Starting phenix.real_space_refine on Sat Mar 7 03:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vq9_21345/03_2026/6vq9_21345.map" } resolution = 3.6 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= -0.001 sd= 0.097 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 173 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: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "R" 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: "S" 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: "C" 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: 7.78, per 1000 atoms: 0.22 Number of scatterers: 36114 At special positions: 0 Unit cell: (174.9, 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: 3.62 Conformation dependent library (CDL) restraints added in 1.5 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: 180 helices and 68 sheets defined 51.3% alpha, 116.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.19 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 319 through 339 removed outlier: 4.692A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.321A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.571A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 558 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.762A pdb=" N LEU A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 4.462A pdb=" N ASP A 588 " --> pdb=" O LYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.661A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 4.453A pdb=" N GLY B 255 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.535A pdb=" N SER B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 319 through 339 removed outlier: 4.568A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.515A pdb=" N TRP B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 412 through 416 removed outlier: 4.129A pdb=" N ASP B 416 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 489 Processing helix chain 'B' and resid 489 through 497 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 583 Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 593 through 614 Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.568A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 280 through 291 removed outlier: 4.029A pdb=" N MET C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 321 through 340 removed outlier: 3.968A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (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 375 through 376 No H-bonds generated for 'chain 'C' and resid 375 through 376' Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.833A pdb=" N ARG C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.472A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.192A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.567A 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 557 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 593 through 616 Processing helix chain 'D' and resid 124 through 128 removed outlier: 4.038A pdb=" N LEU D 128 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 237 through 251 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.807A pdb=" N TYR D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.971A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.520A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 removed outlier: 4.148A pdb=" N LYS D 403 " --> pdb=" O ARG D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.081A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 removed outlier: 4.022A pdb=" N LEU D 444 " --> pdb=" O GLU D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 444' 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 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 237 through 251 removed outlier: 3.604A pdb=" N ASN E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 255 removed outlier: 4.138A pdb=" N ASP E 255 " --> pdb=" O GLY E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 255' Processing helix chain 'E' and resid 269 through 289 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 314 Processing helix chain 'E' and resid 319 through 323 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 371 Processing helix chain 'E' and resid 381 through 386 Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 414 through 440 removed outlier: 3.683A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 462 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 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 removed outlier: 3.669A pdb=" N ARG F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) 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: 4.031A pdb=" N TYR F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.612A pdb=" N HIS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 406 Processing helix chain 'F' and resid 414 through 440 removed outlier: 4.293A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 445 through 462 removed outlier: 4.300A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) 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 removed outlier: 5.038A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) 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 217 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 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 205 Processing helix chain 'I' and resid 207 through 217 removed outlier: 3.565A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 107 Processing helix chain 'J' and resid 109 through 128 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 160 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 195 through 207 Processing helix chain 'J' and resid 207 through 217 Processing helix chain 'K' and resid 67 through 107 Processing helix chain 'K' and resid 108 through 128 removed outlier: 4.593A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) 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 159 Proline residue: K 153 - end of helix removed outlier: 3.534A pdb=" N ILE K 157 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 217 removed outlier: 3.888A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'M' and resid 71 through 104 removed outlier: 3.669A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 91 removed outlier: 3.551A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 105 Processing helix chain 'O' and resid 71 through 89 Processing helix chain 'O' and resid 91 through 105 Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 48 Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 61 through 71 Processing helix chain 'Q' and resid 77 through 97 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 142 removed outlier: 3.841A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 187 Processing helix chain 'Q' and resid 192 through 206 Processing helix chain 'Q' and resid 218 through 234 Processing helix chain 'R' and resid 14 through 37 removed outlier: 3.530A pdb=" N HIS R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 