Starting phenix.real_space_refine on Sat Mar 7 03:21:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqa_21346/03_2026/6vqa_21346.map" } resolution = 3.7 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= 0.092 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 2 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22864 2.51 5 N 6223 2.21 5 O 6821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 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: 36114 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 914 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "I" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1288 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Q" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.25, per 1000 atoms: 0.23 Number of scatterers: 36114 At special positions: 0 Unit cell: (169.6, 171.72, 143.1, 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 203 16.00 P 2 15.00 Mg 1 11.99 O 6821 8.00 N 6223 7.00 C 22864 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8532 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 68 sheets defined 51.2% alpha, 111.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.656A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.388A pdb=" N GLY A 255 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.558A pdb=" N SER A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 319 through 339 removed outlier: 4.513A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.529A pdb=" N TRP A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.707A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.146A pdb=" N ASP A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 489 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 557 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.599A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.828A pdb=" N MET B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 321 through 340 removed outlier: 4.015A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 375 through 376 No H-bonds generated for 'chain 'B' and resid 375 through 376' Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.886A pdb=" N ARG B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.406A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 4.088A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 557 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 574 through 584 Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.532A pdb=" N ASP C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.639A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 319 through 339 removed outlier: 4.646A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.302A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.593A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.874A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 removed outlier: 4.473A pdb=" N ASP C 588 " --> pdb=" O LYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 616 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 237 through 251 removed outlier: 3.554A pdb=" N ASN D 251 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 255 removed outlier: 4.099A pdb=" N ASP D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 269 through 289 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 414 through 440 removed outlier: 3.665A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 462 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 486 through 487 No H-bonds generated for 'chain 'D' and resid 486 through 487' Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 removed outlier: 3.645A pdb=" N ARG E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 299 through 314 removed outlier: 4.070A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.642A pdb=" N HIS E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 414 through 440 removed outlier: 4.358A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 445 through 462 removed outlier: 4.374A pdb=" N TYR E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 486 through 487 No H-bonds generated for 'chain 'E' and resid 486 through 487' Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 496 through 504 removed outlier: 4.956A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 4.090A pdb=" N LEU F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.822A pdb=" N TYR F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.749A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.635A pdb=" N ARG F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 406 removed outlier: 3.838A pdb=" N ILE F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 440 removed outlier: 4.093A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 removed outlier: 3.910A pdb=" N LEU F 444 " --> pdb=" O GLU F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 445 through 462 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 486 through 487 No H-bonds generated for 'chain 'F' and resid 486 through 487' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'H' and resid 12 through 48 Processing helix chain 'H' and resid 155 through 175 Processing helix chain 'H' and resid 175 through 216 Processing helix chain 'I' and resid 67 through 107 Processing helix chain 'I' and resid 109 through 128 Processing helix chain 'I' and resid 137 through 139 No H-bonds generated for 'chain 'I' and resid 137 through 139' Processing helix chain 'I' and resid 140 through 160 removed outlier: 3.534A pdb=" N ALA I 146 " --> pdb=" O PRO I 142 " (cutoff:3.500A) Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 195 through 207 Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'J' and resid 67 through 107 Processing helix chain 'J' and resid 108 through 128 removed outlier: 4.570A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 159 Proline residue: J 153 - end of helix removed outlier: 3.536A pdb=" N ILE J 157 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 217 removed outlier: 3.920A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 67 through 107 Processing helix chain 'K' and resid 109 through 128 Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 removed outlier: 3.503A pdb=" N ALA K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 196 through 205 Processing helix chain 'K' and resid 207 through 217 removed outlier: 3.631A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 91 removed outlier: 4.280A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 105 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 91 through 105 Processing helix chain 'O' and resid 71 through 104 removed outlier: 3.608A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 removed outlier: 3.628A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 77 through 97 Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.795A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 143 No H-bonds generated for 'chain 'Q' and resid 141 through 143' Processing helix chain 'Q' and resid 146 through 167 removed outlier: 3.552A pdb=" N GLN Q 165 " --> pdb=" O MET Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 187 Processing helix chain 'Q' and resid 193 through 207 Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 49 Processing helix chain 'R' and resid 49 through 54 Processing helix chain 'R' and resid 61 through 71 Processing helix chain 'R' and resid 77 through 97 removed outlier: 3.895A pdb=" N LEU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 124 through 140 Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 188 Processing helix chain 'R' and resid 192 through 205 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.587A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'S' and resid 42 through 48 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 61 through 71 Processing helix chain 'S' and resid 77 through 97 Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 142 removed outlier: 3.908A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 187 Processing helix chain 'S' and resid 192 through 206 Processing helix chain 'S' and resid 218 through 234 Processing sheet with id=AA1, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.902A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AE2, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.344A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 163 through 167 removed outlier: 4.007A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.350A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 409 through 410 removed outlier: 7.492A pdb=" N VAL A 410 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 248 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AE7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AE8, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.368A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 273 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 348 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.368A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 273 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 348 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.056A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.587A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AF4, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.660A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.660A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 246 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 245 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 164 through 167 removed outlier: 4.078A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.531A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AF9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AG1, first strand: chain 'D' and resid 131 through 133 removed outlier: 6.646A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR D 298 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 232 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AG3, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.244A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET D 356 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER D 193 " --> pdb=" O MET D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AG5, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.666A pdb=" N PHE E 132 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU E 263 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.411A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.350A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 192 through 193 Processing sheet with id=AG9, first strand: chain 'E' and resid 375 through 376 removed outlier: 3.508A pdb=" N LEU E 398 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AH2, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.723A pdb=" N ARG F 130 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU F 261 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE F 132 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU F 263 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA F 228 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE F 296 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL F 230 " --> pdb=" O ILE F 296 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.976A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.687A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 191 through 193 4860 hydrogen bonds defined for protein. 