17 removed outlier: 4.234A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 67 Processing helix chain 'a' and resid 73 through 94 Processing helix chain 'a' and resid 100 through 119 removed outlier: 3.951A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 146 through 169 removed outlier: 3.771A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 180 removed outlier: 3.833A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.703A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.798A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.833A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.779A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 6.943A pdb=" N ALA W 106 " --> pdb=" O LYS W 137 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN W 139 " --> pdb=" O ALA W 106 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL W 108 " --> pdb=" O ASN W 139 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS W 141 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL W 110 " --> pdb=" O LYS W 141 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 27 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.514A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.535A pdb=" N VAL C 108 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 8.015A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.315A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 66 removed outlier: 6.527A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 35 removed outlier: 4.761A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 9 removed outlier: 3.821A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 89 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS A 42 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AB3, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.341A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.809A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.681A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.889A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.399A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA H 44 " --> pdb=" O GLU G 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.590A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR G 168 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU G 187 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL G 170 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER G 185 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASN G 172 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR G 183 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE G 174 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL G 181 " --> pdb=" O PHE G 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.619A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.351A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.828A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.755A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.182A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.199A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.632A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.345A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 20 through 22 2319 hydrogen bonds defined for protein. 6738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8260 1.32 - 1.45: 7282 1.45 - 1.57: 21658 1.57 - 1.69: 24 1.69 - 1.82: 360 Bond restraints: 37584 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.07e+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 4.30e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.91e+01 bond pdb=" C5 ATP C 600 " pdb=" N7 ATP C 600 " ideal model delta sigma weight residual 1.387 1.329 0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 37579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 50577 4.79 - 9.58: 281 9.58 - 14.37: 10 14.37 - 19.15: 2 19.15 - 23.94: 4 Bond angle restraints: 50874 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 115.93 23.94 1.00e+00 1.00e+00 5.73e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.49 22.38 1.00e+00 1.00e+00 5.01e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.84 19.99 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 117.69 19.14 1.00e+00 1.00e+00 3.66e+02 ... (remaining 50869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 22352 34.82 - 69.65: 409 69.65 - 104.47: 56 104.47 - 139.30: 1 139.30 - 174.12: 4 Dihedral angle restraints: 22822 sinusoidal: 9020 harmonic: 13802 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.12 -174.12 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 151.00 149.01 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 86.42 -146.41 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 22819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5350 0.100 - 0.201: 528 0.201 - 0.301: 40 0.301 - 0.401: 5 0.401 - 0.502: 4 Chirality restraints: 5927 Sorted by residual: chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA PHE R 76 " pdb=" N PHE R 76 " pdb=" C PHE R 76 " pdb=" CB PHE R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE I 63 " pdb=" CA ILE I 63 " pdb=" CG1 ILE I 63 " pdb=" CG2 ILE I 63 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 5924 not shown) Planarity restraints: 6559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 111 " -0.118 9.50e-02 1.11e+02 7.34e-02 3.42e+01 pdb=" NE ARG E 111 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG E 111 " -0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG E 111 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG E 111 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 24 " 0.154 9.50e-02 1.11e+02 8.07e-02 2.48e+01 pdb=" NE ARG D 24 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 24 " 0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG D 24 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG D 24 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 68 " 0.269 9.50e-02 1.11e+02 1.25e-01 2.14e+01 pdb=" NE ARG C 68 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG C 68 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 68 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 68 " 0.030 2.00e-02 2.50e+03 ... (remaining 6556 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 47 2.40 - 3.03: 23711 3.03 - 3.65: 54858 3.65 - 4.28: 82941 4.28 - 4.90: 141108 Nonbonded interactions: 302665 Sorted by model distance: nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.781 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.789 2.170 nonbonded pdb=" O3B ATP B 600 " pdb="MG MG B 601 " model vdw 1.805 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.887 2.170 nonbonded pdb=" O3B ADP F 500 " pdb="MG MG F 501 " model vdw 1.908 2.170 ... (remaining 302660 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 0 through 500) selection = chain 'E' selection = (chain 'F' and resid 0 through 500) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.820 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.012 0.108 37584 Z= 0.530 Angle : 1.163 23.943 50874 Z= 0.720 Chirality : 0.063 0.502 5927 Planarity : 0.008 0.125 6559 Dihedral : 14.620 174.120 13992 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 2.16 % Allowed : 5.94 % Favored : 91.