49 removed outlier: 3.666A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 54 Processing helix chain 'R' and resid 62 through 72 Processing helix chain 'R' and resid 77 through 97 Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 120 through 123 Processing helix chain 'R' and resid 124 through 140 removed outlier: 3.814A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 143 No H-bonds generated for 'chain 'R' and resid 141 through 143' Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 187 Processing helix chain 'R' and resid 193 through 207 Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'S' and resid 42 through 49 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 removed outlier: 3.930A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU S 91 " --> pdb=" O ILE S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 124 through 140 Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 188 Processing helix chain 'S' and resid 192 through 205 Processing helix chain 'S' and resid 218 through 234 removed outlier: 3.528A pdb=" N MET S 229 " --> pdb=" O LEU S 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 164 through 167 removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET J 132 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.090A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (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 164 through 167 removed outlier: 4.097A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.498A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 219 through 221 removed outlier: 4.077A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 219 through 221 removed outlier: 4.077A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR A 246 " --> pdb=" O GLY A 408 " (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: 6.298A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 344 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 163 through 167 removed outlier: 4.010A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.384A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 409 through 410 removed outlier: 7.407A pdb=" N VAL B 410 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE B 248 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AF4, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AF5, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.325A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 273 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 348 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.325A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 273 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 348 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 164 through 167 removed outlier: 3.979A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.507A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) 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 130 through 133 removed outlier: 6.763A pdb=" N ARG D 130 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 261 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE D 132 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU D 263 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.021A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.603A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 191 through 193 removed outlier: 6.493A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AG6, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.722A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA E 228 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE E 296 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 230 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR E 298 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA E 232 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 170 through 171 Processing sheet with id=AG8, first strand: chain 'E' and resid 191 through 194 removed outlier: 6.201A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET E 356 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER E 193 " --> pdb=" O MET E 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AH1, first strand: chain 'F' and resid 131 through 133 removed outlier: 6.629A pdb=" N PHE F 132 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU F 263 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 297 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.407A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.365A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 192 through 193 Processing sheet with id=AH5, first strand: chain 'F' and resid 375 through 376 4884 hydrogen bonds defined for protein. 13857 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: 22.93 Time building geometry restraints manager: 4.59 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: 6986 1.32 - 1.44: 8216 1.44 - 1.57: 21202 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" N PRO E 391 " pdb=" CA PRO E 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.13e+01 bond pdb=" C TYR D 504 " pdb=" N PRO D 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.33e+01 bond pdb=" N PRO D 352 " pdb=" CA PRO D 352 " ideal model delta sigma weight residual 1.466 1.538 -0.072 1.24e-02 6.50e+03 3.38e+01 bond pdb=" C ASP A 290 " pdb=" N PHE A 291 " ideal model delta sigma weight residual 1.331 1.215 0.116 2.07e-02 2.33e+03 3.13e+01 bond pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 1.469 1.539 -0.070 1.25e-02 6.40e+03 3.13e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 47762 2.13 - 4.26: 1757 4.26 - 6.39: 123 6.39 - 8.53: 24 8.53 - 10.66: 10 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE E 189 " pdb=" N PRO E 190 " pdb=" CA PRO E 190 " ideal model delta sigma weight residual 119.85 129.33 -9.48 1.01e+00 9.80e-01 8.80e+01 angle pdb=" C ARG C 215 " pdb=" N PRO C 216 " pdb=" CA PRO C 216 " ideal model delta sigma weight residual 119.76 129.28 -9.52 1.03e+00 9.43e-01 8.54e+01 angle pdb=" C SER A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta sigma weight residual 120.38 129.08 -8.70 1.03e+00 9.43e-01 7.13e+01 angle pdb=" C LEU E 395 " pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 120.04 128.52 -8.48 1.08e+00 8.57e-01 6.16e+01 angle pdb=" C ASN C 397 " pdb=" N PRO C 398 " pdb=" CA PRO C 398 " ideal model delta sigma weight residual 119.82 127.35 -7.53 9.80e-01 1.04e+00 5.90e+01 ... (remaining 49671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 22002 23.68 - 47.36: 426 47.36 - 71.03: 119 71.03 - 94.71: 31 94.71 - 118.39: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.38 118.39 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.44 -98.43 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ILE F 406 " pdb=" C ILE F 406 " pdb=" N GLY F 407 " pdb=" CA GLY F 407 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3825 0.053 - 0.106: 1182 0.106 - 0.159: 462 0.159 - 0.211: 77 0.211 - 0.264: 29 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL E 379 " pdb=" N VAL E 379 " pdb=" C VAL E 379 " pdb=" CB VAL E 379 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP A 529 " pdb=" N ASP A 529 " pdb=" C ASP A 529 " pdb=" CB ASP A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 390 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO E 390 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO E 390 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO E 391 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 584 " -0.016 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C MET C 584 " 0.059 2.00e-02 2.50e+03 pdb=" O MET C 584 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS C 585 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 189 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE E 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE E 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO E 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 8 2.43 - 3.05: 23352 3.05 - 3.66: 53916 3.66 - 4.28: 84353 4.28 - 4.90: 139139 Nonbonded interactions: 300768 Sorted by model distance: nonbonded pdb=" OG1 THR C 257 " pdb="MG MG C 702 " model vdw 1.809 2.170 nonbonded pdb=" OG SER C 269 " pdb=" OG SER C 345 " model vdw 2.377 3.040 nonbonded pdb=" OG SER B 128 " pdb=" OD1 ASP B 130 " model vdw 2.378 3.040 nonbonded pdb=" NE ARG I 135 " pdb=" O ALA I 171 " model vdw 2.389 3.120 nonbonded pdb=" O ILE F 377 " pdb=" OG SER F 397 " model vdw 2.404 3.040 ... (remaining 300763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 17 through 616) } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 55.660 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 0.116 36765 Z= 0.582 Angle : 0.896 10.657 49676 Z= 0.632 Chirality : 0.062 0.264 5575 Planarity : 0.004 0.038 6440 Dihedral : 11.231 118.388 14048 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 0.10 % Allowed : 0.99 % Favored : 98.91 % 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: 0.25 (0.12), residues: 4538 helix: 0.65 (0.10), residues: 2072 sheet: -0.29 (0.19), residues: 679 loop : -0.03 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 208 TYR 0.015 0.000 TYR F 389 PHE 0.011 0.000 PHE C 252 TRP 0.025 0.001 TRP A 450 HIS 0.003 0.000 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00987 (36765) covalent geometry : angle 0.89575 (49676) hydrogen bonds : bond 0.17828 ( 1955) hydrogen bonds : angle 8.90629 (13857) *********************** 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 1504 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1500 time to evaluate : 1.447 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: A 17 THR cc_start: 0.5710 (p) cc_final: 0.5343 (t) REVERT: A 50 LEU cc_start: 0.7642 (mt) cc_final: 0.7370 (mt) REVERT: A 74 SER cc_start: 0.7851 (m) cc_final: 0.7622 (p) REVERT: A 95 MET cc_start: 0.8435 (mmm) cc_final: 0.8217 (mmm) REVERT: A 213 GLN cc_start: 0.6521 (mm-40) cc_final: 0.5895 (mt0) REVERT: A 266 TYR cc_start: 0.6961 (m-80) cc_final: 0.6504 (m-80) REVERT: A 268 ASN cc_start: 0.7000 (t0) cc_final: 0.6574 (t0) REVERT: A 286 GLU cc_start: 0.8707 (tt0) cc_final: 0.8080 (tp30) REVERT: A 296 MET cc_start: 0.7524 (ptm) cc_final: 0.6692 (ptt) REVERT: A 308 ARG cc_start: 0.7569 (ptp-110) cc_final: 0.7091 (ptt180) REVERT: A 340 MET cc_start: 0.8792 (mtt) cc_final: 0.8541 (mtp) REVERT: A 346 MET cc_start: 0.7850 (ttt) cc_final: 0.7429 (ttt) REVERT: A 387 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 399 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6579 (mp0) REVERT: A 428 ILE cc_start: 0.8477 (mm) cc_final: 0.8239 (mt) REVERT: A 438 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7704 (tptp) REVERT: A 491 GLU cc_start: 0.8261 (tp30) cc_final: 0.7754 (tm-30) REVERT: A 500 SER cc_start: 0.8001 (m) cc_final: 0.7377 (p) REVERT: A 517 ASP cc_start: 0.8133 (m-30) cc_final: 0.7853 (m-30) REVERT: A 573 HIS cc_start: 0.7706 (t70) cc_final: 0.7401 (t-170) REVERT: A 604 LEU cc_start: 0.7054 (mp) cc_final: 0.6841 (tt) REVERT: B 56 ARG cc_start: 0.6838 (ttt-90) cc_final: 0.6465 (ttm110) REVERT: B 58 GLU cc_start: 0.7896 (tt0) cc_final: 0.7450 (pm20) REVERT: B 84 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6722 (pttm) REVERT: B 142 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7530 (mmt-90) REVERT: B 147 ILE cc_start: 0.8257 (tt) cc_final: 0.7759 (tt) REVERT: B 252 PHE cc_start: 0.6608 (m-80) cc_final: 0.6251 (m-10) REVERT: B 257 THR cc_start: 0.8158 (m) cc_final: 0.7936 (p) REVERT: B 283 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 303 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7331 (mt-10) REVERT: B 318 MET cc_start: 0.7729 (mmm) cc_final: 0.6252 (mpp) REVERT: B 324 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7267 (t0) REVERT: B 368 MET cc_start: 0.8484 (tpp) cc_final: 0.8243 (tpp) REVERT: B 387 GLU cc_start: 0.8269 (tp30) cc_final: 0.7118 (tm-30) REVERT: B 394 CYS cc_start: 0.6761 (m) cc_final: 0.6487 (m) REVERT: B 419 ASP cc_start: 0.7411 (t70) cc_final: 0.7011 (t70) REVERT: B 436 ASP cc_start: 0.8511 (t0) cc_final: 0.7772 (t70) REVERT: B 466 ASP cc_start: 0.8724 (t70) cc_final: 0.8433 (m-30) REVERT: B 571 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8420 (ttp-110) REVERT: B 584 MET cc_start: 0.8240 (mtm) cc_final: 0.7643 (mtp) REVERT: B 601 TYR cc_start: 0.6793 (m-10) cc_final: 0.6551 (m-80) REVERT: C 163 LYS cc_start: 0.7455 (mttt) cc_final: 0.7177 (mmmt) REVERT: C 189 ASP cc_start: 0.8807 (t0) cc_final: 0.8047 (m-30) REVERT: C 231 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7926 (mm-40) REVERT: C 232 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7091 (mtt90) REVERT: C 235 ASP cc_start: 0.8382 (t70) cc_final: 0.8088 (t0) REVERT: C 254 CYS cc_start: 0.7829 (m) cc_final: 0.7477 (m) REVERT: C 279 GLU cc_start: 0.6319 (tp30) cc_final: 0.6054 (tp30) REVERT: C 283 GLU cc_start: 0.7058 (tp30) cc_final: 0.5310 (tp30) REVERT: C 286 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7368 (tt0) REVERT: C 486 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7930 (tm-30) REVERT: C 487 GLU cc_start: 0.8078 (tp30) cc_final: 0.7745 (tp30) REVERT: C 491 GLU cc_start: 0.8577 (tt0) cc_final: 0.8076 (mm-30) REVERT: C 523 ASN cc_start: 0.6921 (t0) cc_final: 0.6680 (t0) REVERT: C 556 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7986 (tp30) REVERT: D 81 LYS cc_start: 0.8184 (mttt) cc_final: 0.7941 (tttm) REVERT: D 96 VAL cc_start: 0.7876 (t) cc_final: 0.7653 (m) REVERT: D 201 GLU cc_start: 0.7189 (mp0) cc_final: 0.6929 (tp30) REVERT: D 250 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8161 (tm-30) REVERT: D 262 ASN cc_start: 0.8101 (t0) cc_final: 0.7466 (t0) REVERT: D 400 ARG cc_start: 0.6970 (tpm-80) cc_final: 0.6658 (mmm160) REVERT: D 403 LYS cc_start: 0.8571 (pttp) cc_final: 0.8128 (tppt) REVERT: D 460 LYS cc_start: 0.8118 (tttt) cc_final: 0.7583 (ttmm) REVERT: D 497 GLN cc_start: 0.7011 (tp40) cc_final: 0.6788 (tp-100) REVERT: E 108 LYS cc_start: 0.9152 (tttt) cc_final: 