13707 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: 20.98 Time building geometry restraints manager: 3.97 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: 6862 1.32 - 1.44: 8323 1.44 - 1.57: 21219 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" C ASP C 290 " pdb=" N PHE C 291 " ideal model delta sigma weight residual 1.334 1.216 0.119 1.26e-02 6.30e+03 8.85e+01 bond pdb=" N PRO D 391 " pdb=" CA PRO D 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.19e+01 bond pdb=" C TYR F 504 " pdb=" N PRO F 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.33e+01 bond pdb=" C ARG C 104 " pdb=" N PRO C 105 " ideal model delta sigma weight residual 1.333 1.393 -0.060 1.01e-02 9.80e+03 3.48e+01 bond pdb=" N PRO F 352 " pdb=" CA PRO F 352 " ideal model delta sigma weight residual 1.466 1.538 -0.072 1.24e-02 6.50e+03 3.32e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 47782 2.13 - 4.27: 1740 4.27 - 6.40: 122 6.40 - 8.54: 22 8.54 - 10.67: 10 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE D 189 " pdb=" N PRO D 190 " pdb=" CA PRO D 190 " ideal model delta sigma weight residual 119.85 129.30 -9.45 1.01e+00 9.80e-01 8.76e+01 angle pdb=" C ARG B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.76 129.27 -9.51 1.03e+00 9.43e-01 8.53e+01 angle pdb=" C SER C 411 " pdb=" N PRO C 412 " pdb=" CA PRO C 412 " ideal model delta sigma weight residual 120.38 129.05 -8.67 1.03e+00 9.43e-01 7.09e+01 angle pdb=" C LEU D 395 " pdb=" N PRO D 396 " pdb=" CA PRO D 396 " ideal model delta sigma weight residual 120.04 128.53 -8.49 1.08e+00 8.57e-01 6.19e+01 angle pdb=" C ASN B 397 " pdb=" N PRO B 398 " pdb=" CA PRO B 398 " ideal model delta sigma weight residual 119.82 127.35 -7.53 9.80e-01 1.04e+00 5.91e+01 ... (remaining 49671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 22017 23.67 - 47.34: 413 47.34 - 71.01: 117 71.01 - 94.68: 31 94.68 - 118.35: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.41 -98.41 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA VAL B 392 " pdb=" C VAL B 392 " pdb=" N LYS B 393 " pdb=" CA LYS B 393 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3816 0.052 - 0.105: 1167 0.105 - 0.157: 482 0.157 - 0.209: 77 0.209 - 0.261: 33 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL D 379 " pdb=" N VAL D 379 " pdb=" C VAL D 379 " pdb=" CB VAL D 379 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO F 352 " pdb=" N PRO F 352 " pdb=" C PRO F 352 " pdb=" CB PRO F 352 " both_signs ideal model delta sigma weight residual False 2.72 2.97 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 390 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO D 390 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO D 390 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO D 391 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 584 " -0.016 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C MET B 584 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 584 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 585 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 189 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ILE D 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE D 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO D 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10609 2.82 - 3.34: 35486 3.34 - 3.86: 60613 3.86 - 4.38: 72010 4.38 - 4.90: 120813 Nonbonded interactions: 299531 Sorted by model distance: nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 345 " model vdw 2.302 3.040 nonbonded pdb=" NE ARG K 135 " pdb=" O ALA K 171 " model vdw 2.373 3.120 nonbonded pdb=" OG SER A 128 " pdb=" OD1 ASP A 130 " model vdw 2.374 3.040 nonbonded pdb=" OD1 ASP E 266 " pdb=" NZ LYS Q 9 " model vdw 2.380 3.120 nonbonded pdb=" OD1 ASP F 266 " pdb=" NZ LYS R 9 " model vdw 2.392 3.120 ... (remaining 299526 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' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 53.790 Find NCS groups from input model: 0.460 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 36765 Z= 0.585 Angle : 0.895 10.671 49676 Z= 0.632 Chirality : 0.062 0.261 5575 Planarity : 0.004 0.038 6440 Dihedral : 10.831 118.347 14048 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.71 % Favored : 97.09 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.27 (0.12), residues: 4538 helix: 0.63 (0.10), residues: 2081 sheet: -0.24 (0.20), residues: 612 loop : -0.00 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 208 TYR 0.016 0.000 TYR E 389 PHE 0.010 0.000 PHE B 252 TRP 0.010 0.001 TRP R 55 HIS 0.003 0.000 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00990 (36765) covalent geometry : angle 0.89481 (49676) hydrogen bonds : bond 0.18123 ( 1953) hydrogen bonds : angle 8.73976 (13707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1617 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.7946 (m) cc_final: 0.7408 (p) REVERT: A 61 MET cc_start: 0.8166 (mtp) cc_final: 0.7416 (ttm) REVERT: A 142 ARG cc_start: 0.7368 (mmt-90) cc_final: 0.6968 (mmt180) REVERT: A 171 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7774 (mtm180) REVERT: A 224 ASN cc_start: 0.8830 (p0) cc_final: 0.8459 (p0) REVERT: A 254 CYS cc_start: 0.7018 (p) cc_final: 0.6797 (p) REVERT: A 303 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7451 (mt-10) REVERT: A 306 MET cc_start: 0.8866 (mmm) cc_final: 0.8642 (tpp) REVERT: A 324 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 356 GLU cc_start: 0.8700 (tp30) cc_final: 0.8132 (tp30) REVERT: A 417 PHE cc_start: 0.7968 (m-80) cc_final: 0.7742 (m-10) REVERT: A 436 ASP cc_start: 0.8227 (t0) cc_final: 0.7838 (t70) REVERT: A 443 LYS cc_start: 0.9032 (mttt) cc_final: 0.8351 (tptp) REVERT: A 447 SER cc_start: 0.7433 (m) cc_final: 0.6666 (t) REVERT: A 550 MET cc_start: 0.8883 (mmm) cc_final: 0.7913 (mtm) REVERT: A 567 TRP cc_start: 0.8684 (t-100) cc_final: 0.8386 (t-100) REVERT: A 584 MET cc_start: 0.7426 (mtp) cc_final: 0.7222 (mtp) REVERT: A 605 LEU cc_start: 0.8933 (tp) cc_final: 0.8685 (tt) REVERT: A 608 MET cc_start: 0.8454 (mtm) cc_final: 0.8101 (ttp) REVERT: B 30 THR cc_start: 0.8142 (m) cc_final: 0.7724 (p) REVERT: B 77 ASP cc_start: 0.7484 (m-30) cc_final: 0.7039 (m-30) REVERT: B 116 ILE cc_start: 0.8681 (pt) cc_final: 0.8464 (pt) REVERT: B 130 ASP cc_start: 0.8279 (m-30) cc_final: 0.8047 (p0) REVERT: B 219 GLU cc_start: 0.7355 (tt0) cc_final: 0.7078 (tp30) REVERT: B 229 THR cc_start: 0.8968 (m) cc_final: 0.8716 (m) REVERT: B 231 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7410 (mm-40) REVERT: B 254 CYS cc_start: 0.8651 (m) cc_final: 0.8163 (m) REVERT: B 296 MET cc_start: 0.7931 (ttm) cc_final: 0.7482 (ppp) REVERT: B 298 VAL cc_start: 0.8507 (t) cc_final: 0.8171 (t) REVERT: B 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7451 (t0) REVERT: B 360 GLU cc_start: 0.8015 (tt0) cc_final: 0.7793 (tp30) REVERT: B 387 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7804 (tp30) REVERT: B 447 SER cc_start: 0.8374 (p) cc_final: 0.7864 (p) REVERT: B 463 GLU cc_start: 0.8689 (tt0) cc_final: 0.8081 (tt0) REVERT: B 488 ASP cc_start: 0.7400 (m-30) cc_final: 0.6972 (m-30) REVERT: B 530 ARG cc_start: 0.7413 (ptm160) cc_final: 0.7039 (ttp80) REVERT: C 50 LEU cc_start: 0.8570 (mt) cc_final: 0.8349 (mt) REVERT: C 55 ILE cc_start: 0.8090 (mm) cc_final: 0.7802 (mm) REVERT: C 74 SER cc_start: 0.7799 (m) cc_final: 0.7064 (p) REVERT: C 77 ASP cc_start: 0.7614 (m-30) cc_final: 0.7259 (m-30) REVERT: C 168 LEU cc_start: 0.8507 (tp) cc_final: 0.8089 (tp) REVERT: C 173 ARG cc_start: 0.6831 (pmt170) cc_final: 0.6453 (pmt170) REVERT: C 206 VAL cc_start: 0.9243 (t) cc_final: 0.8931 (m) REVERT: C 213 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6227 (mt0) REVERT: C 218 THR cc_start: 0.8783 (m) cc_final: 0.8287 (p) REVERT: C 235 ASP cc_start: 0.8258 (m-30) cc_final: 0.8055 (m-30) REVERT: C 248 ILE cc_start: 0.8265 (mt) cc_final: 0.7692 (pt) REVERT: C 268 ASN cc_start: 0.8080 (t0) cc_final: 0.7335 (t0) REVERT: C 303 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8007 (tp30) REVERT: C 308 ARG cc_start: 0.6875 (ptp-110) cc_final: 0.6567 (ptt180) REVERT: C 349 ASP cc_start: 0.7263 (p0) cc_final: 0.6751 (p0) REVERT: C 531 PHE cc_start: 0.6210 (p90) cc_final: 0.5259 (p90) REVERT: C 532 CYS cc_start: 0.7862 (t) cc_final: 0.6845 (t) REVERT: C 540 MET cc_start: 0.6097 (mtp) cc_final: 0.5824 (mtp) REVERT: C 573 HIS cc_start: 0.7750 (t70) cc_final: 0.7500 (t70) REVERT: C 612 PHE cc_start: 0.7559 (m-80) cc_final: 0.7288 (m-10) REVERT: D 88 GLU cc_start: 0.6981 (tt0) cc_final: 0.6526 (mt-10) REVERT: D 106 ASP cc_start: 0.8470 (p0) cc_final: 0.8091 (p0) REVERT: D 117 ASP cc_start: 0.7341 (t0) cc_final: 0.6969 (p0) REVERT: D 118 ILE cc_start: 0.8243 (pt) cc_final: 0.7820 (pt) REVERT: D 125 GLU cc_start: 0.8505 (tt0) cc_final: 0.8223 (tm-30) REVERT: D 152 ASP cc_start: 0.8354 (t0) cc_final: 0.8116 (t0) REVERT: D 153 ILE cc_start: 0.8639 (pt) cc_final: 0.8411 (pt) REVERT: D 247 ASP cc_start: 0.8031 (t70) cc_final: 0.7628 (t0) REVERT: D 299 ASP cc_start: 0.8340 (m-30) cc_final: 0.7878 (m-30) REVERT: D 368 LEU cc_start: 0.8225 (mt) cc_final: 0.8004 (tt) REVERT: D 380 ASP cc_start: 0.8401 (t0) cc_final: 