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.10), residues: 4813 helix: -0.88 (0.09), residues: 2579 sheet: -0.73 (0.21), residues: 504 loop : -1.24 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.007 ARG E 111 TYR 0.049 0.005 TYR D 26 PHE 0.040 0.004 PHE B 449 TRP 0.035 0.004 TRP X 26 HIS 0.017 0.003 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.01154 (37584) covalent geometry : angle 1.16305 (50874) hydrogen bonds : bond 0.14940 ( 2315) hydrogen bonds : angle 6.75204 ( 6738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 940 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 16 ASP cc_start: 0.8542 (m-30) cc_final: 0.8258 (m-30) REVERT: W 111 ILE cc_start: 0.9492 (mt) cc_final: 0.9221 (tp) REVERT: B 261 ASP cc_start: 0.7775 (t70) cc_final: 0.7404 (t70) REVERT: B 425 GLN cc_start: 0.8584 (tt0) cc_final: 0.8279 (tt0) REVERT: B 481 PRO cc_start: 0.8764 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: A 386 MET cc_start: 0.9132 (mmm) cc_final: 0.8880 (mmm) REVERT: H 46 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8693 (mtmm) REVERT: H 55 GLN cc_start: 0.8248 (pt0) cc_final: 0.7381 (pp30) REVERT: H 111 ASP cc_start: 0.9220 (t0) cc_final: 0.8761 (t0) REVERT: G 68 GLU cc_start: 0.8539 (pt0) cc_final: 0.8138 (pp20) REVERT: G 105 TRP cc_start: 0.8023 (m100) cc_final: 0.7785 (m100) REVERT: E 328 LEU cc_start: 0.9231 (mt) cc_final: 0.8952 (tp) REVERT: E 330 ILE cc_start: 0.8948 (mt) cc_final: 0.8675 (mm) REVERT: E 397 GLN cc_start: 0.8626 (tt0) cc_final: 0.8401 (tm-30) REVERT: I 10 TYR cc_start: 0.7013 (m-10) cc_final: 0.6734 (m-10) REVERT: I 17 MET cc_start: 0.8349 (ptp) cc_final: 0.7987 (mpp) REVERT: I 34 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8629 (mmtp) REVERT: I 35 PHE cc_start: 0.8653 (t80) cc_final: 0.8384 (t80) REVERT: I 42 GLN cc_start: 0.8167 (mm110) cc_final: 0.7833 (mp10) REVERT: I 46 ILE cc_start: 0.9256 (mt) cc_final: 0.9036 (mm) REVERT: I 60 VAL cc_start: 0.7697 (t) cc_final: 0.7444 (t) REVERT: I 73 TYR cc_start: 0.7404 (t80) cc_final: 0.7171 (t80) REVERT: I 74 VAL cc_start: 0.8790 (t) cc_final: 0.8569 (t) REVERT: J 10 TYR cc_start: 0.4704 (m-80) cc_final: 0.4467 (m-80) REVERT: J 11 MET cc_start: 0.6607 (tpp) cc_final: 0.6288 (tmm) REVERT: J 46 ILE cc_start: 0.7645 (mt) cc_final: 0.7410 (mt) REVERT: J 55 ILE cc_start: 0.8689 (mm) cc_final: 0.8400 (mm) REVERT: J 65 MET cc_start: 0.8801 (mmt) cc_final: 0.8496 (mmp) REVERT: M 17 MET cc_start: 0.6698 (mtm) cc_final: 0.6173 (ttm) REVERT: M 35 PHE cc_start: 0.8589 (t80) cc_final: 0.8235 (t80) REVERT: M 50 ARG cc_start: 0.7100 (ttm170) cc_final: 0.6680 (tmt170) REVERT: M 53 PHE cc_start: 0.8519 (t80) cc_final: 0.8017 (t80) REVERT: M 54 PHE cc_start: 0.6850 (m-80) cc_final: 0.6384 (m-80) REVERT: M 56 VAL cc_start: 0.8903 (t) cc_final: 0.8698 (p) REVERT: N 34 LYS cc_start: 0.8515 (mmtm) cc_final: 0.7886 (mmmt) REVERT: N 46 ILE cc_start: 0.7934 (mt) cc_final: 0.7717 (mt) REVERT: O 6 MET cc_start: 0.6816 (ttm) cc_final: 0.6109 (ttt) REVERT: O 34 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7817 (mmmm) REVERT: O 45 LEU cc_start: 0.9065 (mt) cc_final: 0.8731 (mp) REVERT: O 74 VAL cc_start: 0.8980 (t) cc_final: 0.8779 (p) REVERT: P 34 LYS cc_start: 0.8504 (mmtm) cc_final: 0.7907 (mmmm) REVERT: P 42 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8378 (mm110) REVERT: P 65 MET cc_start: 0.8295 (mmm) cc_final: 0.7880 (mmt) REVERT: P 73 TYR cc_start: 0.6941 (t80) cc_final: 0.6707 (t80) REVERT: Q 17 MET cc_start: 0.7822 (mtm) cc_final: 0.7362 (mtm) REVERT: Q 35 PHE cc_start: 0.8724 (t80) cc_final: 0.8466 (t80) REVERT: Q 73 TYR cc_start: 0.5140 (t80) cc_final: 0.4348 (t80) REVERT: R 51 THR cc_start: 0.8794 (m) cc_final: 0.8537 (m) REVERT: R 55 ILE cc_start: 0.8618 (mm) cc_final: 0.8354 (mp) REVERT: S 34 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7782 (mmtt) REVERT: Y 74 VAL cc_start: 0.8660 (t) cc_final: 0.8449 (t) REVERT: a 94 TYR cc_start: 0.6330 (t80) cc_final: 0.5992 (t80) REVERT: a 113 PHE cc_start: 0.8618 (t80) cc_final: 0.8106 (t80) REVERT: a 118 MET cc_start: 0.8188 (tpp) cc_final: 0.7937 (tpt) REVERT: a 186 TRP cc_start: 0.3848 (OUTLIER) cc_final: 0.2679 (t60) REVERT: a 210 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7919 (ttp-110) REVERT: a 248 ILE cc_start: 0.8780 (mm) cc_final: 0.8568 (mt) outliers start: 83 outliers final: 35 residues processed: 1009 average time/residue: 0.2414 time to fit residues: 386.6047 Evaluate side-chains 594 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 558 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 186 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 2.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN W 82 ASN C 14 GLN C 20 ASN C 27 ASN C 333 GLN C 369 ASN B 58 ASN ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN A 140 GLN A 147 GLN A 344 ASN X 4 ASN X 73 GLN H 58 HIS F 35 ASN F 441 GLN E 351 GLN D 73 HIS D 170 HIS J 52 GLN O 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 HIS a 184 ASN a 245 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068266 restraints weight = 98328.018| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.45 r_work: 0.2935 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37584 Z= 0.197 Angle : 0.714 12.139 50874 Z= 0.369 Chirality : 0.046 0.289 5927 Planarity : 0.004 0.043 6559 Dihedral : 8.361 174.214 5399 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 11.72 % Favored : 85.26 % 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: 0.25 (0.12), residues: 4813 helix: 0.88 (0.10), residues: 2584 sheet: -0.39 (0.21), residues: 509 loop : -0.61 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 49 TYR 0.018 0.002 TYR C 236 PHE 0.026 0.002 PHE a 56 TRP 0.015 0.002 TRP a 235 HIS 0.008 0.001 HIS W 97 Details of bonding type rmsd covalent geometry : bond 0.00450 (37584) covalent geometry : angle 0.71395 (50874) hydrogen bonds : bond 0.05815 ( 2315) hydrogen bonds : angle 5.01444 ( 6738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 656 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9343 (tppt) cc_final: 0.8483 (tptp) REVERT: W 16 ASP cc_start: 0.8922 (m-30) cc_final: 0.8708 (m-30) REVERT: C 67 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8541 (mt-10) REVERT: C 411 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8410 (p) REVERT: C 463 LYS cc_start: 0.9298 (tppt) cc_final: 0.9065 (tppp) REVERT: B 68 ARG cc_start: 0.8914 (ttt-90) cc_final: 0.8613 (ttp80) REVERT: B 237 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9044 (mt) REVERT: B 395 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8209 (t) REVERT: B 425 GLN cc_start: 0.8753 (tt0) cc_final: 0.8230 (tt0) REVERT: B 429 GLU cc_start: 0.8691 (tp30) cc_final: 0.8330 (pt0) REVERT: A 513 TRP cc_start: 0.7039 (OUTLIER) cc_final: 0.6279 (m100) REVERT: X 35 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8268 (tptp) REVERT: X 53 ASP cc_start: 0.8665 (t0) cc_final: 0.8451 (t70) REVERT: X 55 ASP cc_start: 0.8212 (m-30) cc_final: 0.7980 (p0) REVERT: X 85 GLN cc_start: 0.8709 (mm110) cc_final: 0.8194 (mm110) REVERT: H 51 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7594 (mtp-110) REVERT: H 60 GLU cc_start: 0.8284 (pt0) cc_final: 0.7783 (pm20) REVERT: H 87 GLN cc_start: 0.8296 (tp40) cc_final: 0.8086 (tp-100) REVERT: H 111 ASP cc_start: 0.9022 (t0) cc_final: 0.8478 (t0) REVERT: G 68 GLU cc_start: 0.9018 (pt0) cc_final: 0.8366 (pp20) REVERT: G 105 TRP cc_start: 0.8168 (m100) cc_final: 0.7961 (m100) REVERT: G 173 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8840 (ttpp) REVERT: E 335 ASP cc_start: 0.8753 (t0) cc_final: 0.8515 (t70) REVERT: D 345 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7805 (p0) REVERT: I 10 TYR cc_start: 0.7113 (m-10) cc_final: 0.6708 (m-10) REVERT: I 11 MET cc_start: 0.6657 (tpp) cc_final: 0.5990 (tmm) REVERT: I 37 GLU cc_start: 0.8863 (tp30) cc_final: 0.8610 (mt-10) REVERT: J 10 TYR cc_start: 0.4866 (m-80) cc_final: 0.4660 (m-80) REVERT: J 55 ILE cc_start: 0.8451 (mm) cc_final: 0.8237 (mm) REVERT: J 65 MET cc_start: 0.8552 (mmt) cc_final: 0.8302 (mmp) REVERT: L 37 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7053 (mm-30) REVERT: M 17 MET cc_start: 0.6912 (mtm) cc_final: 0.5990 (ttm) REVERT: M 35 PHE cc_start: 0.8559 (t80) cc_final: 0.8275 (t80) REVERT: M 41 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7804 (ttm-80) REVERT: N 34 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8009 (mmmt) REVERT: N 65 MET cc_start: 