0.8727 (ttmm) REVERT: E 175 SER cc_start: 0.8671 (m) cc_final: 0.8206 (t) REVERT: E 197 LEU cc_start: 0.8686 (mt) cc_final: 0.8462 (mt) REVERT: E 201 GLU cc_start: 0.7055 (mp0) cc_final: 0.6694 (tt0) REVERT: E 238 MET cc_start: 0.8206 (tpt) cc_final: 0.7451 (tpp) REVERT: E 253 SER cc_start: 0.8006 (p) cc_final: 0.7389 (t) REVERT: E 254 MET cc_start: 0.7075 (tpp) cc_final: 0.6309 (tpp) REVERT: E 256 ASN cc_start: 0.7413 (m-40) cc_final: 0.6710 (p0) REVERT: E 315 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7921 (mm-30) REVERT: E 363 HIS cc_start: 0.7382 (t-90) cc_final: 0.7030 (t-90) REVERT: E 374 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8036 (mt-10) REVERT: E 380 ASP cc_start: 0.7916 (t0) cc_final: 0.7043 (p0) REVERT: E 393 ASN cc_start: 0.7501 (t0) cc_final: 0.6796 (t0) REVERT: E 408 GLU cc_start: 0.7970 (tt0) cc_final: 0.7379 (tp30) REVERT: E 491 MET cc_start: 0.8721 (mtp) cc_final: 0.8297 (mtp) REVERT: F 47 TYR cc_start: 0.7705 (m-80) cc_final: 0.7404 (m-80) REVERT: F 49 THR cc_start: 0.8080 (p) cc_final: 0.7869 (p) REVERT: F 81 LYS cc_start: 0.8710 (mttt) cc_final: 0.8444 (mtpt) REVERT: F 102 THR cc_start: 0.7679 (p) cc_final: 0.7347 (t) REVERT: F 117 ASP cc_start: 0.7277 (t0) cc_final: 0.6946 (m-30) REVERT: F 125 GLU cc_start: 0.8272 (tp30) cc_final: 0.7567 (tp30) REVERT: F 146 LEU cc_start: 0.7795 (tp) cc_final: 0.7408 (tp) REVERT: F 189 ILE cc_start: 0.8055 (mm) cc_final: 0.7634 (mm) REVERT: F 231 PHE cc_start: 0.7554 (t80) cc_final: 0.7185 (t80) REVERT: F 336 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8146 (tp30) REVERT: F 431 ASP cc_start: 0.7871 (m-30) cc_final: 0.7597 (t0) REVERT: F 435 MET cc_start: 0.7052 (ttp) cc_final: 0.6646 (ttm) REVERT: F 469 GLU cc_start: 0.8060 (tp30) cc_final: 0.7676 (tp30) REVERT: H 46 GLN cc_start: 0.8773 (mt0) cc_final: 0.8235 (mt0) REVERT: H 160 GLU cc_start: 0.8426 (tp30) cc_final: 0.8153 (tp30) REVERT: H 181 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7747 (tp30) REVERT: H 182 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7070 (mtm110) REVERT: H 190 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7709 (tp30) REVERT: I 76 MET cc_start: 0.8883 (mmm) cc_final: 0.8388 (mmp) REVERT: I 82 LYS cc_start: 0.8245 (mttt) cc_final: 0.7978 (tptm) REVERT: I 88 ASP cc_start: 0.8891 (t70) cc_final: 0.8617 (t0) REVERT: I 99 LYS cc_start: 0.9184 (mttt) cc_final: 0.8667 (tmtt) REVERT: I 104 LYS cc_start: 0.8985 (tttt) cc_final: 0.8661 (pttt) REVERT: I 113 GLN cc_start: 0.7147 (tp40) cc_final: 0.6945 (tp40) REVERT: I 117 ASP cc_start: 0.8103 (m-30) cc_final: 0.7490 (m-30) REVERT: I 129 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7290 (mm-30) REVERT: I 131 ARG cc_start: 0.6420 (ttm-80) cc_final: 0.6220 (mtp85) REVERT: I 138 LYS cc_start: 0.8460 (tttt) cc_final: 0.8225 (tptt) REVERT: I 154 MET cc_start: 0.8679 (mmp) cc_final: 0.7896 (mtp) REVERT: I 195 THR cc_start: 0.8894 (p) cc_final: 0.8602 (p) REVERT: I 210 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7663 (tm-30) REVERT: J 75 LEU cc_start: 0.8362 (mt) cc_final: 0.7998 (tp) REVERT: J 108 ASP cc_start: 0.6755 (t0) cc_final: 0.6549 (t70) REVERT: J 131 ARG cc_start: 0.7692 (mtp85) cc_final: 0.6931 (mtt-85) REVERT: J 140 ASP cc_start: 0.8387 (m-30) cc_final: 0.7523 (t0) REVERT: J 156 LYS cc_start: 0.8375 (mttt) cc_final: 0.7922 (tptt) REVERT: J 164 ASP cc_start: 0.8412 (t0) cc_final: 0.7552 (t0) REVERT: J 167 ILE cc_start: 0.8971 (mt) cc_final: 0.8715 (tt) REVERT: J 177 ILE cc_start: 0.8778 (mm) cc_final: 0.8427 (mm) REVERT: J 191 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7567 (ptmm) REVERT: J 197 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7876 (tm-30) REVERT: J 207 MET cc_start: 0.8453 (mmm) cc_final: 0.8132 (tpp) REVERT: K 78 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8399 (tt0) REVERT: K 88 ASP cc_start: 0.8735 (t70) cc_final: 0.8475 (t70) REVERT: K 92 THR cc_start: 0.8828 (m) cc_final: 0.8430 (p) REVERT: K 97 GLU cc_start: 0.9106 (tp30) cc_final: 0.8633 (tp30) REVERT: K 132 MET cc_start: 0.8475 (mmt) cc_final: 0.7980 (mmt) REVERT: K 154 MET cc_start: 0.8832 (mtp) cc_final: 0.8563 (mtp) REVERT: K 195 THR cc_start: 0.8884 (p) cc_final: 0.8438 (t) REVERT: K 198 SER cc_start: 0.9276 (m) cc_final: 0.9053 (p) REVERT: N 74 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8404 (pp20) REVERT: N 86 SER cc_start: 0.8878 (t) cc_final: 0.8528 (t) REVERT: N 109 GLN cc_start: 0.8542 (tt0) cc_final: 0.8103 (tp40) REVERT: N 110 VAL cc_start: 0.8617 (t) cc_final: 0.7734 (t) REVERT: O 93 GLU cc_start: 0.8269 (tp30) cc_final: 0.8052 (tm-30) REVERT: O 97 THR cc_start: 0.8865 (m) cc_final: 0.8477 (m) REVERT: Q 16 GLU cc_start: 0.8720 (tp30) cc_final: 0.8300 (tp30) REVERT: Q 46 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7753 (mtt180) REVERT: Q 61 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7826 (mtm110) REVERT: Q 64 GLU cc_start: 0.8667 (tp30) cc_final: 0.8248 (tt0) REVERT: Q 69 SER cc_start: 0.8833 (t) cc_final: 0.8606 (t) REVERT: Q 114 LYS cc_start: 0.9100 (mttt) cc_final: 0.8677 (tppt) REVERT: Q 157 SER cc_start: 0.7097 (m) cc_final: 0.6852 (p) REVERT: Q 191 GLU cc_start: 0.8198 (pm20) cc_final: 0.7988 (pp20) REVERT: Q 195 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7756 (tp30) REVERT: Q 234 MET cc_start: 0.9077 (ttp) cc_final: 0.8469 (tmm) REVERT: R 17 GLN cc_start: 0.8160 (mt0) cc_final: 0.7818 (mm-40) REVERT: R 62 PHE cc_start: 0.7707 (t80) cc_final: 0.7272 (t80) REVERT: R 69 SER cc_start: 0.9117 (t) cc_final: 0.8905 (p) REVERT: R 112 TYR cc_start: 0.8779 (t80) cc_final: 0.8507 (t80) REVERT: R 166 TYR cc_start: 0.8042 (m-80) cc_final: 0.7725 (m-80) REVERT: R 184 HIS cc_start: 0.7358 (t70) cc_final: 0.6667 (t-90) REVERT: R 198 HIS cc_start: 0.8503 (m-70) cc_final: 0.8300 (p-80) REVERT: R 211 SER cc_start: 0.8502 (m) cc_final: 0.8293 (p) REVERT: S 8 ILE cc_start: 0.6485 (mm) cc_final: 0.6111 (mt) REVERT: S 16 GLU cc_start: 0.7747 (tp30) cc_final: 0.7408 (tp30) REVERT: S 28 TYR cc_start: 0.8210 (t80) cc_final: 0.7952 (t80) REVERT: S 33 MET cc_start: 0.7372 (mmm) cc_final: 0.6196 (tpt) REVERT: S 37 ASP cc_start: 0.7164 (t0) cc_final: 0.6123 (t0) REVERT: S 47 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8519 (mm-30) REVERT: S 55 TRP cc_start: 0.7715 (m100) cc_final: 0.7479 (m100) REVERT: S 79 ASP cc_start: 0.8471 (m-30) cc_final: 0.8123 (t0) REVERT: S 101 PHE cc_start: 0.6768 (m-80) cc_final: 0.5650 (m-10) REVERT: S 111 GLN cc_start: 0.9304 (mm-40) cc_final: 0.9098 (mm-40) REVERT: S 114 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8411 (tppt) REVERT: S 161 MET cc_start: 0.7769 (tmm) cc_final: 0.7488 (tmm) REVERT: S 188 MET cc_start: 0.6095 (tpp) cc_final: 0.5597 (ttm) REVERT: S 213 PHE cc_start: 0.7751 (m-80) cc_final: 0.7073 (m-80) REVERT: S 229 MET cc_start: 0.5670 (tpp) cc_final: 0.5102 (tpt) outliers start: 4 outliers final: 1 residues processed: 1501 average time/residue: 0.2575 time to fit residues: 599.5335 Evaluate side-chains 831 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 830 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 123 ASN A 317 ASN B 603 GLN C 261 GLN D 62 HIS D 171 GLN D 187 GLN E 181 ASN E 345 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN K 139 GLN O 80 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN S 134 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101767 restraints weight = 67120.