0.7800 (p0) REVERT: D 388 ILE cc_start: 0.7909 (mt) cc_final: 0.7678 (mm) REVERT: D 393 ASN cc_start: 0.8095 (t0) cc_final: 0.7639 (t0) REVERT: D 431 ASP cc_start: 0.8745 (t70) cc_final: 0.8463 (m-30) REVERT: D 455 LEU cc_start: 0.7592 (tp) cc_final: 0.7333 (tp) REVERT: D 478 ASP cc_start: 0.8314 (m-30) cc_final: 0.8064 (m-30) REVERT: E 47 TYR cc_start: 0.7686 (m-80) cc_final: 0.6893 (m-80) REVERT: E 49 THR cc_start: 0.8178 (p) cc_final: 0.7843 (p) REVERT: E 88 GLU cc_start: 0.7469 (tt0) cc_final: 0.6744 (mt-10) REVERT: E 89 VAL cc_start: 0.8829 (m) cc_final: 0.8564 (p) REVERT: E 118 ILE cc_start: 0.8589 (tt) cc_final: 0.8134 (tt) REVERT: E 201 GLU cc_start: 0.7698 (mp0) cc_final: 0.7010 (tp30) REVERT: E 231 PHE cc_start: 0.8695 (t80) cc_final: 0.8475 (t80) REVERT: E 234 MET cc_start: 0.7021 (ptt) cc_final: 0.6514 (ptt) REVERT: E 262 ASN cc_start: 0.8588 (t0) cc_final: 0.8224 (t0) REVERT: E 268 THR cc_start: 0.8620 (p) cc_final: 0.8059 (t) REVERT: E 270 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 283 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 290 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8078 (mm-30) REVERT: E 309 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 330 ASP cc_start: 0.8274 (t70) cc_final: 0.7591 (t0) REVERT: E 355 THR cc_start: 0.8409 (m) cc_final: 0.7915 (p) REVERT: E 360 ASP cc_start: 0.7517 (t0) cc_final: 0.7302 (t0) REVERT: E 361 ILE cc_start: 0.8174 (tt) cc_final: 0.7866 (mp) REVERT: E 380 ASP cc_start: 0.7842 (p0) cc_final: 0.7619 (p0) REVERT: E 408 GLU cc_start: 0.8294 (tp30) cc_final: 0.8034 (tp30) REVERT: E 442 GLU cc_start: 0.8515 (mp0) cc_final: 0.8221 (mp0) REVERT: E 448 ASP cc_start: 0.8374 (m-30) cc_final: 0.8174 (m-30) REVERT: E 490 GLU cc_start: 0.8848 (mp0) cc_final: 0.8438 (mp0) REVERT: F 49 THR cc_start: 0.8091 (p) cc_final: 0.7802 (p) REVERT: F 53 VAL cc_start: 0.8851 (t) cc_final: 0.8547 (p) REVERT: F 61 ASP cc_start: 0.7477 (t0) cc_final: 0.7250 (m-30) REVERT: F 117 ASP cc_start: 0.7477 (t0) cc_final: 0.7248 (t0) REVERT: F 167 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 178 ASP cc_start: 0.7732 (m-30) cc_final: 0.7093 (m-30) REVERT: F 180 MET cc_start: 0.6732 (mtt) cc_final: 0.5889 (mtp) REVERT: F 201 GLU cc_start: 0.7846 (mp0) cc_final: 0.7064 (mp0) REVERT: F 238 MET cc_start: 0.8309 (tpp) cc_final: 0.7772 (tpt) REVERT: F 249 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8255 (mm-30) REVERT: F 262 ASN cc_start: 0.8876 (t0) cc_final: 0.8190 (t0) REVERT: F 268 THR cc_start: 0.8710 (p) cc_final: 0.8376 (t) REVERT: F 315 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8757 (mt-10) REVERT: F 316 GLU cc_start: 0.8769 (tp30) cc_final: 0.8400 (tp30) REVERT: F 342 GLU cc_start: 0.7441 (tt0) cc_final: 0.6967 (mt-10) REVERT: F 354 LEU cc_start: 0.8690 (mp) cc_final: 0.8447 (mt) REVERT: F 355 THR cc_start: 0.8233 (m) cc_final: 0.7895 (p) REVERT: F 367 ASP cc_start: 0.8249 (t70) cc_final: 0.8010 (t0) REVERT: F 400 ARG cc_start: 0.7039 (tpt90) cc_final: 0.6738 (tpt170) REVERT: F 403 LYS cc_start: 0.8217 (tptt) cc_final: 0.7797 (tptp) REVERT: F 410 MET cc_start: 0.8380 (mtt) cc_final: 0.8039 (mtp) REVERT: F 447 ASP cc_start: 0.8791 (m-30) cc_final: 0.8560 (m-30) REVERT: F 460 LYS cc_start: 0.8658 (tttt) cc_final: 0.8378 (ttpp) REVERT: I 72 MET cc_start: 0.9017 (mmm) cc_final: 0.8296 (mmt) REVERT: I 76 MET cc_start: 0.8781 (mtm) cc_final: 0.8157 (mpp) REVERT: I 89 ASP cc_start: 0.8665 (m-30) cc_final: 0.8088 (t70) REVERT: I 132 MET cc_start: 0.8838 (mtt) cc_final: 0.8493 (mtt) REVERT: I 168 ASP cc_start: 0.8577 (t0) cc_final: 0.7987 (t0) REVERT: I 177 ILE cc_start: 0.8722 (mt) cc_final: 0.8469 (mp) REVERT: I 194 ASN cc_start: 0.8126 (t0) cc_final: 0.7638 (t0) REVERT: I 198 SER cc_start: 0.9061 (m) cc_final: 0.8818 (p) REVERT: I 210 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7525 (tm-30) REVERT: J 68 LYS cc_start: 0.7414 (mttt) cc_final: 0.6318 (tptt) REVERT: J 76 MET cc_start: 0.8983 (mmm) cc_final: 0.8688 (mtm) REVERT: J 89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8147 (t0) REVERT: J 90 LEU cc_start: 0.9452 (mt) cc_final: 0.9233 (mt) REVERT: J 92 THR cc_start: 0.9350 (m) cc_final: 0.9127 (p) REVERT: J 93 ASP cc_start: 0.9105 (m-30) cc_final: 0.8649 (m-30) REVERT: J 96 ASN cc_start: 0.9402 (m-40) cc_final: 0.9195 (m110) REVERT: J 97 GLU cc_start: 0.9132 (tp30) cc_final: 0.8833 (tt0) REVERT: J 129 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8657 (mm-30) REVERT: J 132 MET cc_start: 0.8933 (mmt) cc_final: 0.8478 (mmm) REVERT: J 159 THR cc_start: 0.8837 (p) cc_final: 0.8579 (p) REVERT: J 164 ASP cc_start: 0.8392 (t0) cc_final: 0.8020 (t0) REVERT: J 190 ILE cc_start: 0.8417 (mt) cc_final: 0.8202 (mt) REVERT: J 208 MET cc_start: 0.8292 (tpp) cc_final: 0.7927 (tpp) REVERT: K 72 MET cc_start: 0.8410 (mmm) cc_final: 0.7808 (tmm) REVERT: K 76 MET cc_start: 0.8290 (mtm) cc_final: 0.6970 (ptt) REVERT: K 90 LEU cc_start: 0.9572 (mt) cc_final: 0.9324 (mp) REVERT: K 93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8739 (m-30) REVERT: K 97 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8535 (mt-10) REVERT: K 113 GLN cc_start: 0.8506 (tp40) cc_final: 0.7987 (tm-30) REVERT: K 117 ASP cc_start: 0.8051 (m-30) cc_final: 0.7554 (m-30) REVERT: K 168 ASP cc_start: 0.7967 (t0) cc_final: 0.7527 (t0) REVERT: K 172 TYR cc_start: 0.7764 (m-80) cc_final: 0.7491 (m-10) REVERT: K 173 LEU cc_start: 0.8453 (mt) cc_final: 0.8174 (mt) REVERT: K 197 GLU cc_start: 0.8738 (mp0) cc_final: 0.7962 (tm-30) REVERT: K 198 SER cc_start: 0.8625 (m) cc_final: 0.8304 (p) REVERT: K 206 GLN cc_start: 0.8818 (mt0) cc_final: 0.8439 (mt0) REVERT: K 210 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7691 (tm-30) REVERT: K 219 ASN cc_start: 0.7472 (t0) cc_final: 0.7028 (t0) REVERT: K 221 ASN cc_start: 0.7473 (m-40) cc_final: 0.6693 (t0) REVERT: M 73 VAL cc_start: 0.8374 (t) cc_final: 0.8149 (p) REVERT: M 77 THR cc_start: 0.9303 (m) cc_final: 0.9098 (p) REVERT: M 78 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8603 (ptp-170) REVERT: M 84 MET cc_start: 0.8159 (mtt) cc_final: 0.7931 (mtm) REVERT: M 113 ASN cc_start: 0.8463 (m-40) cc_final: 0.8111 (m-40) REVERT: N 84 MET cc_start: 0.8891 (mtm) cc_final: 0.8337 (mtm) REVERT: N 98 GLN cc_start: 0.8436 (tp40) cc_final: 0.8203 (tp40) REVERT: O 75 GLN cc_start: 0.9070 (mt0) cc_final: 0.8764 (tp40) REVERT: O 78 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8189 (mtm110) REVERT: O 85 GLN cc_start: 0.8839 (mt0) cc_final: 0.8629 (tm-30) REVERT: O 102 MET cc_start: 0.8159 (mtp) cc_final: 0.7558 (mtp) REVERT: O 105 ASP cc_start: 0.7984 (t0) cc_final: 0.7743 (p0) REVERT: Q 43 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8969 (mmtt) REVERT: Q 76 ASN cc_start: 0.7838 (p0) cc_final: 0.7430 (p0) REVERT: Q 104 LYS cc_start: 0.8784 (mttt) cc_final: 0.8577 (mtmm) REVERT: Q 106 ASP cc_start: 0.9167 (m-30) cc_final: 0.8661 (p0) REVERT: Q 109 GLU cc_start: 0.8606 (tt0) cc_final: 0.8059 (tm-30) REVERT: Q 139 TYR cc_start: 0.8590 (t80) cc_final: 0.8229 (t80) REVERT: Q 198 HIS cc_start: 0.8315 (m-70) cc_final: 0.7882 (m170) REVERT: R 42 LEU cc_start: 0.8664 (mt) cc_final: 0.8267 (mp) REVERT: R 79 ASP cc_start: 0.8760 (m-30) cc_final: 0.8261 (t0) REVERT: R 105 LEU cc_start: 0.7853 (mt) cc_final: 0.7598 (mp) REVERT: R 107 LEU cc_start: 0.7836 (tp) cc_final: 0.7327 (tp) REVERT: R 112 TYR cc_start: 0.8422 (t80) cc_final: 0.7980 (t80) REVERT: R 125 ASP cc_start: 0.8802 (m-30) cc_final: 0.8507 (t70) REVERT: R 127 HIS cc_start: 0.8263 (t70) cc_final: 0.7978 (t70) REVERT: R 139 TYR cc_start: 0.8965 (t80) cc_final: 0.8643 (t80) REVERT: R 150 ASN cc_start: 0.7865 (m-40) cc_final: 0.7484 (m-40) REVERT: R 171 ASP cc_start: 0.8470 (m-30) cc_final: 0.8269 (p0) REVERT: R 194 ASP cc_start: 0.8945 (m-30) cc_final: 0.8598 (p0) REVERT: R 195 GLU cc_start: 0.8947 (mp0) cc_final: 0.8715 (mp0) REVERT: R 221 ASP cc_start: 0.8556 (m-30) cc_final: 0.8304 (m-30) REVERT: R 229 MET cc_start: 0.5379 (tpp) cc_final: 0.4998 (tpt) REVERT: S 79 ASP cc_start: 0.8732 (m-30) cc_final: 0.7999 (t0) REVERT: S 113 GLU cc_start: 0.9154 (tp30) cc_final: 0.8853 (tp30) REVERT: S 114 LYS cc_start: 0.8610 (mttt) cc_final: 0.8351 (mmtp) REVERT: S 117 GLN cc_start: 0.8846 (mt0) cc_final: 0.8642 (pp30) REVERT: S 128 VAL cc_start: 0.9288 (t) cc_final: 0.9023 (p) REVERT: S 132 GLN cc_start: 0.8278 (mt0) cc_final: 0.7835 (mp10) REVERT: S 151 PHE cc_start: 0.7764 (m-10) cc_final: 0.7319 (m-10) REVERT: S 153 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7800 (ttm170) REVERT: S 159 LEU cc_start: 0.9130 (tp) cc_final: 0.8922 (tp) REVERT: S 160 GLN cc_start: 0.8205 (mt0) cc_final: 0.7985 (mt0) REVERT: S 172 ASN cc_start: 0.7964 (t0) cc_final: 0.7424 (m-40) REVERT: S 179 PHE cc_start: 0.6811 (m-80) cc_final: 0.6457 (m-80) REVERT: S 196 GLN cc_start: 0.8425 (mt0) cc_final: 0.8116 (mt0) REVERT: S 197 TYR cc_start: 0.7530 (t80) cc_final: 0.6945 (t80) REVERT: S 201 LYS cc_start: 0.7805 (tttt) cc_final: 0.7393 (pttm) REVERT: S 222 GLN cc_start: 0.8533 (mt0) cc_final: 0.7337 (tm-30) outliers start: 2 outliers final: 0 residues processed: 1618 average time/residue: 0.2488 time to fit residues: 633.5804 Evaluate side-chains 936 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 936 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 4.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 HIS C 444 HIS C 468 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 358 ASN E 42 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN F 382 GLN H 27 GLN I 78 GLN J 126 GLN K 77 ASN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN Q 50 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 GLN R 34 GLN R 134 ASN R 172 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088402 restraints weight = 71379.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090898 restraints weight = 37638.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092557 restraints weight = 24156.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093646 restraints weight = 17781.