0.7949 (mmm) cc_final: 0.7686 (mmt) REVERT: O 6 MET cc_start: 0.6466 (ttm) cc_final: 0.4772 (ttp) REVERT: O 10 TYR cc_start: 0.7403 (m-80) cc_final: 0.6547 (m-80) REVERT: O 34 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7726 (mmmm) REVERT: P 11 MET cc_start: 0.8356 (tpp) cc_final: 0.8108 (tpp) REVERT: P 17 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7218 (ppp) REVERT: P 34 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7620 (mmmm) REVERT: P 52 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8665 (mm-40) REVERT: P 65 MET cc_start: 0.8148 (mmm) cc_final: 0.7870 (mmt) REVERT: Q 34 LYS cc_start: 0.9049 (tppt) cc_final: 0.8549 (tppt) REVERT: Q 73 TYR cc_start: 0.5406 (t80) cc_final: 0.4461 (t80) REVERT: R 34 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8189 (ttpt) REVERT: R 55 ILE cc_start: 0.8592 (mm) cc_final: 0.8327 (mp) REVERT: S 34 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8011 (mmtt) REVERT: Y 49 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8067 (tpm170) REVERT: Y 53 ASP cc_start: 0.7099 (m-30) cc_final: 0.6754 (m-30) REVERT: a 16 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8379 (tt) REVERT: a 94 TYR cc_start: 0.7076 (t80) cc_final: 0.6741 (t80) REVERT: a 117 LEU cc_start: 0.9069 (mt) cc_final: 0.8736 (mt) REVERT: a 118 MET cc_start: 0.8767 (tpp) cc_final: 0.8480 (tpt) REVERT: a 153 MET cc_start: 0.9234 (mmp) cc_final: 0.8952 (mmp) REVERT: a 186 TRP cc_start: 0.3644 (OUTLIER) cc_final: 0.2519 (t60) REVERT: a 210 ARG cc_start: 0.8419 (ttm110) cc_final: 0.7892 (ttp-110) REVERT: a 241 TRP cc_start: 0.8273 (t-100) cc_final: 0.7976 (t-100) REVERT: a 257 MET cc_start: 0.8682 (tmm) cc_final: 0.8400 (tmm) REVERT: a 266 MET cc_start: 0.7747 (ptm) cc_final: 0.7514 (ptm) outliers start: 116 outliers final: 52 residues processed: 738 average time/residue: 0.2182 time to fit residues: 263.0360 Evaluate side-chains 597 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 536 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 76 PHE Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 314 optimal weight: 0.0770 chunk 379 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN G 54 HIS G 176 ASN E 353 HIS J 42 GLN Q 5 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS a 148 ASN a 185 HIS a 245 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069339 restraints weight = 97990.183| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.63 r_work: 0.2940 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37584 Z= 0.151 Angle : 0.633 9.473 50874 Z= 0.325 Chirality : 0.043 0.292 5927 Planarity : 0.004 0.045 6559 Dihedral : 7.650 178.096 5367 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.73 % Allowed : 14.01 % Favored : 83.26 % 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: 0.84 (0.12), residues: 4813 helix: 1.39 (0.10), residues: 2581 sheet: -0.20 (0.22), residues: 502 loop : -0.37 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.024 0.001 TYR O 73 PHE 0.027 0.001 PHE a 75 TRP 0.015 0.001 TRP a 235 HIS 0.006 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00334 (37584) covalent geometry : angle 0.63254 (50874) hydrogen bonds : bond 0.05210 ( 2315) hydrogen bonds : angle 4.68068 ( 6738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 597 time to evaluate : 1.173 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: 0.9336 (tppt) cc_final: 0.8396 (tptp) REVERT: W 16 ASP cc_start: 0.8789 (m-30) cc_final: 0.8568 (m-30) REVERT: W 43 MET cc_start: 0.8929 (tpt) cc_final: 0.8713 (tpp) REVERT: C 262 ASP cc_start: 0.8734 (m-30) cc_final: 0.8472 (m-30) REVERT: C 265 LYS cc_start: 0.9247 (mttm) cc_final: 0.8974 (mttt) REVERT: C 463 LYS cc_start: 0.9234 (tppt) cc_final: 0.8883 (tppp) REVERT: B 356 GLU cc_start: 0.8399 (tp30) cc_final: 0.8168 (tp30) REVERT: B 456 LEU cc_start: 0.6326 (mt) cc_final: 0.5655 (pt) REVERT: B 463 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8133 (mtpp) REVERT: A 386 MET cc_start: 0.9216 (mmm) cc_final: 0.8913 (mtp) REVERT: A 513 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6177 (m100) REVERT: X 22 MET cc_start: 0.6611 (ptt) cc_final: 0.6124 (ptt) REVERT: X 55 ASP cc_start: 0.8259 (m-30) cc_final: 0.7981 (p0) REVERT: X 115 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8315 (mtm-85) REVERT: H 81 ASP cc_start: 0.7613 (p0) cc_final: 0.7391 (p0) REVERT: H 111 ASP cc_start: 0.9026 (t0) cc_final: 0.8497 (t0) REVERT: H 132 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: G 68 GLU cc_start: 0.8803 (pt0) cc_final: 0.8084 (pp20) REVERT: F 343 GLN cc_start: 0.8407 (mp10) cc_final: 0.8018 (mp10) REVERT: F 445 MET cc_start: 0.8854 (tpp) cc_final: 0.8646 (mpp) REVERT: E 328 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8976 (tp) REVERT: E 335 ASP cc_start: 0.8555 (t0) cc_final: 0.8286 (t70) REVERT: E 370 LEU cc_start: 0.8702 (mt) cc_final: 0.8436 (mp) REVERT: E 377 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7650 (mm) REVERT: D 335 ASP cc_start: 0.9081 (t0) cc_final: 0.8787 (t70) REVERT: I 11 MET cc_start: 0.6606 (tpp) cc_final: 0.5809 (tmm) REVERT: I 17 MET cc_start: 0.8231 (mtt) cc_final: 0.7853 (mpp) REVERT: I 35 PHE cc_start: 0.8712 (t80) cc_final: 0.8452 (t80) REVERT: I 41 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8174 (mmm160) REVERT: I 42 GLN cc_start: 0.8032 (mm110) cc_final: 0.7607 (mp10) REVERT: I 75 MET cc_start: 0.8644 (mmm) cc_final: 0.8407 (mmm) REVERT: J 50 ARG cc_start: 0.7854 (ptp-110) cc_final: 0.7607 (ptm160) REVERT: L 17 MET cc_start: 0.6834 (tpp) cc_final: 0.6500 (tpp) REVERT: M 17 MET cc_start: 0.6838 (mtm) cc_final: 0.6058 (ttm) REVERT: M 41 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7920 (ttm-80) REVERT: M 50 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6534 (ttm-80) REVERT: N 34 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7980 (mmmt) REVERT: N 65 MET cc_start: 0.7994 (mmm) cc_final: 0.7692 (mmt) REVERT: N 70 LEU cc_start: 0.8424 (mt) cc_final: 0.8047 (tp) REVERT: O 6 MET cc_start: 0.6252 (ttm) cc_final: 0.4909 (ttt) REVERT: O 10 TYR cc_start: 0.7518 (m-80) cc_final: 0.7005 (m-80) REVERT: O 34 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7709 (mmmm) REVERT: P 11 MET cc_start: 0.8387 (tpp) cc_final: 0.8104 (tpp) REVERT: P 52 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8307 (mm-40) REVERT: P 65 MET cc_start: 0.8207 (mmm) cc_final: 0.7858 (mmt) REVERT: Q 17 MET cc_start: 0.6822 (mtt) cc_final: 0.5954 (mmp) REVERT: Q 34 LYS cc_start: 0.8972 (tppt) cc_final: 0.8614 (tppt) REVERT: Q 73 TYR cc_start: 0.5507 (t80) cc_final: 0.4576 (t80) REVERT: R 16 MET cc_start: 0.7201 (ptm) cc_final: 0.6593 (tmm) REVERT: R 55 ILE cc_start: 0.8553 (mm) cc_final: 0.8281 (mt) REVERT: Y 49 ARG cc_start: 0.8502 (tpp-160) cc_final: 0.8289 (tpp-160) REVERT: a 16 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8539 (tt) REVERT: a 92 ASP cc_start: 0.8682 (p0) cc_final: 0.7504 (p0) REVERT: a 94 TYR cc_start: 0.7238 (t80) cc_final: 0.6615 (t80) REVERT: a 118 MET cc_start: 0.8798 (tpp) cc_final: 0.8455 (tpt) REVERT: a 153 MET cc_start: 0.9221 (mmp) cc_final: 0.8948 (mmp) REVERT: a 186 TRP cc_start: 0.3585 (p90) cc_final: 0.2396 (t60) REVERT: a 241 TRP cc_start: 0.8243 (t-100) cc_final: 0.8002 (t-100) outliers start: 105 outliers final: 58 residues processed: 665 average time/residue: 0.2140 time to fit residues: 234.5167 Evaluate side-chains 587 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 251 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 442 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 450 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 ASN C 479 HIS A 479 HIS H 56 HIS G 64 HIS F 121 ASN F 170 HIS J 42 GLN ** Y 10 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 = 0.3593 r_free = 0.3593 target = 0.094034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067335 restraints weight = 