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105107 restraints weight = 30018.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107288 restraints weight = 17397.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108673 restraints weight = 11983.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109515 restraints weight = 9353.552| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36765 Z= 0.180 Angle : 0.665 9.119 49676 Z= 0.347 Chirality : 0.046 0.204 5575 Planarity : 0.005 0.064 6440 Dihedral : 5.020 106.155 5022 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 2.23 % Allowed : 10.95 % Favored : 86.82 % 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: 1.72 (0.11), residues: 2116 sheet: -0.12 (0.20), residues: 604 loop : -0.06 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 31 TYR 0.019 0.002 TYR A 20 PHE 0.026 0.002 PHE A 291 TRP 0.018 0.002 TRP Q 122 HIS 0.014 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00407 (36765) covalent geometry : angle 0.66503 (49676) hydrogen bonds : bond 0.05500 ( 1955) hydrogen bonds : angle 3.34845 (13857) *********************** 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 970 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 882 time to evaluate : 1.473 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: A 74 SER cc_start: 0.9016 (m) cc_final: 0.8713 (p) REVERT: A 248 ILE cc_start: 0.9111 (mt) cc_final: 0.8849 (tt) REVERT: A 268 ASN cc_start: 0.7644 (t0) cc_final: 0.7294 (t0) REVERT: A 296 MET cc_start: 0.8340 (ptm) cc_final: 0.7695 (ptm) REVERT: A 308 ARG cc_start: 0.8306 (ptp-110) cc_final: 0.8070 (ptt-90) REVERT: A 340 MET cc_start: 0.8677 (mtt) cc_final: 0.8450 (mtp) REVERT: A 346 MET cc_start: 0.8315 (ttt) cc_final: 0.8022 (ttt) REVERT: A 387 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7934 (tp30) REVERT: A 438 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8233 (tptp) REVERT: A 500 SER cc_start: 0.8138 (m) cc_final: 0.7799 (p) REVERT: A 604 LEU cc_start: 0.8510 (mp) cc_final: 0.8195 (tt) REVERT: A 607 ASP cc_start: 0.8940 (m-30) cc_final: 0.7985 (t70) REVERT: B 30 THR cc_start: 0.8940 (m) cc_final: 0.8680 (p) REVERT: B 84 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7939 (pttm) REVERT: B 295 THR cc_start: 0.8889 (p) cc_final: 0.8634 (t) REVERT: B 296 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7007 (ptt) REVERT: B 318 MET cc_start: 0.8701 (mmm) cc_final: 0.7927 (mpp) REVERT: B 324 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 334 SER cc_start: 0.9502 (t) cc_final: 0.9250 (t) REVERT: B 346 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7962 (ttt) REVERT: B 368 MET cc_start: 0.8587 (tpp) cc_final: 0.7804 (tpp) REVERT: B 387 GLU cc_start: 0.8166 (tp30) cc_final: 0.7443 (tm-30) REVERT: B 466 ASP cc_start: 0.8409 (t70) cc_final: 0.8105 (t0) REVERT: B 584 MET cc_start: 0.8456 (mtm) cc_final: 0.7657 (mtp) REVERT: B 601 TYR cc_start: 0.7115 (m-10) cc_final: 0.6840 (m-80) REVERT: C 100 ASP cc_start: 0.8554 (p0) cc_final: 0.8316 (p0) REVERT: C 254 CYS cc_start: 0.7957 (m) cc_final: 0.7654 (m) REVERT: C 279 GLU cc_start: 0.6553 (tp30) cc_final: 0.5805 (tp30) REVERT: C 283 GLU cc_start: 0.6569 (tp30) cc_final: 0.6027 (tp30) REVERT: C 318 MET cc_start: 0.8787 (mtt) cc_final: 0.7980 (mtt) REVERT: C 445 PHE cc_start: 0.9253 (m-80) cc_final: 0.8926 (m-80) REVERT: C 486 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 523 ASN cc_start: 0.7960 (t0) cc_final: 0.7727 (t0) REVERT: C 600 ASP cc_start: 0.8249 (t70) cc_final: 0.7966 (t0) REVERT: C 603 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8051 (tm-30) REVERT: D 42 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8453 (mm-40) REVERT: E 51 SER cc_start: 0.8549 (m) cc_final: 0.8256 (t) REVERT: E 83 SER cc_start: 0.8901 (m) cc_final: 0.8427 (p) REVERT: E 88 GLU cc_start: 0.7493 (tt0) cc_final: 0.7250 (tt0) REVERT: E 168 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: E 238 MET cc_start: 0.8613 (tpt) cc_final: 0.8360 (tpp) REVERT: E 250 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8105 (mt-10) REVERT: E 253 SER cc_start: 0.8729 (p) cc_final: 0.8340 (t) REVERT: E 254 MET cc_start: 0.8381 (tpp) cc_final: 0.8000 (tpp) REVERT: E 256 ASN cc_start: 0.8292 (m-40) cc_final: 0.7838 (p0) REVERT: F 49 THR cc_start: 0.8644 (p) cc_final: 0.8423 (p) REVERT: F 299 ASP cc_start: 0.7892 (t0) cc_final: 0.7667 (t0) REVERT: F 300 MET cc_start: 0.8669 (mmm) cc_final: 0.8459 (mmm) REVERT: H 46 GLN cc_start: 0.8649 (mt0) cc_final: 0.8228 (mt0) REVERT: H 160 GLU cc_start: 0.8457 (tp30) cc_final: 0.8120 (tp30) REVERT: I 76 MET cc_start: 0.8466 (mmm) cc_final: 0.8165 (mmp) REVERT: I 88 ASP cc_start: 0.8499 (t70) cc_final: 0.8145 (t0) REVERT: I 97 GLU cc_start: 0.8128 (tt0) cc_final: 0.7544 (tp30) REVERT: I 99 LYS cc_start: 0.9115 (mttt) cc_final: 0.8899 (tmtt) REVERT: I 113 GLN cc_start: 0.7934 (tp40) cc_final: 0.7643 (tp40) REVERT: I 129 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7899 (mm-30) REVERT: I 132 MET cc_start: 0.8006 (mpp) cc_final: 0.7787 (mpp) REVERT: I 194 ASN cc_start: 0.8638 (t0) cc_final: 0.8213 (t0) REVERT: I 207 MET cc_start: 0.7902 (mmt) cc_final: 0.7573 (mmt) REVERT: J 112 TYR cc_start: 0.8744 (t80) cc_final: 0.8488 (t80) REVERT: J 131 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7645 (mtt-85) REVERT: J 162 ASP cc_start: 0.7412 (t0) cc_final: 0.7190 (m-30) REVERT: J 164 ASP cc_start: 0.8241 (t0) cc_final: 0.7515 (t0) REVERT: J 168 ASP cc_start: 0.8264 (t0) cc_final: 0.8021 (t0) REVERT: J 193 SER cc_start: 0.8926 (m) cc_final: 0.8676 (p) REVERT: K 92 THR cc_start: 0.9238 (m) cc_final: 0.8906 (p) REVERT: K 129 GLU cc_start: 0.8636 (tp30) cc_final: 0.8335 (mm-30) REVERT: M 107 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7742 (mtm-85) REVERT: N 102 MET cc_start: 0.8500 (mtm) cc_final: 0.8274 (mtm) REVERT: N 105 ASP cc_start: 0.6993 (m-30) cc_final: 0.6632 (p0) REVERT: N 110 VAL cc_start: 0.8627 (t) cc_final: 0.8077 (t) REVERT: Q 60 TYR cc_start: 0.7630 (m-80) cc_final: 0.7032 (m-80) REVERT: Q 188 MET cc_start: 0.6916 (tpp) cc_final: 0.5843 (ttm) REVERT: Q 226 VAL cc_start: 0.7953 (t) cc_final: 0.7619 (m) REVERT: R 101 PHE cc_start: 0.8128 (m-80) cc_final: 0.7802 (m-10) REVERT: R 112 TYR cc_start: 0.8254 (t80) cc_final: 0.8026 (t80) REVERT: R 115 MET cc_start: 0.8234 (mtp) cc_final: 0.7877 (tpp) REVERT: R 166 TYR cc_start: 0.8150 (m-80) cc_final: 0.7935 (m-10) REVERT: R 198 HIS cc_start: 0.7742 (m-70) cc_final: 0.7541 (m170) REVERT: S 33 MET cc_start: 0.7711 (mmm) cc_final: 0.7205 (tpt) REVERT: S 37 ASP cc_start: 0.7713 (t0) cc_final: 0.7164 (t0) REVERT: S 101 PHE cc_start: 0.7884 (m-80) cc_final: 0.6975 (m-10) REVERT: S 229 MET cc_start: 0.6615 (tpp) cc_final: 0.5887 (tpt) outliers start: 88 outliers final: 48 residues processed: 940 average time/residue: 0.2280 time to fit residues: 346.4907 Evaluate side-chains 750 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 698 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 206 ASP Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 32 optimal weight: 0.0870 chunk 386 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 448 optimal weight: 0.0870 chunk 285 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 484 GLN D 156 GLN D 456 GLN E 62 HIS ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 187 GLN R 19 HIS ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097735 restraints weight = 67690.