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094381 restraints weight = 14488.400| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36765 Z= 0.169 Angle : 0.662 7.986 49676 Z= 0.346 Chirality : 0.046 0.189 5575 Planarity : 0.005 0.065 6440 Dihedral : 4.950 116.359 5018 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.13 % Rotamer: Outliers : 2.73 % Allowed : 11.15 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.15 (0.12), residues: 4538 helix: 1.74 (0.11), residues: 2111 sheet: -0.09 (0.21), residues: 557 loop : -0.00 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 45 TYR 0.033 0.002 TYR R 197 PHE 0.023 0.002 PHE A 469 TRP 0.011 0.001 TRP E 481 HIS 0.006 0.001 HIS S 118 Details of bonding type rmsd covalent geometry : bond 0.00366 (36765) covalent geometry : angle 0.66241 (49676) hydrogen bonds : bond 0.05545 ( 1953) hydrogen bonds : angle 3.35607 (13707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1033 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: symmetry clash REVERT: A 130 ASP cc_start: 0.6868 (t0) cc_final: 0.6585 (t0) REVERT: A 194 LEU cc_start: 0.8325 (pt) cc_final: 0.7967 (pt) REVERT: A 203 LEU cc_start: 0.9011 (mt) cc_final: 0.8728 (mp) REVERT: A 224 ASN cc_start: 0.8822 (p0) cc_final: 0.8458 (p0) REVERT: A 428 ILE cc_start: 0.9324 (mm) cc_final: 0.9120 (mm) REVERT: A 447 SER cc_start: 0.7882 (m) cc_final: 0.7447 (t) REVERT: A 475 LEU cc_start: 0.8636 (mt) cc_final: 0.8416 (mt) REVERT: A 505 ASP cc_start: 0.7519 (t0) cc_final: 0.7288 (t0) REVERT: A 532 CYS cc_start: 0.7934 (t) cc_final: 0.7629 (t) REVERT: A 612 PHE cc_start: 0.8288 (m-80) cc_final: 0.8034 (m-80) REVERT: B 18 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: B 30 THR cc_start: 0.9279 (m) cc_final: 0.8929 (p) REVERT: B 224 ASN cc_start: 0.8651 (p0) cc_final: 0.8321 (p0) REVERT: B 274 TYR cc_start: 0.8695 (t80) cc_final: 0.8372 (t80) REVERT: B 297 GLU cc_start: 0.8160 (mp0) cc_final: 0.7758 (mm-30) REVERT: B 447 SER cc_start: 0.8858 (p) cc_final: 0.8571 (p) REVERT: B 458 MET cc_start: 0.8045 (mmm) cc_final: 0.7801 (mmm) REVERT: B 488 ASP cc_start: 0.7822 (m-30) cc_final: 0.7508 (m-30) REVERT: B 558 THR cc_start: 0.7321 (p) cc_final: 0.7065 (p) REVERT: C 74 SER cc_start: 0.8520 (m) cc_final: 0.7445 (p) REVERT: C 248 ILE cc_start: 0.8680 (mt) cc_final: 0.8427 (pt) REVERT: C 284 MET cc_start: 0.8692 (mmm) cc_final: 0.8488 (mmm) REVERT: C 340 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8218 (mtm) REVERT: C 349 ASP cc_start: 0.7470 (p0) cc_final: 0.7180 (p0) REVERT: C 485 GLU cc_start: 0.8563 (tt0) cc_final: 0.8247 (tt0) REVERT: C 531 PHE cc_start: 0.5984 (p90) cc_final: 0.5669 (p90) REVERT: D 118 ILE cc_start: 0.8901 (pt) cc_final: 0.8682 (pt) REVERT: D 368 LEU cc_start: 0.9126 (mt) cc_final: 0.8895 (tt) REVERT: E 187 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: E 327 MET cc_start: 0.8035 (tpp) cc_final: 0.7751 (tpp) REVERT: E 358 ASN cc_start: 0.8382 (t0) cc_final: 0.8095 (t0) REVERT: E 360 ASP cc_start: 0.8283 (t0) cc_final: 0.8034 (t0) REVERT: F 49 THR cc_start: 0.8142 (p) cc_final: 0.7936 (p) REVERT: F 96 VAL cc_start: 0.9396 (t) cc_final: 0.9148 (m) REVERT: F 178 ASP cc_start: 0.8227 (m-30) cc_final: 0.7871 (m-30) REVERT: F 403 LYS cc_start: 0.8221 (tptt) cc_final: 0.7972 (tptp) REVERT: H 12 SER cc_start: 0.8006 (p) cc_final: 0.7667 (p) REVERT: H 173 GLU cc_start: 0.7823 (tt0) cc_final: 0.7488 (tt0) REVERT: I 164 ASP cc_start: 0.7998 (t0) cc_final: 0.7768 (t0) REVERT: I 194 ASN cc_start: 0.8449 (t0) cc_final: 0.8064 (t0) REVERT: J 68 LYS cc_start: 0.6920 (mttt) cc_final: 0.6353 (tttt) REVERT: J 185 ASN cc_start: 0.8473 (p0) cc_final: 0.8240 (p0) REVERT: J 190 ILE cc_start: 0.9277 (mt) cc_final: 0.8970 (mt) REVERT: K 76 MET cc_start: 0.7583 (mtm) cc_final: 0.7256 (ptt) REVERT: K 88 ASP cc_start: 0.7786 (t70) cc_final: 0.7480 (t0) REVERT: K 92 THR cc_start: 0.9216 (m) cc_final: 0.8995 (p) REVERT: K 197 GLU cc_start: 0.7576 (mp0) cc_final: 0.7216 (tm-30) REVERT: M 84 MET cc_start: 0.8721 (mtt) cc_final: 0.8519 (mtm) REVERT: N 104 CYS cc_start: 0.8135 (m) cc_final: 0.7867 (m) REVERT: O 100 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8451 (mp) REVERT: O 102 MET cc_start: 0.8663 (mtp) cc_final: 0.8143 (mtp) REVERT: Q 85 SER cc_start: 0.8662 (t) cc_final: 0.8455 (p) REVERT: Q 198 HIS cc_start: 0.7744 (m-70) cc_final: 0.7165 (m-70) REVERT: R 37 ASP cc_start: 0.7623 (t0) cc_final: 0.7330 (t0) REVERT: R 79 ASP cc_start: 0.8374 (m-30) cc_final: 0.7969 (t0) REVERT: R 107 LEU cc_start: 0.7854 (tp) cc_final: 0.7374 (tp) REVERT: R 112 TYR cc_start: 0.8025 (t80) cc_final: 0.7800 (t80) REVERT: R 197 TYR cc_start: 0.7625 (m-80) cc_final: 0.7109 (m-80) REVERT: R 228 THR cc_start: 0.8212 (m) cc_final: 0.7690 (p) REVERT: R 229 MET cc_start: 0.7185 (tpp) cc_final: 0.6513 (tpt) REVERT: S 33 MET cc_start: 0.8098 (tpp) cc_final: 0.7719 (mtp) REVERT: S 54 ILE cc_start: 0.8585 (tp) cc_final: 0.8368 (tp) REVERT: S 60 TYR cc_start: 0.7529 (m-80) cc_final: 0.6958 (m-80) REVERT: S 151 PHE cc_start: 0.7711 (m-10) cc_final: 0.7487 (m-10) REVERT: S 201 LYS cc_start: 0.7892 (tttt) cc_final: 0.7661 (pttm) REVERT: S 222 GLN cc_start: 0.7784 (mt0) cc_final: 0.6786 (tm-30) outliers start: 108 outliers final: 61 residues processed: 1085 average time/residue: 0.2268 time to fit residues: 405.4760 Evaluate side-chains 867 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 802 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 34 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 32 optimal weight: 5.9990 chunk 386 optimal weight: 0.9980 chunk 406 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 448 optimal weight: 0.4980 chunk 285 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 610 ASN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 251 ASN M 113 ASN O 75 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN R 198 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087295 restraints weight = 71773.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089781 restraints weight = 37908.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091431 restraints weight = 24394.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092533 restraints weight = 18026.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093171 restraints weight = 14675.242| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36765 Z= 0.152 Angle : 0.632 9.083 49676 Z= 0.324 Chirality : 0.045 0.180 5575 Planarity : 0.005 0.051 6440 Dihedral : 4.835 121.593 5018 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 13.99 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.10 (0.12), residues: 4538 helix: 1.81 (0.11), residues: 2124 sheet: -0.27 (0.21), residues: 585 loop : -0.13 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG F 400 TYR 0.037 0.002 TYR Q 112 PHE 0.029 0.002 PHE R 200 TRP 0.010 0.001 TRP R 55 HIS 0.008 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00318 (36765) covalent geometry : angle 0.63206 (49676) hydrogen bonds : bond 0.04739 ( 1953) hydrogen bonds : angle 3.08309 (13707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 871 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.8871 (p0) cc_final: 0.8470 (p0) REVERT: A 258 VAL cc_start: 0.9232 (p) cc_final: 0.9022 (m) REVERT: A 387 GLU cc_start: 0.8065 (tp30) cc_final: 0.7863 (tp30) REVERT: A 475 LEU cc_start: 0.8659 (mt) cc_final: 0.8425 (mt) REVERT: A 505 ASP cc_start: 0.7665 (t0) cc_final: 0.7322 (t0) REVERT: A 532 CYS cc_start: 0.8068 (t) cc_final: 0.7804 (t) REVERT: B 18 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: B 30 THR cc_start: 0.9389 (m) cc_final: 0.9027 (p) REVERT: B 224 ASN cc_start: 0.8734 (p0) cc_final: 0.8421 (p0) REVERT: B 447 SER cc_start: 0.8856 (p) cc_final: 0.8610 (p) REVERT: C 218 THR cc_start: 0.8788 (m) cc_final: 0.8538 (m) REVERT: C 248 ILE cc_start: 0.8709 (mt) cc_final: 0.8473 (pt) REVERT: C 284 MET cc_start: 0.8724 (mmm) cc_final: 0.8434 (mmm) REVERT: C 295 THR cc_start: 0.8827 (p) cc_final: 0.8445 (t) REVERT: C 340 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: C 349 ASP cc_start: 0.7445 (p0) cc_final: 0.7164 (p0) REVERT: C 485 GLU cc_start: 0.8557 (tt0) cc_final: 0.8275 (tt0) REVERT: C 531 PHE cc_start: 0.5793 (p90) cc_final: 0.5454 (p90) REVERT: D 169 MET cc_start: 0.7740 (ttt) cc_final: 0.7465 (ttt) REVERT: D 187 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: D 270 GLU cc_start: 0.8177 (tp30) cc_final: 0.7898 (tp30) REVERT: D 446 SER cc_start: 0.8588 (m) cc_final: 0.8369 (p) REVERT: E 47 TYR cc_start: 0.7946 (m-80) cc_final: 0.7435 (m-80) REVERT: E 49 THR cc_start: 0.8313 (p) cc_final: 0.8004 (p) REVERT: E 178 ASP cc_start: 0.7956 (m-30) cc_final: 0.7742 (p0) REVERT: E 238 MET cc_start: 0.6872 (tmm) cc_final: 0.6504 (tmm) REVERT: E 327 MET cc_start: 0.8235 (tpp) cc_final: 0.7857 (tpp) REVERT: E 358 ASN cc_start: 0.8468 (t0) cc_final: 0.8105 (t0) REVERT: E 360 ASP cc_start: 0.8336 (t0) cc_final: 0.8033 (t0) REVERT: F 178 ASP cc_start: 0.8188 (m-30) cc_final: 0.7843 (m-30) REVERT: F 180 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6893 (mtm) REVERT: F 355 THR cc_start: 0.8829 (m) cc_final: 0.8317 (p) REVERT: F 403 LYS cc_start: 0.8298 (tptt) cc_final: 0.8042 (tptp) REVERT: H 168 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7605 (ttp-170) REVERT: H 173 GLU cc_start: 0.7795 (tt0) cc_final: 0.7446 (tt0) REVERT: H 191 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8447 (mp) REVERT: I 129 GLU cc_start: 0.7981 (tp30) cc_final: 0.7769 (tp30) REVERT: I 194 ASN cc_start: 0.8503 (t0) cc_final: 0.8203 (t0) REVERT: J 68 LYS cc_start: 0.6939 (mttt) cc_final: 0.6399 (tttt) REVERT: J 120 VAL cc_start: 0.9426 (m) cc_final: 0.8943 (p) REVERT: K 72 MET cc_start: 0.8110 (tmm) cc_final: 0.7709 (tmm) REVERT: K 112 TYR cc_start: 0.7930 (t80) cc_final: 0.7325 (t80) REVERT: K 155 TYR cc_start: 0.8683 (t80) cc_final: 0.8386 (t80) REVERT: M 75 GLN cc_start: 0.8776 (mp10) cc_final: 0.8234 (pm20) REVERT: N 75 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8373 (mm-40) REVERT: N 78 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8061 (mtm180) REVERT: O 75 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8164 (tm-30) REVERT: Q 198 HIS cc_start: 0.7760 (m-70) cc_final: 0.7143 (m-70) REVERT: R 28 TYR cc_start: 0.8753 (t80) cc_final: 0.8540 (t80) REVERT: R 33 MET cc_start: 0.8678 (tpp) cc_final: 0.8381 (tpp) REVERT: R 107 LEU cc_start: 0.8050 (tp) cc_final: 0.7799 (tp) REVERT: R 115 MET cc_start: 0.8784 (mtp) cc_final: 0.8543 (mtp) REVERT: R 228 THR cc_start: 0.8429 (m) cc_final: 0.7819 (p) REVERT: S 33 MET cc_start: 0.8099 (tpp) cc_final: 0.7752 (mtp) REVERT: S 151 PHE cc_start: 0.7858 (m-10) cc_final: 0.7432 (m-10) REVERT: S 201 LYS cc_start: 0.8030 (tttt) cc_final: 0.7700 (pttm) REVERT: S 222 GLN cc_start: 0.7707 (mt0) cc_final: 0.6812 (tm-30) outliers start: 117 outliers final: 63 residues processed: 930 average time/residue: 0.2195 time to fit residues: 338.7286 Evaluate side-chains 845 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 776 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 34 GLN Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 439 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 441 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 164 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 610 ASN C 65 GLN C 103 GLN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN J 139 GLN K 194 ASN M 91 ASN M 98 GLN N 98 GLN O 82 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 HIS R 134 ASN R 150 ASN R 198 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082476 restraints weight = 72963.