98426.714| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.54 r_work: 0.2902 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37584 Z= 0.222 Angle : 0.664 14.210 50874 Z= 0.340 Chirality : 0.045 0.237 5927 Planarity : 0.004 0.053 6559 Dihedral : 7.515 176.330 5364 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.46 % Allowed : 14.87 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.12), residues: 4813 helix: 1.46 (0.10), residues: 2589 sheet: -0.29 (0.22), residues: 524 loop : -0.34 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 51 TYR 0.019 0.002 TYR F 297 PHE 0.029 0.002 PHE Q 35 TRP 0.014 0.001 TRP a 235 HIS 0.019 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00518 (37584) covalent geometry : angle 0.66378 (50874) hydrogen bonds : bond 0.05183 ( 2315) hydrogen bonds : angle 4.69860 ( 6738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 544 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: symmetry clash REVERT: W 12 LYS cc_start: 0.9460 (tppt) cc_final: 0.8654 (tptp) REVERT: W 16 ASP cc_start: 0.9133 (m-30) cc_final: 0.8780 (m-30) REVERT: C 262 ASP cc_start: 0.9007 (m-30) cc_final: 0.8774 (m-30) REVERT: C 265 LYS cc_start: 0.9353 (mttm) cc_final: 0.9072 (mttt) REVERT: C 343 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8945 (p) REVERT: C 463 LYS cc_start: 0.9293 (tppt) cc_final: 0.8966 (tppp) REVERT: B 237 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9028 (mt) REVERT: B 456 LEU cc_start: 0.6336 (mt) cc_final: 0.5672 (pt) REVERT: B 463 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8199 (mtpp) REVERT: A 513 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.6148 (m100) REVERT: X 22 MET cc_start: 0.6460 (ptt) cc_final: 0.6053 (ptt) REVERT: X 55 ASP cc_start: 0.8322 (m-30) cc_final: 0.7992 (p0) REVERT: X 115 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: H 81 ASP cc_start: 0.7835 (p0) cc_final: 0.7606 (p0) REVERT: H 111 ASP cc_start: 0.9110 (t0) cc_final: 0.8579 (t0) REVERT: G 68 GLU cc_start: 0.9041 (pt0) cc_final: 0.8145 (pp20) REVERT: G 180 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8116 (mp-120) REVERT: G 198 LEU cc_start: 0.8156 (mt) cc_final: 0.7682 (tp) REVERT: F 343 GLN cc_start: 0.8734 (mp10) cc_final: 0.8474 (mp10) REVERT: F 445 MET cc_start: 0.9092 (tpp) cc_final: 0.8832 (mpp) REVERT: E 125 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9083 (mp) REVERT: E 328 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8965 (tp) REVERT: E 335 ASP cc_start: 0.8808 (t0) cc_final: 0.8532 (t0) REVERT: E 377 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7631 (mm) REVERT: D 122 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8458 (p) REVERT: D 243 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: D 335 ASP cc_start: 0.9171 (t0) cc_final: 0.8846 (t70) REVERT: I 11 MET cc_start: 0.6362 (tpp) cc_final: 0.5712 (tmm) REVERT: I 17 MET cc_start: 0.8400 (mtt) cc_final: 0.8137 (tpp) REVERT: I 41 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8365 (mmm160) REVERT: I 42 GLN cc_start: 0.8118 (mm110) cc_final: 0.7673 (mp10) REVERT: I 75 MET cc_start: 0.8838 (mmm) cc_final: 0.8616 (mmm) REVERT: J 50 ARG cc_start: 0.7945 (ptp-110) cc_final: 0.7655 (ptm160) REVERT: L 16 MET cc_start: 0.6016 (ptp) cc_final: 0.5557 (tpp) REVERT: L 17 MET cc_start: 0.6642 (tpp) cc_final: 0.6251 (tpp) REVERT: M 11 MET cc_start: 0.8236 (mmm) cc_final: 0.7635 (mmm) REVERT: M 17 MET cc_start: 0.6543 (mtm) cc_final: 0.5744 (ttm) REVERT: N 34 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7907 (mmmt) REVERT: N 37 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8210 (tm-30) REVERT: N 70 LEU cc_start: 0.8357 (mt) cc_final: 0.7953 (tp) REVERT: O 6 MET cc_start: 0.6236 (ttm) cc_final: 0.5031 (ttt) REVERT: O 10 TYR cc_start: 0.7613 (m-80) cc_final: 0.7201 (m-80) REVERT: O 17 MET cc_start: 0.7386 (mtt) cc_final: 0.7132 (mtt) REVERT: O 28 ILE cc_start: 0.8326 (mm) cc_final: 0.7975 (mm) REVERT: O 34 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7780 (mmmm) REVERT: O 41 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7184 (ttp-170) REVERT: P 11 MET cc_start: 0.8481 (tpp) cc_final: 0.8163 (tpp) REVERT: Q 73 TYR cc_start: 0.5462 (t80) cc_final: 0.4532 (t80) REVERT: R 55 ILE cc_start: 0.8576 (mm) cc_final: 0.8306 (mt) REVERT: Y 49 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8377 (tpp-160) REVERT: Y 77 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: a 16 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8386 (tt) REVERT: a 94 TYR cc_start: 0.7376 (t80) cc_final: 0.6908 (t80) REVERT: a 118 MET cc_start: 0.8792 (tpp) cc_final: 0.8489 (tpt) REVERT: a 186 TRP cc_start: 0.3577 (p90) cc_final: 0.2330 (t60) REVERT: a 210 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8044 (mtp-110) REVERT: a 214 ASN cc_start: 0.9545 (m-40) cc_final: 0.9168 (m110) REVERT: a 231 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (p90) REVERT: a 241 TRP cc_start: 0.8241 (t-100) cc_final: 0.7965 (t-100) outliers start: 133 outliers final: 76 residues processed: 640 average time/residue: 0.2119 time to fit residues: 226.0140 Evaluate side-chains 607 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 519 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 411 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 260 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 420 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 21 HIS A 140 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070063 restraints weight = 97695.723| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.59 r_work: 0.2957 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 37584 Z= 0.122 Angle : 0.595 11.229 50874 Z= 0.302 Chirality : 0.042 0.357 5927 Planarity : 0.004 0.047 6559 Dihedral : 7.063 163.559 5363 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.71 % Allowed : 16.19 % Favored : 81.10 % 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: 1.23 (0.12), residues: 4813 helix: 1.71 (0.10), residues: 2602 sheet: -0.02 (0.22), residues: 504 loop : -0.23 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 41 TYR 0.021 0.001 TYR F 116 PHE 0.019 0.001 PHE Q 53 TRP 0.019 0.001 TRP a 235 HIS 0.004 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00256 (37584) covalent geometry : angle 0.59471 (50874) hydrogen bonds : bond 0.04547 ( 2315) hydrogen bonds : angle 4.42356 ( 6738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 583 time to evaluate : 1.379 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 12 LYS cc_start: 0.9474 (tppt) cc_final: 0.8739 (tptp) REVERT: W 16 ASP cc_start: 0.9114 (m-30) cc_final: 0.8781 (m-30) REVERT: W 160 ASP cc_start: 0.8623 (t0) cc_final: 0.6924 (p0) REVERT: C 262 ASP cc_start: 0.8917 (m-30) cc_final: 0.8499 (m-30) REVERT: C 265 LYS cc_start: 0.9207 (mttm) cc_final: 0.8943 (mttt) REVERT: C 327 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9222 (mp) REVERT: C 463 LYS cc_start: 0.9252 (tppt) cc_final: 0.8910 (tppp) REVERT: B 171 ARG cc_start: 0.9107 (ptt90) cc_final: 0.8828 (ptp90) REVERT: B 456 LEU cc_start: 0.6312 (mt) cc_final: 0.5636 (pt) REVERT: A 408 GLN cc_start: 0.8213 (mp10) cc_final: 0.7871 (mp10) REVERT: A 513 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.5979 (m100) REVERT: X 14 PHE cc_start: 0.8513 (t80) cc_final: 0.8204 (t80) REVERT: X 42 ASP cc_start: 0.5612 (m-30) cc_final: 0.5384 (m-30) REVERT: X 55 ASP cc_start: 0.8362 (m-30) cc_final: 0.8022 (p0) REVERT: H 51 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8091 (ptm-80) REVERT: H 81 ASP cc_start: 0.7743 (p0) cc_final: 0.7513 (p0) REVERT: H 87 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7800 (tp40) REVERT: H 111 ASP cc_start: 0.9085 (t0) cc_final: 0.8516 (t0) REVERT: H 132 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: G 68 GLU cc_start: 0.9005 (pt0) cc_final: 0.8099 (pp20) REVERT: G 180 