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101005 restraints weight = 30361.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103112 restraints weight = 17719.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104449 restraints weight = 12299.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105300 restraints weight = 9668.188| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36765 Z= 0.192 Angle : 0.637 9.494 49676 Z= 0.329 Chirality : 0.046 0.204 5575 Planarity : 0.005 0.047 6440 Dihedral : 4.913 109.372 5022 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.31 % Allowed : 12.57 % Favored : 84.12 % 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: 1.06 (0.12), residues: 4538 helix: 1.88 (0.11), residues: 2108 sheet: -0.34 (0.20), residues: 602 loop : -0.25 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 208 TYR 0.027 0.002 TYR S 112 PHE 0.029 0.002 PHE B 612 TRP 0.012 0.001 TRP Q 122 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00432 (36765) covalent geometry : angle 0.63668 (49676) hydrogen bonds : bond 0.04738 ( 1955) hydrogen bonds : angle 3.08312 (13857) *********************** 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 902 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 771 time to evaluate : 1.321 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 61 MET cc_start: 0.7521 (mtp) cc_final: 0.7134 (ttm) REVERT: A 74 SER cc_start: 0.8995 (m) cc_final: 0.8736 (p) REVERT: A 268 ASN cc_start: 0.7737 (t0) cc_final: 0.7455 (t0) REVERT: A 296 MET cc_start: 0.8435 (ptm) cc_final: 0.7762 (ptt) REVERT: A 308 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.8060 (ptt-90) REVERT: A 438 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8317 (tptp) REVERT: A 491 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7698 (tp30) REVERT: A 500 SER cc_start: 0.8331 (m) cc_final: 0.7897 (p) REVERT: A 573 HIS cc_start: 0.7736 (t-170) cc_final: 0.7525 (t70) REVERT: B 30 THR cc_start: 0.9053 (m) cc_final: 0.8803 (p) REVERT: B 39 MET cc_start: 0.8191 (ttt) cc_final: 0.7944 (ttt) REVERT: B 84 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8110 (pttm) REVERT: B 318 MET cc_start: 0.8753 (mmm) cc_final: 0.7817 (mpp) REVERT: B 324 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 334 SER cc_start: 0.9491 (t) cc_final: 0.9256 (t) REVERT: B 340 MET cc_start: 0.8380 (mtm) cc_final: 0.7954 (mtm) REVERT: B 345 SER cc_start: 0.9233 (t) cc_final: 0.8815 (p) REVERT: B 346 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7797 (ttt) REVERT: B 387 GLU cc_start: 0.8180 (tp30) cc_final: 0.7592 (tm-30) REVERT: B 466 ASP cc_start: 0.8466 (t70) cc_final: 0.8224 (t0) REVERT: B 584 MET cc_start: 0.8626 (mtm) cc_final: 0.7850 (mtp) REVERT: B 601 TYR cc_start: 0.7132 (m-10) cc_final: 0.6870 (m-80) REVERT: C 254 CYS cc_start: 0.7818 (m) cc_final: 0.7559 (m) REVERT: C 318 MET cc_start: 0.8808 (mtt) cc_final: 0.8122 (mtt) REVERT: C 445 PHE cc_start: 0.9236 (m-80) cc_final: 0.8972 (m-80) REVERT: C 448 VAL cc_start: 0.9182 (t) cc_final: 0.8937 (m) REVERT: C 600 ASP cc_start: 0.8312 (t70) cc_final: 0.7959 (t0) REVERT: C 603 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8214 (tm-30) REVERT: D 316 GLU cc_start: 0.8414 (tp30) cc_final: 0.8017 (tt0) REVERT: E 83 SER cc_start: 0.8917 (m) cc_final: 0.8471 (p) REVERT: E 168 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: E 254 MET cc_start: 0.8416 (tpp) cc_final: 0.8027 (tpp) REVERT: E 256 ASN cc_start: 0.8366 (m-40) cc_final: 0.7785 (p0) REVERT: E 327 MET cc_start: 0.8271 (ttt) cc_final: 0.8049 (ttt) REVERT: E 500 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8558 (mm) REVERT: F 47 TYR cc_start: 0.8397 (m-80) cc_final: 0.8117 (m-80) REVERT: F 266 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: F 300 MET cc_start: 0.8795 (mmm) cc_final: 0.8590 (mmm) REVERT: F 336 GLU cc_start: 0.7577 (tp30) cc_final: 0.7345 (tp30) REVERT: H 46 GLN cc_start: 0.8650 (mt0) cc_final: 0.8199 (mp10) REVERT: H 160 GLU cc_start: 0.8473 (tp30) cc_final: 0.8010 (tp30) REVERT: H 193 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8135 (tm-30) REVERT: I 76 MET cc_start: 0.8472 (mmm) cc_final: 0.8260 (mmp) REVERT: I 88 ASP cc_start: 0.8530 (t70) cc_final: 0.8157 (t0) REVERT: I 97 GLU cc_start: 0.8127 (tt0) cc_final: 0.7564 (tp30) REVERT: I 113 GLN cc_start: 0.7936 (tp40) cc_final: 0.7614 (tp40) REVERT: I 129 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7567 (mm-30) REVERT: I 132 MET cc_start: 0.8049 (mpp) cc_final: 0.7485 (mpp) REVERT: I 163 VAL cc_start: 0.8782 (p) cc_final: 0.8339 (p) REVERT: I 194 ASN cc_start: 0.8485 (t0) cc_final: 0.8189 (t0) REVERT: J 89 ASP cc_start: 0.8734 (m-30) cc_final: 0.8529 (m-30) REVERT: J 97 GLU cc_start: 0.8675 (tt0) cc_final: 0.8345 (tt0) REVERT: J 112 TYR cc_start: 0.8858 (t80) cc_final: 0.8649 (t80) REVERT: J 131 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7519 (mtt-85) REVERT: J 162 ASP cc_start: 0.7455 (t0) cc_final: 0.7162 (m-30) REVERT: J 164 ASP cc_start: 0.8272 (t0) cc_final: 0.7429 (t0) REVERT: J 168 ASP cc_start: 0.8465 (t0) cc_final: 0.8183 (t0) REVERT: J 182 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7905 (mm-30) REVERT: J 194 ASN cc_start: 0.8881 (t0) cc_final: 0.8615 (t0) REVERT: K 92 THR cc_start: 0.9222 (m) cc_final: 0.8920 (p) REVERT: K 125 TYR cc_start: 0.8748 (m-10) cc_final: 0.8527 (m-10) REVERT: K 182 GLU cc_start: 0.6401 (mt-10) cc_final: 0.6192 (mt-10) REVERT: M 107 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7887 (ttm-80) REVERT: M 109 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7640 (mm-40) REVERT: M 115 ARG cc_start: 0.7723 (mtm180) cc_final: 0.7520 (mtm180) REVERT: N 102 MET cc_start: 0.8506 (mtm) cc_final: 0.8183 (mtm) REVERT: N 105 ASP cc_start: 0.6938 (m-30) cc_final: 0.6547 (p0) REVERT: O 78 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: O 94 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8447 (tmm-80) REVERT: Q 188 MET cc_start: 0.7323 (tpp) cc_final: 0.6236 (ttm) REVERT: R 101 PHE cc_start: 0.8089 (m-80) cc_final: 0.7869 (m-10) REVERT: R 111 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7751 (mm110) REVERT: R 115 MET cc_start: 0.8309 (mtp) cc_final: 