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084944 restraints weight = 38424.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086560 restraints weight = 24642.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087647 restraints weight = 18200.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088365 restraints weight = 14792.764| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36765 Z= 0.218 Angle : 0.668 9.818 49676 Z= 0.342 Chirality : 0.046 0.176 5575 Planarity : 0.005 0.062 6440 Dihedral : 4.890 133.336 5018 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.97 % Allowed : 14.85 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.12), residues: 4538 helix: 1.76 (0.11), residues: 2134 sheet: -0.23 (0.21), residues: 571 loop : -0.39 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 137 TYR 0.037 0.002 TYR Q 126 PHE 0.027 0.002 PHE R 200 TRP 0.013 0.002 TRP B 433 HIS 0.008 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00495 (36765) covalent geometry : angle 0.66775 (49676) hydrogen bonds : bond 0.04557 ( 1953) hydrogen bonds : angle 3.05566 (13707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 808 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.9063 (mt) cc_final: 0.8814 (mp) REVERT: A 387 GLU cc_start: 0.8271 (tp30) cc_final: 0.8064 (tp30) REVERT: A 505 ASP cc_start: 0.8022 (t0) cc_final: 0.7610 (t0) REVERT: A 532 CYS cc_start: 0.8381 (t) cc_final: 0.8141 (t) REVERT: B 18 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: B 30 THR cc_start: 0.9530 (m) cc_final: 0.9043 (p) REVERT: B 224 ASN cc_start: 0.8977 (p0) cc_final: 0.8722 (p0) REVERT: B 400 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8510 (mtm-85) REVERT: C 218 THR cc_start: 0.8871 (m) cc_final: 0.8638 (m) REVERT: C 248 ILE cc_start: 0.8932 (mt) cc_final: 0.8645 (pt) REVERT: C 284 MET cc_start: 0.8819 (mmm) cc_final: 0.8600 (mmm) REVERT: C 349 ASP cc_start: 0.7716 (p0) cc_final: 0.7431 (p0) REVERT: C 458 MET cc_start: 0.7778 (mmt) cc_final: 0.7159 (mmt) REVERT: C 531 PHE cc_start: 0.5767 (p90) cc_final: 0.5405 (p90) REVERT: C 574 MET cc_start: 0.8189 (ppp) cc_final: 0.7634 (ppp) REVERT: D 149 ASP cc_start: 0.7666 (m-30) cc_final: 0.7379 (m-30) REVERT: D 169 MET cc_start: 0.8183 (ttt) cc_final: 0.7865 (ttt) REVERT: D 270 GLU cc_start: 0.8426 (tp30) cc_final: 0.8095 (mm-30) REVERT: D 302 SER cc_start: 0.8914 (m) cc_final: 0.8603 (t) REVERT: D 446 SER cc_start: 0.8685 (m) cc_final: 0.8474 (p) REVERT: E 47 TYR cc_start: 0.8278 (m-80) cc_final: 0.7601 (m-80) REVERT: E 154 MET cc_start: 0.8128 (mmm) cc_final: 0.7738 (mmt) REVERT: E 178 ASP cc_start: 0.8018 (m-30) cc_final: 0.7802 (p0) REVERT: E 201 GLU cc_start: 0.7480 (tp30) cc_final: 0.7253 (tp30) REVERT: E 238 MET cc_start: 0.6971 (tmm) cc_final: 0.6684 (tmm) REVERT: E 327 MET cc_start: 0.8575 (tpp) cc_final: 0.8192 (tpp) REVERT: E 358 ASN cc_start: 0.8707 (t0) cc_final: 0.8285 (t0) REVERT: E 360 ASP cc_start: 0.8526 (t0) cc_final: 0.8140 (t0) REVERT: F 178 ASP cc_start: 0.8392 (m-30) cc_final: 0.7971 (m-30) REVERT: F 201 GLU cc_start: 0.7629 (mp0) cc_final: 0.7343 (mp0) REVERT: F 259 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9016 (mm) REVERT: F 269 ILE cc_start: 0.9237 (mm) cc_final: 0.9018 (mm) REVERT: F 330 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8012 (t0) REVERT: F 336 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7554 (tp30) REVERT: F 403 LYS cc_start: 0.8432 (tptt) cc_final: 0.8078 (tptp) REVERT: H 168 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: H 173 GLU cc_start: 0.7838 (tt0) cc_final: 0.7586 (tt0) REVERT: I 194 ASN cc_start: 0.8800 (t0) cc_final: 0.8472 (t0) REVERT: J 68 LYS cc_start: 0.6949 (mttt) cc_final: 0.6415 (tttt) REVERT: J 185 ASN cc_start: 0.8745 (p0) cc_final: 0.8374 (p0) REVERT: K 72 MET cc_start: 0.8094 (tmm) cc_final: 0.7817 (tmm) REVERT: K 112 TYR cc_start: 0.8067 (t80) cc_final: 0.7510 (t80) REVERT: K 133 ILE cc_start: 0.8813 (mt) cc_final: 0.8591 (mt) REVERT: K 197 GLU cc_start: 0.7636 (mp0) cc_final: 0.6785 (tm-30) REVERT: N 75 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8348 (mm-40) REVERT: N 78 ARG cc_start: 0.8484 (mtm110) cc_final: 0.8097 (mtm110) REVERT: O 79 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8397 (ttp-110) REVERT: O 90 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7530 (ptt-90) REVERT: Q 198 HIS cc_start: 0.7903 (m-70) cc_final: 0.7461 (m170) REVERT: R 33 MET cc_start: 0.8913 (tpp) cc_final: 0.8577 (tpp) REVERT: R 83 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.8090 (ttp-170) REVERT: R 103 MET cc_start: 0.7480 (ttm) cc_final: 0.7175 (ttm) REVERT: R 107 LEU cc_start: 0.8165 (tp) cc_final: 0.7928 (tp) REVERT: R 196 GLN cc_start: 0.7772 (mt0) cc_final: 0.7477 (mt0) REVERT: S 33 MET cc_start: 0.8203 (tpp) cc_final: 0.7753 (mtp) REVERT: S 151 PHE cc_start: 0.7981 (m-10) cc_final: 0.7424 (m-10) REVERT: S 201 LYS cc_start: 0.8156 (tttt) cc_final: 0.7725 (pttm) REVERT: S 222 GLN cc_start: 0.7909 (mt0) cc_final: 0.6850 (tm-30) outliers start: 157 outliers final: 110 residues processed: 884 average time/residue: 0.2244 time to fit residues: 330.2945 Evaluate side-chains 860 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 745 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain S residue 34 GLN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 198 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 339 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 610 ASN C 103 GLN ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN H 27 GLN M 91 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 HIS R 134 ASN S 196 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083778 restraints weight = 71788.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086246 restraints weight = 37635.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.087879 restraints weight = 24039.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088972 restraints weight = 17721.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089649 restraints weight = 14421.397| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36765 Z= 0.154 Angle : 0.610 9.627 49676 Z= 0.311 Chirality : 0.044 0.191 5575 Planarity : 0.004 0.048 6440 Dihedral : 4.772 134.425 5018 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 3.21 % Allowed : 17.05 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.99 (0.12), residues: 4538 helix: 1.85 (0.11), residues: 2130 sheet: -0.21 (0.22), residues: 541 loop : -0.44 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 79 TYR 0.042 0.001 TYR E 328 PHE 0.029 0.002 PHE R 200 TRP 0.013 0.001 TRP A 567 HIS 0.014 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00350 (36765) covalent geometry : angle 0.60968 (49676) hydrogen bonds : bond 0.04244 ( 1953) hydrogen bonds : angle 2.94652 (13707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 801 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.9050 (mt) cc_final: 0.8838 (mp) REVERT: A 505 ASP cc_start: 0.8100 (t0) cc_final: 0.7662 (t0) REVERT: A 532 CYS cc_start: 0.8397 (t) cc_final: 0.8145 (t) REVERT: A 574 MET cc_start: 0.6742 (ptp) cc_final: 0.6517 (ptp) REVERT: A 584 MET cc_start: 0.8474 (tpp) cc_final: 0.7958 (tpp) REVERT: B 18 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: B 30 THR cc_start: 0.9525 (m) cc_final: 0.9004 (p) REVERT: C 218 THR cc_start: 0.8817 (m) cc_final: 0.8566 (m) REVERT: C 458 MET cc_start: 0.7758 (mmt) cc_final: 0.7225 (mmt) REVERT: C 531 PHE cc_start: 0.5753 (p90) cc_final: 0.5414 (p90) REVERT: C 565 ILE cc_start: 0.6947 (mt) cc_final: 0.6517 (tp) REVERT: D 149 ASP cc_start: 0.7837 (m-30) cc_final: 0.7579 (m-30) REVERT: D 302 SER cc_start: 0.8870 (m) cc_final: 0.8592 (t) REVERT: E 47 TYR cc_start: 0.8262 (m-80) cc_final: 0.7467 (m-80) REVERT: E 49 THR cc_start: 0.8518 (p) cc_final: 0.8202 (p) REVERT: E 154 MET cc_start: 0.8170 (mmm) cc_final: 0.7865 (mmt) REVERT: E 201 GLU cc_start: 0.7332 (tp30) cc_final: 0.7002 (tp30) REVERT: E 327 MET cc_start: 0.8608 (tpp) cc_final: 0.8220 (tpp) REVERT: E 358 ASN cc_start: 0.8658 (t0) cc_final: 0.8232 (t0) REVERT: E 360 ASP cc_start: 0.8459 (t0) cc_final: 0.8076 (t0) REVERT: F 178 ASP cc_start: 0.8374 (m-30) cc_final: 0.7980 (m-30) REVERT: F 180 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7412 (mtp) REVERT: F 201 GLU cc_start: 0.7502 (mp0) cc_final: 0.7292 (mp0) REVERT: F 259 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8956 (mm) REVERT: F 300 MET cc_start: 0.8766 (mmm) cc_final: 0.8549 (mmp) REVERT: F 330 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7824 (t0) REVERT: F 336 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7478 (tp30) REVERT: F 403 LYS cc_start: 0.8399 (tptt) cc_final: 0.7983 (tptp) REVERT: H 14 MET cc_start: 0.8446 (mmm) cc_final: 0.8197 (mmm) REVERT: H 24 LYS cc_start: 0.9004 (tppt) cc_final: 0.8792 (tppt) REVERT: H 168 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7730 (ttp-170) REVERT: H 173 GLU cc_start: 0.7861 (tt0) cc_final: 0.7602 (tt0) REVERT: J 68 LYS cc_start: 0.6934 (mttt) cc_final: 0.6408 (tttt) REVERT: J 185 ASN cc_start: 0.8780 (p0) cc_final: 0.8361 (p0) REVERT: K 112 TYR cc_start: 0.8081 (t80) cc_final: 0.7653 (t80) REVERT: K 197 GLU cc_start: 0.7625 (mp0) cc_final: 0.6711 (tm-30) REVERT: M 109 GLN cc_start: 0.8184 (tt0) cc_final: 0.7787 (tp-100) REVERT: O 90 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7570 (ptt-90) REVERT: O 102 MET cc_start: 0.8566 (mtp) cc_final: 0.8225 (ttm) REVERT: Q 39 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: Q 161 MET cc_start: 0.8446 (tpp) cc_final: 0.8242 (tmm) REVERT: Q 198 HIS cc_start: 0.7972 (m-70) cc_final: 0.7558 (m-70) REVERT: R 33 MET cc_start: 0.8933 (tpp) cc_final: 0.8460 (tpp) REVERT: R 83 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8073 (ttp-170) REVERT: R 103 MET cc_start: 0.7508 (ttm) cc_final: 0.7197 (ttm) REVERT: R 107 LEU cc_start: 0.8101 (tp) cc_final: 0.7865 (tp) REVERT: R 115 MET cc_start: 0.8881 (mtp) cc_final: 0.8675 (mtp) REVERT: S 33 MET cc_start: 0.8251 (tpp) cc_final: 0.7784 (mtp) REVERT: S 151 PHE cc_start: 0.7964 (m-10) cc_final: 0.7407 (m-10) REVERT: S 197 TYR cc_start: 0.7379 (m-80) cc_final: 0.7174 (m-80) REVERT: S 201 LYS cc_start: 0.8140 (tttt) cc_final: 0.7693 (pttm) REVERT: S 222 GLN cc_start: 0.7892 (mt0) cc_final: 0.6817 (tm-30) outliers start: 127 outliers final: 87 residues processed: 861 average time/residue: 0.2189 time to fit residues: 313.7843 Evaluate side-chains 839 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 745 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 150 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 309 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 449 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 610 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN O 82 GLN O 88 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084665 restraints weight = 71915.