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8174 (mp-120) REVERT: G 198 LEU cc_start: 0.8307 (mt) cc_final: 0.7786 (tp) REVERT: F 445 MET cc_start: 0.8982 (tpp) cc_final: 0.8756 (mpp) REVERT: E 265 VAL cc_start: 0.9604 (t) cc_final: 0.9381 (t) REVERT: E 328 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9012 (tp) REVERT: E 335 ASP cc_start: 0.8787 (t0) cc_final: 0.8515 (t0) REVERT: E 377 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7417 (mm) REVERT: D 243 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7745 (m-40) REVERT: D 422 ASP cc_start: 0.8692 (m-30) cc_final: 0.8292 (t0) REVERT: D 458 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7383 (tptp) REVERT: I 11 MET cc_start: 0.6392 (tpp) cc_final: 0.5832 (tmm) REVERT: I 42 GLN cc_start: 0.8082 (mm110) cc_final: 0.7613 (mp10) REVERT: I 75 MET cc_start: 0.8875 (mmm) cc_final: 0.8591 (mmm) REVERT: J 50 ARG cc_start: 0.7898 (ptp-110) cc_final: 0.7663 (ptm160) REVERT: L 17 MET cc_start: 0.6518 (tpp) cc_final: 0.6295 (tpp) REVERT: M 6 MET cc_start: 0.6428 (ppp) cc_final: 0.6210 (ppp) REVERT: M 17 MET cc_start: 0.6451 (mtm) cc_final: 0.5827 (ttm) REVERT: N 34 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7957 (mmmt) REVERT: N 70 LEU cc_start: 0.8445 (mt) cc_final: 0.8158 (tp) REVERT: O 6 MET cc_start: 0.6223 (ttm) cc_final: 0.5571 (mtt) REVERT: O 10 TYR cc_start: 0.7676 (m-80) cc_final: 0.7154 (m-80) REVERT: O 41 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7147 (ttp-170) REVERT: P 11 MET cc_start: 0.8612 (tpp) cc_final: 0.8330 (tpp) REVERT: P 42 GLN cc_start: 0.8290 (mm110) cc_final: 0.8082 (mm-40) REVERT: P 65 MET cc_start: 0.7702 (mmt) cc_final: 0.7402 (tpp) REVERT: Q 54 PHE cc_start: 0.8223 (m-10) cc_final: 0.7823 (t80) REVERT: Q 57 MET cc_start: 0.6396 (tmm) cc_final: 0.5920 (tmm) REVERT: Q 73 TYR cc_start: 0.5349 (t80) cc_final: 0.4430 (t80) REVERT: R 11 MET cc_start: 0.6321 (tpp) cc_final: 0.5780 (tpp) REVERT: R 55 ILE cc_start: 0.8624 (mm) cc_final: 0.8330 (mt) REVERT: Y 49 ARG cc_start: 0.8690 (tpp-160) cc_final: 0.8433 (tpp-160) REVERT: Y 117 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8333 (tmt90) REVERT: Y 138 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8443 (mmm160) REVERT: a 10 ASP cc_start: 0.8650 (t0) cc_final: 0.8302 (t70) REVERT: a 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8558 (tt) REVERT: a 94 TYR cc_start: 0.7466 (t80) cc_final: 0.6861 (t80) REVERT: a 153 MET cc_start: 0.9266 (mmp) cc_final: 0.8878 (mmp) REVERT: a 186 TRP cc_start: 0.3684 (p90) cc_final: 0.2537 (t60) REVERT: a 209 LEU cc_start: 0.9127 (mt) cc_final: 0.8143 (mt) REVERT: a 210 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.7825 (mtp-110) REVERT: a 214 ASN cc_start: 0.9516 (m-40) cc_final: 0.9315 (m110) REVERT: a 241 TRP cc_start: 0.8213 (t-100) cc_final: 0.7900 (t-100) outliers start: 104 outliers final: 52 residues processed: 661 average time/residue: 0.2162 time to fit residues: 237.1087 Evaluate side-chains 589 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 526 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 305 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 178 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 GLN H 56 HIS ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** Y 10 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 = 0.3612 r_free = 0.3612 target = 0.095078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068501 restraints weight = 98566.839| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.56 r_work: 0.2933 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37584 Z= 0.160 Angle : 0.620 11.835 50874 Z= 0.313 Chirality : 0.043 0.299 5927 Planarity : 0.004 0.113 6559 Dihedral : 6.925 155.161 5361 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.42 % Allowed : 17.16 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 4813 helix: 1.75 (0.10), residues: 2601 sheet: -0.00 (0.22), residues: 510 loop : -0.21 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 115 TYR 0.021 0.001 TYR F 116 PHE 0.018 0.001 PHE O 53 TRP 0.028 0.002 TRP a 231 HIS 0.023 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00370 (37584) covalent geometry : angle 0.62041 (50874) hydrogen bonds : bond 0.04669 ( 2315) hydrogen bonds : angle 4.46655 ( 6738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 531 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9478 (tppt) cc_final: 0.8798 (tptp) REVERT: W 16 ASP cc_start: 0.9166 (m-30) cc_final: 0.8834 (m-30) REVERT: W 160 ASP cc_start: 0.8642 (t0) cc_final: 0.6947 (p0) REVERT: C 262 ASP cc_start: 0.8988 (m-30) cc_final: 0.8608 (m-30) REVERT: C 265 LYS cc_start: 0.9258 (mttm) cc_final: 0.8978 (mttt) REVERT: C 463 LYS cc_start: 0.9256 (tppt) cc_final: 0.8923 (tppp) REVERT: B 171 ARG cc_start: 0.9120 (ptt90) cc_final: 0.8844 (ptp90) REVERT: B 456 LEU cc_start: 0.6327 (mt) cc_final: 0.5709 (pt) REVERT: A 513 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.6050 (m100) REVERT: X 55 ASP cc_start: 0.8365 (m-30) cc_final: 0.8023 (p0) REVERT: H 13 GLN cc_start: 0.8451 (pm20) cc_final: 0.7983 (pm20) REVERT: H 51 ARG cc_start: 0.8622 (ptm160) cc_final: 0.7978 (ptm-80) REVERT: H 72 GLN cc_start: 0.7513 (mt0) cc_final: 0.7239 (mt0) REVERT: H 111 ASP cc_start: 0.9129 (t0) cc_final: 0.8593 (t0) REVERT: H 132 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: G 68 GLU cc_start: 0.9013 (pt0) cc_final: 0.8110 (pp20) REVERT: G 180 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8134 (mp-120) REVERT: G 198 LEU cc_start: 0.8286 (mt) cc_final: 0.7759 (tp) REVERT: F 445 MET cc_start: 0.9009 (tpp) cc_final: 0.8743 (mpp) REVERT: E 328 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9017 (tp) REVERT: E 335 ASP cc_start: 0.8776 (t0) cc_final: 0.8511 (t0) REVERT: E 377 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7416 (mm) REVERT: D 122 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8400 (p) REVERT: D 422 ASP cc_start: 0.8700 (m-30) cc_final: 0.8366 (t0) REVERT: D 458 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7351 (tptp) REVERT: I 11 MET cc_start: 0.6271 (tpp) cc_final: 0.5721 (tmm) REVERT: I 17 MET cc_start: 0.8304 (mmt) cc_final: 0.8049 (mmp) REVERT: J 50 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7663 (ptm160) REVERT: M 6 MET cc_start: 0.6637 (ppp) cc_final: 0.6223 (ppp) REVERT: M 17 MET cc_start: 0.6627 (mtm) cc_final: 0.5591 (ttm) REVERT: O 6 MET cc_start: 0.6288 (ttm) cc_final: 0.5143 (ttt) REVERT: O 10 TYR cc_start: 0.7717 (m-80) cc_final: 0.7312 (m-80) REVERT: O 41 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7133 (ttp-170) REVERT: O 75 MET cc_start: 0.8816 (mtp) cc_final: 0.8195 (mtp) REVERT: P 11 MET cc_start: 0.8603 (tpp) cc_final: 0.8251 (tpp) REVERT: P 65 MET cc_start: 0.7748 (mmt) cc_final: 0.7471 (tpp) REVERT: Q 54 PHE cc_start: 0.8332 (m-10) cc_final: 0.7777 (t80) REVERT: Q 57 MET cc_start: 0.6407 (tmm) cc_final: 0.5858 (tmm) REVERT: Q 73 TYR cc_start: 0.5368 (t80) cc_final: 0.4461 (t80) REVERT: R 11 MET cc_start: 0.6219 (tpp) cc_final: 0.5733 (tpp) REVERT: R 55 ILE cc_start: 0.8568 (mm) cc_final: 0.8274 (mt) REVERT: S 11 MET cc_start: 0.8733 (tpp) cc_final: 0.8364 (mmm) REVERT: Y 49 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8355 (tpp-160) REVERT: Y 117 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8259 (tmt90) REVERT: a 10 ASP cc_start: 0.8679 (t0) cc_final: 0.8254 (t70) REVERT: a 94 TYR cc_start: 0.7508 (t80) cc_final: 0.6848 (t80) REVERT: a 118 MET cc_start: 0.8563 (tpt) cc_final: 0.8195 (tpp) REVERT: a 186 TRP cc_start: 0.3550 (p90) cc_final: 0.2408 (t60) REVERT: a 209 LEU cc_start: 0.9076 (mt) cc_final: 0.8308 (mt) REVERT: a 210 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8008 (mtp-110) REVERT: a 231 TRP cc_start: 0.7423 (p90) cc_final: 0.6597 (p-90) REVERT: a 235 TRP cc_start: 0.7307 (p-90) cc_final: 0.6863 (p-90) REVERT: a 241 TRP cc_start: 0.8247 (t-100) cc_final: 0.7954 (t-100) outliers start: 93 outliers final: 70 residues processed: 595 average time/residue: 0.2110 time to fit residues: 208.6565 Evaluate side-chains 582 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 504 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 261 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 41 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 451 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 212 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 210 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068758 restraints weight = 98163.559| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.60 r_work: 0.2930 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37584 Z= 0.148 Angle : 0.617 11.403 50874 Z= 0.310 Chirality : 0.043 0.319 5927 Planarity : 0.004 0.100 6559 Dihedral : 6.742 142.086 5361 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.50 % Allowed : 17.47 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.12), residues: 4813 helix: 1.81 (0.10), residues: 2604 sheet: 0.04 (0.23), residues: 510 loop : -0.17 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 41 TYR 0.022 0.001 TYR F 116 PHE 0.019 0.001 PHE Q 53 TRP 0.030 0.002 TRP X 26 HIS 0.004 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00341 (37584) covalent geometry : angle 0.61725 (50874) hydrogen bonds : bond 0.04575 ( 2315) hydrogen bonds : angle 4.45370 ( 6738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 527 time to evaluate : 1.470 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 12 LYS cc_start: 0.9483 (tppt) cc_final: 0.8812 (tptp) REVERT: W 16 ASP cc_start: 0.9188 (m-30) cc_final: 0.8854 (m-30) REVERT: C 463 LYS cc_start: 0.9252 (tppt) cc_final: 0.8918 (tppp) REVERT: B 171 ARG cc_start: 0.9107 (ptt90) cc_final: 0.8850 (ptp90) REVERT: B 429 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8210 (pt0) REVERT: B 456 LEU cc_start: 0.6308 (mt) cc_final: 0.5777 (pt) REVERT: A 76 MET cc_start: 0.9057 (mmm) cc_final: 0.8750 (mmm) REVERT: A 386 MET cc_start: 0.9355 (tpp) cc_final: 0.8812 (mmm) REVERT: A 418 ARG cc_start: 0.8311 (ttp80) cc_final: 0.8040 (ttm110) REVERT: A 488 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 513 TRP cc_start: 0.7358 (OUTLIER) cc_final: 0.5878 (m100) REVERT: X 14 PHE cc_start: 0.8694 (t80) cc_final: 0.8417 (t80) REVERT: X 42 ASP cc_start: 0.5978 (m-30) cc_final: 0.5625 (p0) REVERT: X 55 ASP cc_start: 0.8369 (m-30) cc_final: 0.8027 (p0) REVERT: H 72 GLN cc_start: 0.7502 (mt0) cc_final: 0.7241 (mt0) REVERT: H 111 ASP cc_start: 0.9144 (t0) cc_final: 0.8512 (t0) REVERT: H 132 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7260 (pp20) REVERT: G 68 GLU cc_start: 0.9017 (pt0) cc_final: 0.8118 (pp20) REVERT: G 139 MET cc_start: 0.8690 (mtp) cc_final: 0.8425 (mtp) REVERT: G 180 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: G 198 LEU cc_start: 0.8346 (mt) cc_final: 0.7870 (tp) REVERT: F 445 MET cc_start: 0.9007 (tpp) cc_final: 0.8768 (tpp) REVERT: E 328 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9018 (tp) REVERT: E 335 ASP cc_start: 0.8788 (t0) cc_final: 0.8501 (t0) REVERT: E 377 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7413 (mm) REVERT: D 422 ASP cc_start: 0.8722 (m-30) cc_final: 0.8367 (t0) REVERT: I 11 MET cc_start: 0.6270 (tpp) cc_final: 0.5716 (tmm) REVERT: I 17 MET cc_start: 0.8180 (mmt) cc_final: 0.7872 (mmp) REVERT: I 75 MET cc_start: 0.8845 (mmm) cc_final: 0.8544 (mmm) REVERT: J 50 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7608 (ptm160) REVERT: M 6 MET cc_start: 0.6606 (ppp) cc_final: 0.6361 (ppp) REVERT: M 17 MET cc_start: 0.6529 (mtm) cc_final: 0.5847 (ttt) REVERT: O 6 MET cc_start: 0.6518 (ttm) cc_final: 0.5336 (ttt) REVERT: O 10 TYR cc_start: 0.7666 (m-80) cc_final: 0.7221 (m-80) REVERT: O 16 MET cc_start: 0.8104 (ppp) cc_final: 0.7859 (ppp) REVERT: O 34 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7444 (mmmt) REVERT: O 37 GLU cc_start: 0.8626 (pp20) cc_final: 0.8323 (pp20) REVERT: O 41 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: O 75 MET cc_start: 0.8705 (mtp) cc_final: 0.7948 (mtm) REVERT: P 11 MET cc_start: 0.8626 (tpp) cc_final: 0.8335 (tpp) REVERT: P 65 MET cc_start: 0.7695 (mmt) cc_final: 0.7389 (tpp) REVERT: Q 54 PHE cc_start: 0.8402 (m-10) cc_final: 0.7673 (t80) REVERT: Q 57 MET cc_start: 0.6409 (tmm) cc_final: 0.5849 (tmm) REVERT: Q 73 TYR cc_start: 0.5363 (t80) cc_final: 0.4453 (t80) REVERT: R 11 MET cc_start: 0.6394 (tpp) cc_final: 0.5929 (tpp) REVERT: R 55 ILE cc_start: 0.8552 (mm) cc_final: 0.8266 (mt) REVERT: Y 49 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8377 (tpp-160) REVERT: Y 56 LEU cc_start: 0.7125 (pp) cc_final: 0.6910 (pp) REVERT: Y 117 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8226 (tmt90) REVERT: a 6 MET cc_start: 0.5851 (tpp) cc_final: 0.5573 (tpp) REVERT: a 10 ASP cc_start: 0.8697 (t0) cc_final: 0.8276 (t70) REVERT: a 60 PHE cc_start: 0.8478 (m-80) cc_final: 0.8210 (m-80) REVERT: a 94 TYR cc_start: 0.7533 (t80) cc_final: 0.6869 (t80) REVERT: a 118 MET cc_start: 0.8452 (tpt) cc_final: 0.8068 (tpp) REVERT: a 186 TRP cc_start: 0.3383 (p90) cc_final: 0.2905 (p-90) REVERT: a 209 LEU cc_start: 0.9008 (mt) cc_final: 0.8217 (mt) REVERT: a 210 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.8057 (mtp-110) REVERT: a 235 TRP cc_start: 0.7319 (p-90) cc_final: 0.6898 (p-90) REVERT: a 241 TRP cc_start: 0.8170 (t-100) cc_final: 0.7877 (t-100) outliers start: 96 outliers final: 75 residues processed: 594 average time/residue: 0.2160 time to fit residues: 212.8825 Evaluate side-chains 586 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 504 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 238 optimal weight: 2.9990 chunk 376 optimal weight: 0.0030 chunk 439 optimal weight: 7.9990 chunk 446 optimal weight: 0.8980 chunk 373 optimal weight: 1.9990 chunk 421 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 42 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069763 restraints weight = 98218.167| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.57 r_work: 0.2959 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 37584 Z= 0.124 Angle : 0.612 11.242 50874 Z= 0.306 Chirality : 0.042 0.356 5927 Planarity : 0.004 0.102 6559 Dihedral : 6.463 139.247 5359 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.37 % Allowed : 17.91 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 4813 helix: 1.88 (0.10), residues: 2595 sheet: 0.19 (0.23), residues: 498 loop : -0.14 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 115 TYR 0.021 0.001 TYR F 116 PHE 0.023 0.001 PHE a 256 TRP 0.022 0.002 TRP a 231 HIS 0.027 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00270 (37584) covalent geometry : angle 0.61167 (50874) hydrogen bonds : bond 0.04399 ( 2315) hydrogen bonds : angle 4.37757 ( 6738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 528 time to evaluate : 1.517 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 12 LYS cc_start: 0.9468 (tppt) cc_final: 0.8842 (tptp) REVERT: W 16 ASP cc_start: 0.9167 (m-30) cc_final: 0.8836 (m-30) REVERT: W 160 ASP cc_start: 0.8452 (t0) cc_final: 0.6830 (p0) REVERT: C 52 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8619 (tpp) REVERT: C 463 LYS cc_start: 0.9234 (tppt) cc_final: 0.8905 (tppp) REVERT: B 171 ARG cc_start: 0.9070 (ptt90) cc_final: 0.8843 (ptp90) REVERT: B 456 LEU cc_start: 0.6292 (mt) cc_final: 0.5802 (pt) REVERT: A 76 MET cc_start: 0.9049 (mmm) cc_final: 0.8757 (mmm) REVERT: X 42 ASP cc_start: 0.5970 (m-30) cc_final: 0.5658 (p0) REVERT: H 51 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8010 (ptm-80) REVERT: H 72 GLN cc_start: 0.7470 (mt0) cc_final: 0.7164 (mt0) REVERT: H 99 ARG cc_start: 0.8794 (tmm-80) cc_final: 0.8578 (tmm-80) REVERT: H 111 ASP cc_start: 0.9149 (t0) cc_final: 0.8601 (t0) REVERT: H 127 GLN cc_start: 0.7834 (pp30) cc_final: 0.7458 (pp30) REVERT: H 132 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: G 68 GLU cc_start: 0.9014 (pt0) cc_final: 0.8122 (pp20) REVERT: G 180 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: G 198 LEU cc_start: 0.8365 (mt) cc_final: 0.7885 (tp) REVERT: E 265 VAL cc_start: 0.9559 (t) cc_final: 0.9313 (t) REVERT: E 328 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9014 (tp) REVERT: E 335 ASP cc_start: 0.8726 (t0) cc_final: 0.8462 (t0) REVERT: E 377 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7425 (mm) REVERT: E 445 MET cc_start: 0.8989 (mmm) cc_final: 0.8672 (mmm) REVERT: D 122 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8629 (m) REVERT: D 422 ASP cc_start: 0.8704 (m-30) cc_final: 0.8436 (t0) REVERT: I 17 MET cc_start: 0.8134 (mmt) cc_final: 0.7770 (mmp) REVERT: I 35 PHE cc_start: 0.8786 (t80) cc_final: 0.8545 (t80) REVERT: I 75 MET cc_start: 0.8856 (mmm) cc_final: 0.8569 (mmm) REVERT: M 6 MET cc_start: 0.6565 (ppp) cc_final: 0.6247 (ppp) REVERT: M 11 MET cc_start: 0.7882 (mmm) cc_final: 0.7307 (mmm) REVERT: M 17 MET cc_start: 0.6628 (mtm) cc_final: 0.5944 (ttm) REVERT: M 54 PHE cc_start: 0.7342 (m-80) cc_final: 0.7123 (m-80) REVERT: N 75 MET cc_start: 0.8826 (tpt) cc_final: 0.8399 (tpt) REVERT: O 6 MET cc_start: 0.6544 (ttm) cc_final: 0.5343 (ttt) REVERT: O 10 TYR cc_start: 0.7600 (m-80) cc_final: 0.7232 (m-80) REVERT: O 16 MET cc_start: 0.7842 (ppp) cc_final: 0.7446 (ppp) REVERT: O 34 LYS cc_start: 0.7675 (mmtm) cc_final: 0.7286 (mmmt) REVERT: O 37 GLU cc_start: 0.8587 (pp20) cc_final: 0.8259 (pp20) REVERT: O 41 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: O 70 LEU cc_start: 0.8978 (mm) cc_final: 0.8642 (pp) REVERT: P 11 MET cc_start: 0.8564 (tpp) cc_final: 0.7597 (ppp) REVERT: P 65 MET cc_start: 0.7547 (mmt) cc_final: 0.7319 (tpp) REVERT: Q 54 PHE cc_start: 0.8437 (m-10) cc_final: 0.7631 (t80) REVERT: Q 57 MET cc_start: 0.6497 (tmm) cc_final: 0.5890 (tmm) REVERT: Q 73 TYR cc_start: 0.5345 (t80) cc_final: 0.4545 (t80) REVERT: R 11 MET cc_start: 0.6244 (tpp) cc_final: 0.5774 (tpp) REVERT: R 55 ILE cc_start: 0.8558 (mm) cc_final: 0.8275 (mt) REVERT: S 11 MET cc_start: 0.8773 (tpp) cc_final: 0.8318 (mmm) REVERT: Y 49 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8402 (tpp-160) REVERT: a 10 ASP cc_start: 0.8621 (t0) cc_final: 0.8225 (t70) REVERT: a 60 PHE cc_start: 0.8525 (m-80) cc_final: 0.8311 (m-80) REVERT: a 94 TYR cc_start: 0.7692 (t80) cc_final: 0.6995 (t80) REVERT: a 118 MET cc_start: 0.8488 (tpt) cc_final: 0.8130 (tpp) REVERT: a 186 TRP cc_start: 0.3308 (p90) cc_final: 0.2844 (p-90) REVERT: a 209 LEU cc_start: 0.8960 (mt) cc_final: 0.8135 (mt) REVERT: a 210 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.7672 (mtp-110) REVERT: a 214 ASN cc_start: 0.9522 (m-40) cc_final: 0.9263 (m110) REVERT: a 241 TRP cc_start: 0.8230 (t-100) cc_final: 0.8014 (t-100) outliers start: 91 outliers final: 74 residues processed: 598 average time/residue: 0.2091 time to fit residues: 208.3833 Evaluate side-chains 578 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 497 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 464 optimal weight: 5.9990 chunk 376 optimal weight: 0.8980 chunk 385 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 234 optimal weight: 0.2980 chunk 194 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN B 2 GLN B 425 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** 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 = 0.3637 r_free = 0.3637 target = 0.096566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069675 restraints weight = 98353.484| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.51 r_work: 0.2969 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 37584 Z= 0.126 Angle : 0.621 15.815 50874 Z= 0.308 Chirality : 0.042 0.353 5927 Planarity : 0.004 0.089 6559 Dihedral : 6.246 134.228 5359 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.24 % Allowed : 18.43 % Favored : 79.33 % 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: 1.52 (0.12), residues: 4813 helix: 1.92 (0.10), residues: 2606 sheet: 0.17 (0.23), residues: 510 loop : -0.09 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 115 TYR 0.022 0.001 TYR F 116 PHE 0.024 0.001 PHE a 256 TRP 0.025 0.002 TRP a 235 HIS 0.004 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00280 (37584) covalent geometry : angle 0.62129 (50874) hydrogen bonds : bond 0.04321 ( 2315) hydrogen bonds : angle 4.35085 ( 6738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 521 time to evaluate : 1.356 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 12 LYS cc_start: 0.9411 (tppt) cc_final: 0.8763 (tptp) REVERT: W 16 ASP cc_start: 0.9034 (m-30) cc_final: 0.8716 (m-30) REVERT: W 30 MET cc_start: 0.8910 (tpp) cc_final: 0.8687 (ttt) REVERT: W 160 ASP cc_start: 0.8269 (t0) cc_final: 0.6721 (p0) REVERT: C 52 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8384 (tpp) REVERT: C 463 LYS cc_start: 0.9145 (tppt) cc_final: 0.8800 (tppp) REVERT: B 456 LEU cc_start: 0.6283 (mt) cc_final: 0.5823 (pt) REVERT: A 76 MET cc_start: 0.8852 (mmm) cc_final: 0.8520 (mmm) REVERT: X 42 ASP cc_start: 0.6114 (m-30) cc_final: 0.5914 (p0) REVERT: H 7 ASP cc_start: 0.8446 (m-30) cc_final: 0.7811 (p0) REVERT: H 13 GLN cc_start: 0.8408 (pm20) cc_final: 0.8084 (pm20) REVERT: H 51 ARG cc_start: 0.8488 (ptm160) cc_final: 0.7982 (ptm-80) REVERT: H 72 GLN cc_start: 0.7223 (mt0) cc_final: 0.6964 (mt0) REVERT: H 99 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.8544 (tmm-80) REVERT: H 111 ASP cc_start: 0.9150 (t0) cc_final: 0.8543 (t0) REVERT: H 132 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: G 198 LEU cc_start: 0.8397 (mt) cc_final: 0.7928 (tp) REVERT: E 265 VAL cc_start: 0.9515 (t) cc_final: 0.9269 (t) REVERT: E 328 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9014 (tp) REVERT: E 335 ASP cc_start: 0.8512 (t0) cc_final: 0.8279 (t0) REVERT: E 377 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7506 (mm) REVERT: E 425 ARG cc_start: 0.8469 (mtm110) cc_final: 0.8049 (tmm-80) REVERT: E 445 MET cc_start: 0.8816 (mmm) cc_final: 0.8536 (mmm) REVERT: D 122 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8526 (m) REVERT: I 11 MET cc_start: 0.6537 (tmm) cc_final: 0.5997 (tpp) REVERT: I 17 MET cc_start: 0.8122 (mmt) cc_final: 0.7692 (mmp) REVERT: I 42 GLN cc_start: 0.8046 (mm110) cc_final: 0.7609 (mp10) REVERT: I 75 MET cc_start: 0.8833 (mmm) cc_final: 0.8576 (mmm) REVERT: J 50 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7285 (ptm160) REVERT: L 53 PHE cc_start: 0.7238 (t80) cc_final: 0.6938 (t80) REVERT: M 6 MET cc_start: 0.6325 (ppp) cc_final: 0.6008 (ppp) REVERT: M 17 MET cc_start: 0.6654 (mtm) cc_final: 0.5894 (ttm) REVERT: M 57 MET cc_start: 0.8410 (tmm) cc_final: 0.8203 (tmm) REVERT: N 75 MET cc_start: 0.8740 (tpt) cc_final: 0.8527 (tpp) REVERT: O 6 MET cc_start: 0.6763 (ttm) cc_final: 0.5610 (ttt) REVERT: O 10 TYR cc_start: 0.7536 (m-80) cc_final: 0.7197 (m-80) REVERT: O 16 MET cc_start: 0.7960 (ppp) cc_final: 0.7517 (ppp) REVERT: O 34 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7394 (mmmt) REVERT: O 41 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7413 (ttp-170) REVERT: O 70 LEU cc_start: 0.8988 (mm) cc_final: 0.8755 (pp) REVERT: O 75 MET cc_start: 0.8830 (mtp) cc_final: 0.8100 (mtm) REVERT: P 17 MET cc_start: 0.7529 (ptp) cc_final: 0.6866 (ptp) REVERT: P 50 ARG cc_start: 0.7445 (ptt180) cc_final: 0.7240 (ptp-170) REVERT: Q 54 PHE cc_start: 0.8450 (m-10) cc_final: 0.7788 (t80) REVERT: Q 73 TYR cc_start: 0.5310 (t80) cc_final: 0.4540 (t80) REVERT: R 11 MET cc_start: 0.6445 (tpp) cc_final: 0.5939 (tpp) REVERT: R 55 ILE cc_start: 0.8536 (mm) cc_final: 0.8263 (mt) REVERT: S 10 TYR cc_start: 0.7688 (m-10) cc_final: 0.7455 (m-10) REVERT: S 11 