0.8093 (mtp) REVERT: R 135 GLN cc_start: 0.8678 (tt0) cc_final: 0.8466 (tt0) REVERT: R 139 TYR cc_start: 0.8601 (t80) cc_final: 0.7814 (t80) REVERT: R 166 TYR cc_start: 0.8138 (m-80) cc_final: 0.7771 (m-10) REVERT: S 33 MET cc_start: 0.7672 (mmm) cc_final: 0.7409 (tpt) REVERT: S 37 ASP cc_start: 0.7460 (t0) cc_final: 0.6940 (t0) REVERT: S 101 PHE cc_start: 0.7982 (m-80) cc_final: 0.7125 (m-10) REVERT: S 229 MET cc_start: 0.6898 (tpp) cc_final: 0.6315 (tpt) outliers start: 131 outliers final: 81 residues processed: 852 average time/residue: 0.2211 time to fit residues: 310.5097 Evaluate side-chains 748 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 663 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain J residue 75 LEU 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 70 SER Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain S residue 175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 439 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 441 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 314 ASN B 261 GLN M 75 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092666 restraints weight = 68488.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095780 restraints weight = 31071.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097805 restraints weight = 18373.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099103 restraints weight = 12918.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099915 restraints weight = 10255.284| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 36765 Z= 0.277 Angle : 0.701 9.782 49676 Z= 0.361 Chirality : 0.048 0.224 5575 Planarity : 0.005 0.073 6440 Dihedral : 5.124 109.627 5022 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.10 % Allowed : 13.94 % Favored : 81.97 % 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: 0.77 (0.12), residues: 4538 helix: 1.72 (0.11), residues: 2119 sheet: -0.51 (0.20), residues: 595 loop : -0.53 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 78 TYR 0.034 0.002 TYR Q 232 PHE 0.021 0.002 PHE A 252 TRP 0.015 0.002 TRP Q 122 HIS 0.006 0.001 HIS B 444 Details of bonding type rmsd covalent geometry : bond 0.00633 (36765) covalent geometry : angle 0.70121 (49676) hydrogen bonds : bond 0.04689 ( 1955) hydrogen bonds : angle 3.10870 (13857) *********************** 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 876 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 714 time to evaluate : 1.290 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 74 SER cc_start: 0.8987 (m) cc_final: 0.8620 (p) REVERT: A 142 ARG cc_start: 0.7841 (mmt180) cc_final: 0.7380 (mmt180) REVERT: A 268 ASN cc_start: 0.7826 (t0) cc_final: 0.7621 (t0) REVERT: A 296 MET cc_start: 0.8701 (ptm) cc_final: 0.7961 (ptt) REVERT: A 308 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.8053 (ptt-90) REVERT: A 438 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8443 (tptp) REVERT: A 500 SER cc_start: 0.8598 (m) cc_final: 0.8136 (p) REVERT: A 610 ASN cc_start: 0.7897 (m-40) cc_final: 0.7450 (m-40) REVERT: B 30 THR cc_start: 0.9204 (m) cc_final: 0.8882 (p) REVERT: B 39 MET cc_start: 0.8370 (ttt) cc_final: 0.8027 (ttt) REVERT: B 84 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8250 (pttm) REVERT: B 324 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 334 SER cc_start: 0.9566 (t) cc_final: 0.9346 (t) REVERT: B 346 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7789 (ttt) REVERT: B 387 GLU cc_start: 0.8342 (tp30) cc_final: 0.7749 (tm-30) REVERT: B 466 ASP cc_start: 0.8604 (t70) cc_final: 0.8305 (t0) REVERT: B 584 MET cc_start: 0.8771 (mtm) cc_final: 0.7995 (mtp) REVERT: B 613 ARG cc_start: 0.8993 (mtp-110) cc_final: 0.8475 (mtm180) REVERT: C 254 CYS cc_start: 0.7854 (m) cc_final: 0.7499 (m) REVERT: C 350 SER cc_start: 0.8119 (p) cc_final: 0.7859 (t) REVERT: C 420 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8706 (Cg_endo) REVERT: C 445 PHE cc_start: 0.9265 (m-80) cc_final: 0.9040 (m-80) REVERT: C 448 VAL cc_start: 0.9361 (t) cc_final: 0.9160 (m) REVERT: D 201 GLU cc_start: 0.7546 (tp30) cc_final: 0.7247 (tp30) REVERT: D 400 ARG cc_start: 0.7138 (tpm-80) cc_final: 0.6589 (tpm170) REVERT: E 83 SER cc_start: 0.8982 (m) cc_final: 0.8477 (p) REVERT: E 168 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: E 253 SER cc_start: 0.8766 (p) cc_final: 0.8369 (t) REVERT: E 254 MET cc_start: 0.8294 (tpp) cc_final: 0.7894 (tpp) REVERT: E 327 MET cc_start: 0.8319 (ttt) cc_final: 0.8058 (ttt) REVERT: E 500 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8722 (mm) REVERT: F 74 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8796 (mt) REVERT: F 189 ILE cc_start: 0.8929 (mm) cc_final: 0.8581 (tt) REVERT: F 238 MET cc_start: 0.7998 (tpt) cc_final: 0.7773 (tmm) REVERT: F 266 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: F 336 GLU cc_start: 0.7855 (tp30) cc_final: 0.7605 (tp30) REVERT: H 46 GLN cc_start: 0.8686 (mt0) cc_final: 0.8210 (mp10) REVERT: H 160 GLU cc_start: 0.8552 (tp30) cc_final: 0.8098 (tp30) REVERT: I 76 MET cc_start: 0.8506 (mmm) cc_final: 0.8269 (mmp) REVERT: I 88 ASP cc_start: 0.8533 (t70) cc_final: 0.8164 (t0) REVERT: I 97 GLU cc_start: 0.8301 (tt0) cc_final: 0.7589 (tp30) REVERT: I 113 GLN cc_start: 0.8113 (tp40) cc_final: 0.7902 (tp40) REVERT: I 129 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7803 (mm-30) REVERT: I 132 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: I 163 VAL cc_start: 0.8933 (p) cc_final: 0.7577 (p) REVERT: J 89 ASP cc_start: 0.8782 (m-30) cc_final: 0.8560 (m-30) REVERT: J 131 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7578 (mtt-85) REVERT: J 162 ASP cc_start: 0.7482 (t0) cc_final: 0.7014 (m-30) REVERT: J 164 ASP cc_start: 0.8312 (t0) cc_final: 0.7492 (t0) REVERT: J 168 ASP cc_start: 0.8654 (t0) cc_final: 0.8417 (t0) REVERT: J 182 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8058 (mm-30) REVERT: J 207 MET cc_start: 0.8589 (mmm) cc_final: 0.7989 (mtm) REVERT: K 125 TYR cc_start: 0.8854 (m-10) cc_final: 0.8572 (m-10) REVERT: K 182 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6483 (mt-10) REVERT: N 79 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7629 (ptp-110) REVERT: N 82 GLN cc_start: 0.8605 (pt0) cc_final: 0.8397 (tm-30) REVERT: N 89 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8454 (tp40) REVERT: N 94 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8139 (ptt90) REVERT: N 102 MET cc_start: 0.8446 (mtm) cc_final: 0.7661 (mtm) REVERT: N 105 ASP cc_start: 0.6889 (m-30) cc_final: 0.6596 (p0) REVERT: N 107 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8435 (mmp80) REVERT: O 79 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8210 (ptp90) REVERT: Q 230 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8134 (tt) REVERT: Q 231 ASP cc_start: 0.8346 (m-30) cc_final: 0.8115 (m-30) REVERT: Q 232 TYR cc_start: 0.8127 (t80) cc_final: 0.7772 (t80) REVERT: R 48 ASP cc_start: 0.8140 (t0) cc_final: 0.7864 (t0) REVERT: R 101 PHE cc_start: 