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087157 restraints weight = 37560.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088807 restraints weight = 23946.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089918 restraints weight = 17550.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090647 restraints weight = 14171.222| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36765 Z= 0.140 Angle : 0.617 12.310 49676 Z= 0.312 Chirality : 0.044 0.185 5575 Planarity : 0.004 0.049 6440 Dihedral : 4.712 135.179 5018 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 3.06 % Allowed : 18.21 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.05 (0.13), residues: 4538 helix: 1.96 (0.11), residues: 2116 sheet: -0.22 (0.23), residues: 534 loop : -0.45 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 90 TYR 0.034 0.001 TYR C 535 PHE 0.032 0.002 PHE R 200 TRP 0.017 0.001 TRP A 567 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00314 (36765) covalent geometry : angle 0.61695 (49676) hydrogen bonds : bond 0.04051 ( 1953) hydrogen bonds : angle 2.89295 (13707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 799 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7287 (t0) cc_final: 0.6879 (t0) REVERT: A 203 LEU cc_start: 0.9107 (mt) cc_final: 0.8880 (mp) REVERT: A 218 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 505 ASP cc_start: 0.8126 (t0) cc_final: 0.7724 (t70) REVERT: A 532 CYS cc_start: 0.8389 (t) cc_final: 0.8134 (t) REVERT: A 574 MET cc_start: 0.6530 (ptp) cc_final: 0.6288 (ptp) REVERT: B 18 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: B 30 THR cc_start: 0.9515 (m) cc_final: 0.8958 (p) REVERT: B 279 GLU cc_start: 0.7005 (tp30) cc_final: 0.6736 (tp30) REVERT: B 520 LEU cc_start: 0.8669 (mp) cc_final: 0.8405 (mp) REVERT: C 218 THR cc_start: 0.8776 (m) cc_final: 0.8522 (m) REVERT: C 458 MET cc_start: 0.7753 (mmt) cc_final: 0.7208 (mmt) REVERT: C 531 PHE cc_start: 0.5735 (p90) cc_final: 0.5404 (p90) REVERT: C 565 ILE cc_start: 0.6934 (mt) cc_final: 0.6556 (tp) REVERT: D 464 THR cc_start: 0.9127 (m) cc_final: 0.8726 (p) REVERT: E 47 TYR cc_start: 0.8288 (m-80) cc_final: 0.7473 (m-80) REVERT: E 49 THR cc_start: 0.8451 (p) cc_final: 0.8133 (p) REVERT: E 125 GLU cc_start: 0.8554 (tt0) cc_final: 0.8073 (tm-30) REVERT: E 201 GLU cc_start: 0.7248 (tp30) cc_final: 0.6909 (tp30) REVERT: E 327 MET cc_start: 0.8512 (tpp) cc_final: 0.8038 (tpp) REVERT: E 358 ASN cc_start: 0.8564 (t0) cc_final: 0.8103 (t0) REVERT: E 360 ASP cc_start: 0.8475 (t0) cc_final: 0.8111 (t0) REVERT: F 178 ASP cc_start: 0.8340 (m-30) cc_final: 0.7953 (m-30) REVERT: F 259 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8956 (mm) REVERT: F 314 ARG cc_start: 0.7662 (ptm-80) cc_final: 0.7291 (ttp-170) REVERT: F 330 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7749 (t0) REVERT: F 373 THR cc_start: 0.9275 (p) cc_final: 0.9037 (t) REVERT: F 403 LYS cc_start: 0.8323 (tptt) cc_final: 0.7850 (tptp) REVERT: H 168 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7773 (ttp-170) REVERT: H 173 GLU cc_start: 0.7860 (tt0) cc_final: 0.7627 (tt0) REVERT: J 68 LYS cc_start: 0.6889 (mttt) cc_final: 0.6380 (tptt) REVERT: J 185 ASN cc_start: 0.8785 (p0) cc_final: 0.8406 (p0) REVERT: K 112 TYR cc_start: 0.8143 (t80) cc_final: 0.7712 (t80) REVERT: K 196 LEU cc_start: 0.8922 (mt) cc_final: 0.8682 (mt) REVERT: M 91 ASN cc_start: 0.7602 (p0) cc_final: 0.7137 (p0) REVERT: M 107 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7809 (tpp80) REVERT: M 109 GLN cc_start: 0.8178 (tt0) cc_final: 0.7782 (tp-100) REVERT: N 78 ARG cc_start: 0.8540 (mtm110) cc_final: 0.8188 (mtm110) REVERT: N 109 GLN cc_start: 0.7975 (pt0) cc_final: 0.7767 (pm20) REVERT: N 115 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7688 (mmt180) REVERT: O 102 MET cc_start: 0.8379 (mtp) cc_final: 0.8101 (mtp) REVERT: Q 161 MET cc_start: 0.8427 (tpp) cc_final: 0.8221 (tmm) REVERT: Q 198 HIS cc_start: 0.7891 (m-70) cc_final: 0.7483 (m-70) REVERT: R 33 MET cc_start: 0.8975 (tpp) cc_final: 0.8500 (tpp) REVERT: R 83 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8099 (ttp-170) REVERT: R 103 MET cc_start: 0.7438 (ttm) cc_final: 0.7166 (ttm) REVERT: R 105 LEU cc_start: 0.7668 (mm) cc_final: 0.7282 (mp) REVERT: R 107 LEU cc_start: 0.8010 (tp) cc_final: 0.7779 (tp) REVERT: R 115 MET cc_start: 0.8803 (mtp) cc_final: 0.8526 (mtp) REVERT: R 153 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8542 (tpp80) REVERT: R 229 MET cc_start: 0.6932 (tpt) cc_final: 0.6620 (tpt) REVERT: S 33 MET cc_start: 0.8231 (tpp) cc_final: 0.7751 (mtp) REVERT: S 151 PHE cc_start: 0.7897 (m-10) cc_final: 0.7346 (m-10) REVERT: S 201 LYS cc_start: 0.8139 (tttt) cc_final: 0.7721 (pttm) REVERT: S 222 GLN cc_start: 0.7845 (mt0) cc_final: 0.6776 (tm-30) outliers start: 121 outliers final: 87 residues processed: 860 average time/residue: 0.2237 time to fit residues: 318.9110 Evaluate side-chains 838 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 746 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 126 TYR Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 414 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN H 27 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081621 restraints weight = 72743.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084060 restraints weight = 38079.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085689 restraints weight = 24364.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086768 restraints weight = 17897.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087480 restraints weight = 14549.428| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36765 Z= 0.209 Angle : 0.666 14.853 49676 Z= 0.339 Chirality : 0.046 0.227 5575 Planarity : 0.005 0.063 6440 Dihedral : 4.793 136.005 5018 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 3.39 % Allowed : 18.56 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4538 helix: 1.89 (0.11), residues: 2124 sheet: -0.35 (0.23), residues: 538 loop : -0.51 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 79 TYR 0.039 0.002 TYR R 197 PHE 0.036 0.002 PHE R 200 TRP 0.019 0.002 TRP A 567 HIS 0.010 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00477 (36765) covalent geometry : angle 0.66604 (49676) hydrogen bonds : bond 0.04160 ( 1953) hydrogen bonds : angle 2.93044 (13707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 751 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7268 (t0) cc_final: 0.6870 (t0) REVERT: A 171 ARG cc_start: 0.7775 (ptp90) cc_final: 0.7532 (ptt180) REVERT: A 203 LEU cc_start: 0.9100 (mt) cc_final: 0.8877 (mp) REVERT: A 505 ASP cc_start: 0.8173 (t0) cc_final: 0.7787 (t70) REVERT: A 532 CYS cc_start: 0.8470 (t) cc_final: 0.8218 (t) REVERT: B 18 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: B 30 THR cc_start: 0.9559 (m) cc_final: 0.9059 (p) REVERT: B 279 GLU cc_start: 0.7100 (tp30) cc_final: 0.6842 (tp30) REVERT: C 218 THR cc_start: 0.8832 (m) cc_final: 0.8583 (m) REVERT: C 531 PHE cc_start: 0.5725 (p90) cc_final: 0.5356 (p90) REVERT: D 302 SER cc_start: 0.8968 (m) cc_final: 0.8665 (t) REVERT: E 47 TYR cc_start: 0.8320 (m-80) cc_final: 0.7553 (m-80) REVERT: E 49 THR cc_start: 0.8569 (p) cc_final: 0.8278 (p) REVERT: E 125 GLU cc_start: 0.8582 (tt0) cc_final: 0.8095 (tm-30) REVERT: E 154 MET cc_start: 0.8211 (mmm) cc_final: 0.7770 (mmt) REVERT: E 201 GLU cc_start: 0.7426 (tp30) cc_final: 0.7022 (tp30) REVERT: E 327 MET cc_start: 0.8561 (tpp) cc_final: 0.7933 (tpp) REVERT: E 358 ASN cc_start: 0.8651 (t0) cc_final: 0.8205 (t0) REVERT: E 360 ASP cc_start: 0.8593 (t0) cc_final: 0.8240 (t0) REVERT: F 158 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8516 (mt) REVERT: F 178 ASP cc_start: 0.8403 (m-30) cc_final: 0.7994 (m-30) REVERT: F 259 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8981 (mm) REVERT: F 330 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7810 (t0) REVERT: H 24 LYS cc_start: 0.9063 (tppt) cc_final: 0.8717 (tppt) REVERT: H 168 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7754 (ttp-170) REVERT: H 173 GLU cc_start: 0.7910 (tt0) cc_final: 0.7640 (tt0) REVERT: J 68 LYS cc_start: 0.7003 (mttt) cc_final: 0.6448 (tptt) REVERT: J 185 ASN cc_start: 0.8872 (p0) cc_final: 0.8445 (p0) REVERT: J 208 MET cc_start: 0.8364 (tpp) cc_final: 0.8016 (tpp) REVERT: K 112 TYR cc_start: 0.8178 (t80) cc_final: 0.7763 (t80) REVERT: K 197 GLU cc_start: 0.7743 (mp0) cc_final: 0.6728 (tm-30) REVERT: M 107 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7811 (tpp80) REVERT: N 78 ARG cc_start: 0.8520 (mtm110) cc_final: 0.8218 (mtm110) REVERT: N 80 GLN cc_start: 0.8564 (mt0) cc_final: 0.8120 (mt0) REVERT: N 109 GLN cc_start: 0.8072 (pt0) cc_final: 0.7804 (pm20) REVERT: O 102 MET cc_start: 0.8459 (mtp) cc_final: 0.7950 (mtp) REVERT: Q 85 SER cc_start: 0.9014 (m) cc_final: 0.8270 (t) REVERT: Q 123 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7716 (mttp) REVERT: Q 139 TYR cc_start: 0.8616 (t80) cc_final: 0.8194 (t80) REVERT: Q 198 HIS cc_start: 0.7974 (m-70) cc_final: 0.7540 (m-70) REVERT: R 33 MET cc_start: 0.9016 (tpp) cc_final: 0.8628 (tpp) REVERT: R 83 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8127 (ttp-170) REVERT: R 103 MET cc_start: 0.7455 (ttm) cc_final: 0.7173 (ttm) REVERT: R 105 LEU cc_start: 0.7785 (mm) cc_final: 0.7397 (mp) REVERT: R 107 LEU cc_start: 0.8034 (tp) cc_final: 0.7795 (tp) REVERT: R 115 MET cc_start: 0.8875 (mtp) cc_final: 0.8624 (mtp) REVERT: S 33 MET cc_start: 0.8245 (tpp) cc_final: 0.7722 (mtp) REVERT: S 74 CYS cc_start: 0.7762 (m) cc_final: 0.7281 (m) REVERT: S 151 PHE cc_start: 0.7949 (m-10) cc_final: 0.7356 (m-10) REVERT: S 201 LYS cc_start: 0.8208 (tttt) cc_final: 0.7819 (pttm) REVERT: S 222 GLN cc_start: 0.7900 (mt0) cc_final: 0.6817 (tm-30) outliers start: 134 outliers final: 105 residues processed: 825 average time/residue: 0.2228 time to fit residues: 305.8963 Evaluate side-chains 820 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 710 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 126 TYR Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 411 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS B 610 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN Q 165 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083039 restraints weight = 72569.