MET cc_start: 0.8741 (tpp) cc_final: 0.8302 (mmm) REVERT: Y 49 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8374 (tpp-160) REVERT: a 6 MET cc_start: 0.5604 (tpp) cc_final: 0.5173 (tpp) REVERT: a 10 ASP cc_start: 0.8651 (t0) cc_final: 0.8225 (t70) REVERT: a 94 TYR cc_start: 0.7579 (t80) cc_final: 0.6902 (t80) REVERT: a 118 MET cc_start: 0.8412 (tpt) cc_final: 0.8174 (tpp) REVERT: a 151 LEU cc_start: 0.9226 (mm) cc_final: 0.8996 (mm) REVERT: a 186 TRP cc_start: 0.3265 (p90) cc_final: 0.2831 (p-90) REVERT: a 209 LEU cc_start: 0.8935 (mt) cc_final: 0.8036 (mt) REVERT: a 210 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7717 (mtp-110) REVERT: a 214 ASN cc_start: 0.9509 (m-40) cc_final: 0.9277 (m110) outliers start: 86 outliers final: 70 residues processed: 584 average time/residue: 0.2125 time to fit residues: 205.7405 Evaluate side-chains 568 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 492 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 329 optimal weight: 0.0770 chunk 314 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 466 optimal weight: 10.0000 chunk 235 optimal weight: 0.0020 chunk 25 optimal weight: 9.9990 chunk 443 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 369 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 overall best weight: 1.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 GLN A 484 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS ** a 116 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.096598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069861 restraints weight = 98301.536| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.49 r_work: 0.2972 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 37584 Z= 0.132 Angle : 0.633 13.500 50874 Z= 0.316 Chirality : 0.043 0.347 5927 Planarity : 0.004 0.091 6559 Dihedral : 6.141 132.338 5359 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 19.08 % Favored : 78.83 % 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: 1.52 (0.12), residues: 4813 helix: 1.91 (0.10), residues: 2602 sheet: 0.16 (0.22), residues: 519 loop : -0.05 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 115 TYR 0.022 0.001 TYR F 116 PHE 0.050 0.001 PHE J 53 TRP 0.031 0.002 TRP a 231 HIS 0.004 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00298 (37584) covalent geometry : angle 0.63337 (50874) hydrogen bonds : bond 0.04356 ( 2315) hydrogen bonds : angle 4.37495 ( 6738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 496 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 12 LYS cc_start: 0.9457 (tppt) cc_final: 0.8874 (tptp) REVERT: W 16 ASP cc_start: 0.9198 (m-30) cc_final: 0.8871 (m-30) REVERT: W 30 MET cc_start: 0.8904 (tpp) cc_final: 0.8483 (ttt) REVERT: W 160 ASP cc_start: 0.8402 (t0) cc_final: 0.6802 (p0) REVERT: C 52 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (tpp) REVERT: C 463 LYS cc_start: 0.9228 (tppt) cc_final: 0.8892 (tppp) REVERT: B 456 LEU cc_start: 0.6305 (mt) cc_final: 0.5794 (pt) REVERT: A 76 MET cc_start: 0.9079 (mmm) cc_final: 0.8774 (mmm) REVERT: A 418 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8003 (ttm110) REVERT: X 42 ASP cc_start: 0.6259 (m-30) cc_final: 0.5923 (p0) REVERT: H 7 ASP cc_start: 0.8449 (m-30) cc_final: 0.7942 (p0) REVERT: H 13 GLN cc_start: 0.8502 (pm20) cc_final: 0.8190 (pm20) REVERT: H 51 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8082 (ptm-80) REVERT: H 72 GLN cc_start: 0.7394 (mt0) cc_final: 0.7130 (mt0) REVERT: H 111 ASP cc_start: 0.9154 (t0) cc_final: 0.8512 (t0) REVERT: H 132 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: G 198 LEU cc_start: 0.8500 (mt) cc_final: 0.8041 (tp) REVERT: E 265 VAL cc_start: 0.9577 (t) cc_final: 0.9331 (t) REVERT: E 328 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9010 (tp) REVERT: E 335 ASP cc_start: 0.8732 (t0) cc_final: 0.8458 (t0) REVERT: E 377 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7343 (mm) REVERT: E 425 ARG cc_start: 0.8625 (mtm110) cc_final: 0.8207 (tmm-80) REVERT: E 445 MET cc_start: 0.8969 (mmm) cc_final: 0.8695 (mmm) REVERT: I 11 MET cc_start: 0.6450 (tmm) cc_final: 0.5905 (tpp) REVERT: I 17 MET cc_start: 0.8152 (mmt) cc_final: 0.7722 (mmp) REVERT: I 42 GLN cc_start: 0.8098 (mm110) cc_final: 0.7627 (mp10) REVERT: I 75 MET cc_start: 0.8900 (mmm) cc_final: 0.8657 (mmm) REVERT: J 17 MET cc_start: 0.8111 (pmm) cc_final: 0.7863 (pmm) REVERT: J 50 ARG cc_start: 0.7647 (ptm160) cc_final: 0.7259 (ptm160) REVERT: L 53 PHE cc_start: 0.7260 (t80) cc_final: 0.7006 (t80) REVERT: M 6 MET cc_start: 0.6370 (ppp) cc_final: 0.6084 (ppp) REVERT: M 17 MET cc_start: 0.6745 (mtm) cc_final: 0.5892 (ttt) REVERT: M 54 PHE cc_start: 0.7133 (m-80) cc_final: 0.6531 (m-80) REVERT: N 53 PHE cc_start: 0.8585 (t80) cc_final: 0.8379 (t80) REVERT: N 75 MET cc_start: 0.8713 (tpt) cc_final: 0.8478 (tpp) REVERT: O 6 MET cc_start: 0.6642 (ttm) cc_final: 0.5507 (ttt) REVERT: O 10 TYR cc_start: 0.7568 (m-80) cc_final: 0.7280 (m-80) REVERT: O 41 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7430 (ttp-170) REVERT: O 70 LEU cc_start: 0.8973 (mm) cc_final: 0.8710 (pp) REVERT: O 75 MET cc_start: 0.8857 (mtp) cc_final: 0.8146 (mtm) REVERT: P 17 MET cc_start: 0.7628 (ptp) cc_final: 0.6986 (ptp) REVERT: Q 60 VAL cc_start: 0.7838 (t) cc_final: 0.7596 (p) REVERT: Q 73 TYR cc_start: 0.5306 (t80) cc_final: 0.4512 (t80) REVERT: R 11 MET cc_start: 0.6370 (tpp) cc_final: 0.5928 (tpp) REVERT: R 55 ILE cc_start: 0.8532 (mm) cc_final: 0.8251 (mt) REVERT: S 10 TYR cc_start: 0.7719 (m-10) cc_final: 0.7488 (m-10) REVERT: S 11 MET cc_start: 0.8749 (tpp) cc_final: 0.8342 (mmm) REVERT: Y 49 ARG cc_start: 0.8684 (tpp-160) cc_final: 0.8421 (tpp-160) REVERT: a 6 MET cc_start: 0.5678 (tpp) cc_final: 0.5165 (tpp) REVERT: a 10 ASP cc_start: 0.8654 (t0) cc_final: 0.8227 (t70) REVERT: a 94 TYR cc_start: 0.7713 (t80) cc_final: 0.7062 (t80) REVERT: a 118 MET cc_start: 0.8576 (tpt) cc_final: 0.8296 (tpp) REVERT: a 140 ARG cc_start: 0.6637 (ttp80) cc_final: 0.6107 (ttp-110) REVERT: a 151 LEU cc_start: 0.9250 (mm) cc_final: 0.9025 (mm) REVERT: a 186 TRP cc_start: 0.3287 (p90) cc_final: 0.2838 (p-90) REVERT: a 209 LEU cc_start: 0.8646 (mt) cc_final: 0.8443 (mt) outliers start: 80 outliers final: 68 residues processed: 553 average time/residue: 0.2077 time to fit residues: 191.3965 Evaluate side-chains 563 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 490 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 203 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 143 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 367 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 463 optimal weight: 10.0000 chunk 15 optimal weight: 0.0030 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.0170 chunk 190 optimal weight: 2.9990 overall best weight: 1.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070201 restraints weight = 98189.938| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.57 r_work: 0.2974 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 37584 Z= 0.130 Angle : 0.641 14.123 50874 Z= 0.319 Chirality : 0.043 0.351 5927 Planarity : 0.004 0.086 6559 Dihedral : 6.040 130.865 5359 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 19.01 % Favored : 78.91 % 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: 1.53 (0.12), residues: 4813 helix: 1.90 (0.10), residues: 2602 sheet: 0.19 (0.22), residues: 519 loop : -0.03 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 115 TYR 0.021 0.001 TYR F 116 PHE 0.035 0.001 PHE a 256 TRP 0.042 0.002 TRP a 231 HIS 0.019 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00288 (37584) covalent geometry : angle 0.64084 (50874) hydrogen bonds : bond 0.04346 ( 2315) hydrogen bonds : angle 4.37231 ( 6738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11494.99 seconds wall clock time: 196 minutes 9.16 seconds (11769.16 seconds total)