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085574 restraints weight = 38110.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087245 restraints weight = 24312.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088356 restraints weight = 17931.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089094 restraints weight = 14584.657| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36765 Z= 0.146 Angle : 0.643 14.096 49676 Z= 0.325 Chirality : 0.045 0.259 5575 Planarity : 0.004 0.060 6440 Dihedral : 4.729 134.567 5018 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 2.86 % Allowed : 19.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4538 helix: 1.95 (0.11), residues: 2113 sheet: -0.37 (0.23), residues: 535 loop : -0.54 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 79 TYR 0.050 0.001 TYR R 197 PHE 0.037 0.002 PHE R 200 TRP 0.023 0.001 TRP A 567 HIS 0.010 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00332 (36765) covalent geometry : angle 0.64346 (49676) hydrogen bonds : bond 0.03964 ( 1953) hydrogen bonds : angle 2.87820 (13707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 748 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7765 (ptp90) cc_final: 0.7486 (ptt180) REVERT: A 203 LEU cc_start: 0.9134 (mt) cc_final: 0.8918 (mp) REVERT: A 484 GLN cc_start: 0.8032 (tp40) cc_final: 0.7383 (tp-100) REVERT: A 505 ASP cc_start: 0.8287 (t0) cc_final: 0.7829 (t70) REVERT: A 584 MET cc_start: 0.8405 (tpp) cc_final: 0.7998 (tpp) REVERT: B 18 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: B 30 THR cc_start: 0.9512 (m) cc_final: 0.8977 (p) REVERT: B 279 GLU cc_start: 0.7138 (tp30) cc_final: 0.6898 (tp30) REVERT: B 284 MET cc_start: 0.9237 (mmm) cc_final: 0.9029 (tpp) REVERT: C 218 THR cc_start: 0.8874 (m) cc_final: 0.8641 (m) REVERT: C 458 MET cc_start: 0.7759 (mmt) cc_final: 0.7133 (mmt) REVERT: C 531 PHE cc_start: 0.5683 (p90) cc_final: 0.5330 (p90) REVERT: D 302 SER cc_start: 0.8919 (m) cc_final: 0.8592 (t) REVERT: D 447 ASP cc_start: 0.7723 (m-30) cc_final: 0.7463 (t0) REVERT: D 464 THR cc_start: 0.9141 (m) cc_final: 0.8698 (p) REVERT: E 47 TYR cc_start: 0.8360 (m-80) cc_final: 0.7585 (m-80) REVERT: E 49 THR cc_start: 0.8512 (p) cc_final: 0.8190 (p) REVERT: E 125 GLU cc_start: 0.8630 (tt0) cc_final: 0.8088 (tm-30) REVERT: E 127 MET cc_start: 0.8945 (tpp) cc_final: 0.8738 (tpp) REVERT: E 154 MET cc_start: 0.8284 (mmm) cc_final: 0.7820 (mmt) REVERT: E 201 GLU cc_start: 0.7349 (tp30) cc_final: 0.7043 (tp30) REVERT: E 238 MET cc_start: 0.6383 (tmm) cc_final: 0.6088 (tmm) REVERT: E 327 MET cc_start: 0.8596 (tpp) cc_final: 0.7923 (tpp) REVERT: E 358 ASN cc_start: 0.8667 (t0) cc_final: 0.8195 (t0) REVERT: E 360 ASP cc_start: 0.8516 (t0) cc_final: 0.8112 (t0) REVERT: E 474 TYR cc_start: 0.7673 (m-10) cc_final: 0.7435 (m-80) REVERT: E 491 MET cc_start: 0.8461 (mtm) cc_final: 0.8175 (mtm) REVERT: F 90 SER cc_start: 0.9050 (t) cc_final: 0.8685 (m) REVERT: F 178 ASP cc_start: 0.8373 (m-30) cc_final: 0.7930 (m-30) REVERT: F 259 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8956 (mm) REVERT: F 330 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7715 (t0) REVERT: H 24 LYS cc_start: 0.9026 (tppt) cc_final: 0.8647 (tppt) REVERT: H 173 GLU cc_start: 0.7908 (tt0) cc_final: 0.7655 (tt0) REVERT: H 190 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8302 (mm-30) REVERT: I 76 MET cc_start: 0.8665 (mpp) cc_final: 0.8346 (mpp) REVERT: J 68 LYS cc_start: 0.7015 (mttt) cc_final: 0.6432 (tptt) REVERT: J 185 ASN cc_start: 0.8852 (p0) cc_final: 0.8421 (p0) REVERT: J 208 MET cc_start: 0.8529 (tpp) cc_final: 0.8321 (tpp) REVERT: K 112 TYR cc_start: 0.8312 (t80) cc_final: 0.7810 (t80) REVERT: K 196 LEU cc_start: 0.8987 (mt) cc_final: 0.8629 (mt) REVERT: K 197 GLU cc_start: 0.7877 (mp0) cc_final: 0.6786 (tm-30) REVERT: M 107 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7848 (tpp80) REVERT: N 78 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8245 (mtm180) REVERT: N 109 GLN cc_start: 0.8145 (pt0) cc_final: 0.7832 (pm20) REVERT: N 115 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7870 (mmt-90) REVERT: O 102 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8032 (mtp) REVERT: Q 85 SER cc_start: 0.8968 (m) cc_final: 0.8256 (t) REVERT: Q 123 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7646 (mttp) REVERT: Q 139 TYR cc_start: 0.8654 (t80) cc_final: 0.8164 (t80) REVERT: Q 198 HIS cc_start: 0.8009 (m-70) cc_final: 0.7546 (m-70) REVERT: R 33 MET cc_start: 0.9032 (tpp) cc_final: 0.8559 (tpp) REVERT: R 83 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8103 (ttp-170) REVERT: R 105 LEU cc_start: 0.7794 (mm) cc_final: 0.7420 (mp) REVERT: R 107 LEU cc_start: 0.8047 (tp) cc_final: 0.7841 (tp) REVERT: R 115 MET cc_start: 0.8906 (mtp) cc_final: 0.8586 (mtp) REVERT: R 153 ARG cc_start: 0.8889 (tpp80) cc_final: 0.8489 (tpp80) REVERT: S 33 MET cc_start: 0.8309 (tpp) cc_final: 0.7807 (mtp) REVERT: S 74 CYS cc_start: 0.7741 (m) cc_final: 0.7182 (m) REVERT: S 127 HIS cc_start: 0.9121 (t70) cc_final: 0.8859 (t70) REVERT: S 151 PHE cc_start: 0.7915 (m-10) cc_final: 0.7330 (m-10) REVERT: S 201 LYS cc_start: 0.8167 (tttt) cc_final: 0.7775 (pttm) outliers start: 113 outliers final: 88 residues processed: 808 average time/residue: 0.2188 time to fit residues: 293.8978 Evaluate side-chains 809 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 717 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 126 TYR Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 445 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 381 optimal weight: 7.9990 chunk 433 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 347 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN B 610 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 444 HIS C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078901 restraints weight = 73788.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.081282 restraints weight = 38751.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082861 restraints weight = 24941.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083906 restraints weight = 18511.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084606 restraints weight = 15163.780| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 36765 Z= 0.278 Angle : 0.737 12.572 49676 Z= 0.377 Chirality : 0.048 0.296 5575 Planarity : 0.005 0.062 6440 Dihedral : 4.989 136.970 5018 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 3.03 % Allowed : 19.32 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.67 (0.12), residues: 4538 helix: 1.75 (0.11), residues: 2122 sheet: -0.59 (0.23), residues: 523 loop : -0.72 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 79 TYR 0.034 0.002 TYR C 535 PHE 0.037 0.002 PHE R 151 TRP 0.024 0.002 TRP A 567 HIS 0.007 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00632 (36765) covalent geometry : angle 0.73686 (49676) hydrogen bonds : bond 0.04452 ( 1953) hydrogen bonds : angle 3.06036 (13707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 714 time to evaluate : 1.742 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: A 130 ASP cc_start: 0.7503 (t0) cc_final: 0.7151 (t0) REVERT: A 203 LEU cc_start: 0.9184 (mt) cc_final: 0.8916 (mp) REVERT: A 505 ASP cc_start: 0.8258 (t0) cc_final: 0.7862 (t70) REVERT: A 584 MET cc_start: 0.8483 (tpp) cc_final: 0.8112 (tpp) REVERT: B 18 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: B 30 THR cc_start: 0.9525 (m) cc_final: 0.9016 (p) REVERT: B 289 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8225 (tmm-80) REVERT: B 335 GLU cc_start: 0.8635 (tt0) cc_final: 0.8418 (tp30) REVERT: C 218 THR cc_start: 0.8881 (m) cc_final: 0.8656 (m) REVERT: C 284 MET cc_start: 0.8678 (mmm) cc_final: 0.8376 (mmm) REVERT: C 517 ASP cc_start: 0.7543 (m-30) cc_final: 0.6924 (t0) REVERT: C 531 PHE cc_start: 0.5890 (p90) cc_final: 0.5472 (p90) REVERT: C 565 ILE cc_start: 0.7148 (mt) cc_final: 0.6828 (tp) REVERT: D 302 SER cc_start: 0.9029 (m) cc_final: 0.8728 (t) REVERT: D 447 ASP cc_start: 0.7844 (m-30) cc_final: 0.7441 (t0) REVERT: E 47 TYR cc_start: 0.8406 (m-80) cc_final: 0.7651 (m-80) REVERT: E 125 GLU cc_start: 0.8603 (tt0) cc_final: 0.8038 (tm-30) REVERT: E 180 MET cc_start: 0.8723 (mmm) cc_final: 0.8297 (mtp) REVERT: E 201 GLU cc_start: 0.7568 (tp30) cc_final: 0.7169 (tp30) REVERT: E 263 LEU cc_start: 0.8783 (mt) cc_final: 0.8529 (mt) REVERT: E 327 MET cc_start: 0.8778 (tpp) cc_final: 0.7974 (tpp) REVERT: E 358 ASN cc_start: 0.8731 (t0) cc_final: 0.8359 (t0) REVERT: E 359 ASP cc_start: 0.8265 (t0) cc_final: 0.7895 (t0) REVERT: E 360 ASP cc_start: 0.8521 (t0) cc_final: 0.8139 (t0) REVERT: F 178 ASP cc_start: 0.8472 (m-30) cc_final: 0.8149 (m-30) REVERT: F 256 ASN cc_start: 0.8778 (m-40) cc_final: 0.8345 (p0) REVERT: F 259 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9009 (mm) REVERT: F 330 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7811 (t0) REVERT: F 398 LEU cc_start: 0.8191 (mt) cc_final: 0.7952 (mt) REVERT: H 173 GLU cc_start: 0.7996 (tt0) cc_final: 0.7653 (tt0) REVERT: H 190 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8380 (mm-30) REVERT: J 68 LYS cc_start: 0.7093 (mttt) cc_final: 0.6574 (tptt) REVERT: J 185 ASN cc_start: 0.8988 (p0) cc_final: 0.8596 (p0) REVERT: J 208 MET cc_start: 0.8524 (tpp) cc_final: 0.8300 (tpp) REVERT: K 77 ASN cc_start: 0.9045 (t0) cc_final: 0.8834 (t0) REVERT: K 112 TYR cc_start: 0.8348 (t80) cc_final: 0.7848 (t80) REVERT: K 197 GLU cc_start: 0.8061 (mp0) cc_final: 0.7053 (tm-30) REVERT: N 78 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8214 (mtm180) REVERT: N 109 GLN cc_start: 0.8265 (pt0) cc_final: 0.7917 (pm20) REVERT: N 115 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7909 (mmt-90) REVERT: Q 48 ASP cc_start: 0.8124 (m-30) cc_final: 0.7612 (t0) REVERT: Q 85 SER cc_start: 0.9166 (m) cc_final: 0.8487 (t) REVERT: Q 121 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8948 (tp) REVERT: Q 123 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7772 (mttp) REVERT: Q 139 TYR cc_start: 0.8722 (t80) cc_final: 0.8130 (t80) REVERT: Q 161 MET cc_start: 0.8587 (tpp) cc_final: 0.8177 (tmm) REVERT: Q 188 MET cc_start: 0.8804 (ttm) cc_final: 0.8589 (ttt) REVERT: Q 198 HIS cc_start: 0.8169 (m-70) cc_final: 0.7734 (m-70) REVERT: R 33 MET cc_start: 0.9049 (tpp) cc_final: 0.8722 (tpp) REVERT: R 79 ASP cc_start: 0.8684 (m-30) cc_final: 0.7730 (t0) REVERT: R 83 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8203 (ttp-170) REVERT: R 103 MET cc_start: 0.7497 (ttm) cc_final: 0.7147 (ttm) REVERT: R 107 LEU cc_start: 0.8280 (tp) cc_final: 0.8035 (tp) REVERT: R 112 TYR cc_start: 0.8409 (t80) cc_final: 0.7387 (t80) REVERT: R 153 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8650 (tpp80) REVERT: S 33 MET cc_start: 0.8371 (tpp) cc_final: 0.7829 (mtp) REVERT: S 74 CYS cc_start: 0.7824 (m) cc_final: 0.7351 (m) REVERT: S 151 PHE cc_start: 0.7901 (m-10) cc_final: 0.7189 (m-10) REVERT: S 201 LYS cc_start: 0.8219 (tttt) cc_final: 0.7796 (pttm) outliers start: 120 outliers final: 106 residues processed: 785 average time/residue: 0.2166 time to fit residues: 283.4367 Evaluate side-chains 799 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 689 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 197 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 573 HIS B 610 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN O 88 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.083817 restraints weight = 72652.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086352 restraints weight = 37716.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088012 restraints weight = 23846.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089115 restraints weight = 17449.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.089770 restraints weight = 14115.421| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36765 Z= 0.137 Angle : 0.669 13.098 49676 Z= 0.336 Chirality : 0.045 0.363 5575 Planarity : 0.005 0.087 6440 Dihedral : 4.816 132.208 5018 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 2.30 % Allowed : 20.69 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.78 (0.13), residues: 4538 helix: 1.82 (0.11), residues: 2123 sheet: -0.56 (0.23), residues: 537 loop : -0.64 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 79 TYR 0.035 0.001 TYR C 535 PHE 0.036 0.002 PHE R 200 TRP 0.028 0.001 TRP A 567 HIS 0.009 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00307 (36765) covalent geometry : angle 0.66851 (49676) hydrogen bonds : bond 0.03996 ( 1953) hydrogen bonds : angle 2.92705 (13707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9076 Ramachandran restraints generated. 4538 Oldfield, 0 Emsley, 4538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 777 time to evaluate : 1.545 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: A 130 ASP cc_start: 0.7431 (t0) cc_final: 0.7050 (t0) REVERT: A 218 THR cc_start: 0.8590 (m) cc_final: 0.8154 (m) REVERT: A 283 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7786 (mt-10) REVERT: A 484 GLN cc_start: 0.8300 (tp40) cc_final: 0.8060 (tp-100) REVERT: A 505 ASP cc_start: 0.8147 (t0) cc_final: 0.7770 (t70) REVERT: B 18 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: B 30 THR cc_start: 0.9508 (m) cc_final: 0.8991 (p) REVERT: B 53 GLU cc_start: 0.7857 (tt0) cc_final: 0.7458 (pp20) REVERT: B 324 GLU cc_start: 0.8136 (tt0) cc_final: 0.7841 (tt0) REVERT: B 405 SER cc_start: 0.9351 (m) cc_final: 0.9131 (t) REVERT: B 450 TRP cc_start: 0.8931 (p90) cc_final: 0.8469 (p90) REVERT: C 61 MET cc_start: 0.7605 (mtp) cc_final: 0.7293 (ttm) REVERT: C 218 THR cc_start: 0.8868 (m) cc_final: 0.8647 (m) REVERT: C 458 MET cc_start: 0.7642 (mmt) cc_final: 0.7052 (mmt) REVERT: C 517 ASP cc_start: 0.7348 (m-30) cc_final: 0.6823 (t0) REVERT: C 531 PHE cc_start: 0.5652 (p90) cc_final: 0.5303 (p90) REVERT: C 565 ILE cc_start: 0.7126 (mt) cc_final: 0.6689 (tp) REVERT: D 358 ASN cc_start: 0.7171 (t0) cc_final: 0.6950 (t0) REVERT: D 464 THR cc_start: 0.9111 (m) cc_final: 0.8678 (p) REVERT: E 47 TYR cc_start: 0.8329 (m-80) cc_final: 0.7722 (m-80) REVERT: E 49 THR cc_start: 0.8536 (p) cc_final: 0.8233 (p) REVERT: E 125 GLU cc_start: 0.8641 (tt0) cc_final: 0.8109 (tm-30) REVERT: E 154 MET cc_start: 0.8257 (mmm) cc_final: 0.8055 (mmt) REVERT: E 201 GLU cc_start: 0.7225 (tp30) cc_final: 0.6941 (tp30) REVERT: E 238 MET cc_start: 0.6633 (tmm) cc_final: 0.6376 (tmm) REVERT: E 327 MET cc_start: 0.8571 (tpp) cc_final: 0.7830 (tpp) REVERT: E 358 ASN cc_start: 0.8681 (t0) cc_final: 0.8226 (t0) REVERT: E 359 ASP cc_start: 0.8210 (t0) cc_final: 0.7816 (t0) REVERT: E 360 ASP cc_start: 0.8487 (t0) cc_final: 0.8159 (t0) REVERT: E 408 GLU cc_start: 0.7577 (tp30) cc_final: 0.7208 (mm-30) REVERT: E 491 MET cc_start: 0.8513 (mtm) cc_final: 0.8236 (mtm) REVERT: F 90 SER cc_start: 0.9023 (t) cc_final: 0.8632 (m) REVERT: F 178 ASP cc_start: 0.8476 (m-30) cc_final: 0.8158 (m-30) REVERT: F 256 ASN cc_start: 0.8689 (m-40) cc_final: 0.8377 (p0) REVERT: F 259 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8945 (mm) REVERT: F 330 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7692 (t0) REVERT: H 24 LYS cc_start: 0.9021 (tppt) cc_final: 0.8708 (tppt) REVERT: H 173 GLU cc_start: 0.7934 (tt0) cc_final: 0.7653 (tt0) REVERT: H 190 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8309 (mm-30) REVERT: J 68 LYS cc_start: 0.6938 (mttt) cc_final: 0.6464 (tptt) REVERT: J 185 ASN cc_start: 0.8966 (p0) cc_final: 0.8579 (p0) REVERT: J 201 ASP cc_start: 0.8363 (t70) cc_final: 0.8137 (t0) REVERT: J 208 MET cc_start: 0.8438 (tpp) cc_final: 0.8225 (tpp) REVERT: K 112 TYR cc_start: 0.8398 (t80) cc_final: 0.7918 (t80) REVERT: K 197 GLU cc_start: 0.7956 (mp0) cc_final: 0.6882 (tm-30) REVERT: M 107 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7830 (tpp80) REVERT: N 78 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8198 (mtm180) REVERT: N 109 GLN cc_start: 0.8193 (pt0) cc_final: 0.7834 (pm20) REVERT: O 90 ARG cc_start: 0.7869 (ptt-90) cc_final: 0.7535 (ptt90) REVERT: O 107 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8494 (mmm-85) REVERT: Q 48 ASP cc_start: 0.8027 (m-30) cc_final: 0.7525 (t0) REVERT: Q 85 SER cc_start: 0.9074 (m) cc_final: 0.8344 (t) REVERT: Q 123 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7575 (mttp) REVERT: Q 139 TYR cc_start: 0.8583 (t80) cc_final: 0.8031 (t80) REVERT: Q 198 HIS cc_start: 0.8067 (m-70) cc_final: 0.7621 (m-70) REVERT: R 33 MET cc_start: 0.9050 (tpp) cc_final: 0.8565 (tpp) REVERT: R 79 ASP cc_start: 0.8655 (m-30) cc_final: 0.7724 (t0) REVERT: R 83 ARG cc_start: 0.8445 (ttp-170) cc_final: 0.8095 (ttp-170) REVERT: R 107 LEU cc_start: 0.8154 (tp) cc_final: 0.7873 (tp) REVERT: R 112 TYR cc_start: 0.8353 (t80) cc_final: 0.7493 (t80) REVERT: R 153 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8581 (tpp80) REVERT: S 33 MET cc_start: 0.8324 (tpp) cc_final: 0.7925 (ttt) REVERT: S 74 CYS cc_start: 0.7692 (m) cc_final: 0.7245 (m) REVERT: S 127 HIS cc_start: 0.9097 (t70) cc_final: 0.8859 (t70) REVERT: S 151 PHE cc_start: 0.7789 (m-10) cc_final: 0.7235 (m-10) REVERT: S 201 LYS cc_start: 0.8120 (tttt) cc_final: 0.7720 (pttm) outliers start: 91 outliers final: 73 residues processed: 822 average time/residue: 0.2254 time to fit residues: 308.9667 Evaluate side-chains 806 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 730 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 299 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 437 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 344 optimal weight: 8.9990 chunk 280 optimal weight: 0.0570 chunk 131 optimal weight: 7.9990 chunk 397 optimal weight: 0.6980 chunk 383 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN B 610 ASN C 103 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN F 181 ASN J 122 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082352 restraints weight = 72685.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084839 restraints weight = 38092.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.086479 restraints weight = 24358.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087569 restraints weight = 17964.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088291 restraints weight = 14644.967| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36765 Z= 0.160 Angle : 0.675 14.927 49676 Z= 0.340 Chirality : 0.046 0.355 5575 Planarity : 0.004 0.066 6440 Dihedral : 4.762 131.067 5018 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 2.33 % Allowed : 20.51 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.82 (0.13), residues: 4538 helix: 1.88 (0.11), residues: 2119 sheet: -0.55 (0.23), residues: 527 loop : -0.65 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 78 TYR 0.035 0.001 TYR C 535 PHE 0.033 0.002 PHE R 200 TRP 0.027 0.001 TRP A 567 HIS 0.007 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00369 (36765) covalent geometry : angle 0.67529 (49676) hydrogen bonds : bond 0.03964 ( 1953) hydrogen bonds : angle 2.90323 (13707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.82 seconds wall clock time: 132 minutes 24.81 seconds (7944.81 seconds total)