0.8099 (m-80) cc_final: 0.7804 (m-10) REVERT: R 111 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7898 (mm110) REVERT: R 115 MET cc_start: 0.8489 (mtp) cc_final: 0.8236 (mtp) REVERT: S 37 ASP cc_start: 0.7421 (t0) cc_final: 0.7018 (t0) REVERT: S 101 PHE cc_start: 0.8157 (m-80) cc_final: 0.7272 (m-10) REVERT: S 188 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6468 (tmm) REVERT: S 229 MET cc_start: 0.7076 (tpp) cc_final: 0.6803 (tpt) outliers start: 162 outliers final: 106 residues processed: 814 average time/residue: 0.2172 time to fit residues: 290.3076 Evaluate side-chains 768 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 654 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 175 ILE Chi-restraints excluded: chain S residue 188 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 198 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 339 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 297 optimal weight: 0.0050 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN E 85 GLN F 181 ASN H 206 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096623 restraints weight = 66826.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099913 restraints weight = 29853.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102031 restraints weight = 17464.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103399 restraints weight = 12170.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104223 restraints weight = 9574.088| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36765 Z= 0.130 Angle : 0.604 10.178 49676 Z= 0.305 Chirality : 0.044 0.219 5575 Planarity : 0.004 0.065 6440 Dihedral : 4.891 109.546 5022 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.93 % Allowed : 15.78 % Favored : 81.28 % 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: 1.03 (0.13), residues: 4538 helix: 1.97 (0.11), residues: 2120 sheet: -0.43 (0.20), residues: 564 loop : -0.43 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 613 TYR 0.028 0.001 TYR Q 197 PHE 0.022 0.001 PHE B 612 TRP 0.013 0.001 TRP C 567 HIS 0.011 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00283 (36765) covalent geometry : angle 0.60360 (49676) hydrogen bonds : bond 0.04171 ( 1955) hydrogen bonds : angle 2.89825 (13857) *********************** 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 857 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 741 time to evaluate : 0.934 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: A 61 MET cc_start: 0.7447 (mtp) cc_final: 0.7053 (ttm) REVERT: A 74 SER cc_start: 0.8900 (m) cc_final: 0.8645 (p) REVERT: A 141 LEU cc_start: 0.9184 (mt) cc_final: 0.8907 (mt) REVERT: A 142 ARG cc_start: 0.7737 (mmt180) cc_final: 0.7288 (mmt180) REVERT: A 268 ASN cc_start: 0.7702 (t0) cc_final: 0.7501 (t0) REVERT: A 296 MET cc_start: 0.8680 (ptm) cc_final: 0.8014 (ptt) REVERT: A 308 ARG cc_start: 0.8342 (ptp-110) cc_final: 0.8017 (ptt-90) REVERT: A 438 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8371 (tptp) REVERT: A 500 SER cc_start: 0.8538 (m) cc_final: 0.8064 (p) REVERT: A 576 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: B 30 THR cc_start: 0.9099 (m) cc_final: 0.8841 (p) REVERT: B 39 MET cc_start: 0.8350 (ttt) cc_final: 0.8128 (ttt) REVERT: B 84 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8089 (ptpp) REVERT: B 95 MET cc_start: 0.7606 (mmm) cc_final: 0.7141 (mtp) REVERT: B 117 TYR cc_start: 0.8908 (m-80) cc_final: 0.8577 (m-80) REVERT: B 324 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 334 SER cc_start: 0.9508 (t) cc_final: 0.9250 (t) REVERT: B 345 SER cc_start: 0.9298 (t) cc_final: 0.8962 (p) REVERT: B 346 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7742 (ttt) REVERT: B 387 GLU cc_start: 0.8246 (tp30) cc_final: 0.7879 (tm-30) REVERT: B 466 ASP cc_start: 0.8560 (t70) cc_final: 0.8269 (t0) REVERT: B 613 ARG cc_start: 0.9027 (mtp-110) cc_final: 0.8516 (mtm180) REVERT: C 193 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6855 (tt0) REVERT: C 254 CYS cc_start: 0.7817 (m) cc_final: 0.7503 (m) REVERT: C 283 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 350 SER cc_start: 0.7834 (p) cc_final: 0.7586 (t) REVERT: C 445 PHE cc_start: 0.9291 (m-80) cc_final: 0.9021 (m-80) REVERT: C 448 VAL cc_start: 0.9302 (t) cc_final: 0.9088 (m) REVERT: C 600 ASP cc_start: 0.8385 (t70) cc_final: 0.8151 (t0) REVERT: C 603 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8001 (tm-30) REVERT: D 39 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.6144 (p90) REVERT: D 161 GLN cc_start: 0.9013 (tp40) cc_final: 0.8705 (tm-30) REVERT: D 201 GLU cc_start: 0.7515 (tp30) cc_final: 0.7241 (tp30) REVERT: D 316 GLU cc_start: 0.8584 (tp30) cc_final: 0.8147 (tt0) REVERT: D 402 MET cc_start: 0.8599 (tpt) cc_final: 0.8102 (tpt) REVERT: D 419 SER cc_start: 0.8994 (t) cc_final: 0.8738 (m) REVERT: D 456 GLN cc_start: 0.8285 (tp40) cc_final: 0.7961 (tp-100) REVERT: E 83 SER cc_start: 0.8948 (m) cc_final: 0.8379 (p) REVERT: E 168 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: E 187 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: E 254 MET cc_start: 0.8300 (tpp) cc_final: 0.7863 (tpp) REVERT: E 327 MET cc_start: 0.8264 (ttt) cc_final: 0.8034 (ttt) REVERT: E 500 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8510 (mm) REVERT: F 74 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (mt) REVERT: F 189 ILE cc_start: 0.8777 (mm) cc_final: 0.8411 (tt) REVERT: F 238 MET cc_start: 0.7894 (tpt) cc_final: 0.7653 (tmm) REVERT: F 266 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: H 46 GLN cc_start: 0.8724 (mt0) cc_final: 0.8231 (mp10) REVERT: H 160 GLU cc_start: 0.8548 (tp30) cc_final: 0.8067 (tp30) REVERT: H 190 GLU cc_start: 0.8055 (tp30) cc_final: 0.7779 (tp30) REVERT: H 193 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8129 (tm-30) REVERT: I 76 MET cc_start: 0.8560 (mmm) cc_final: 0.8298 (mmp) REVERT: I 88 ASP cc_start: 0.8496 (t70) cc_final: 0.8121 (t0) REVERT: I 97 GLU cc_start: 0.8416 (tt0) cc_final: 0.7664 (tp30) REVERT: I 129 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7601 (mm-30) REVERT: I 132 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: I 163 VAL cc_start: 0.8963 (p) cc_final: 0.8429 (p) REVERT: J 89 ASP cc_start: 0.8849 (m-30) cc_final: 0.8608 (m-30) REVERT: J 131 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7446 (mtt-85) REVERT: J 132 MET cc_start: 0.7910 (mmt) cc_final: 0.7654 (mmt) REVERT: J 162 ASP cc_start: 0.7529 (t0) cc_final: 0.7079 (m-30) REVERT: J 164 ASP cc_start: 0.8329 (t0) cc_final: 0.7382 (t0) REVERT: J 168 ASP cc_start: 0.8638 (t0) cc_final: 0.8353 (t0) REVERT: J 182 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7976 (mm-30) REVERT: K 121 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8649 (mm) REVERT: K 125 TYR cc_start: 0.8708 (m-10) cc_final: 0.8442 (m-10) REVERT: K 182 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6260 (mt-10) REVERT: M 107 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7999 (mtm-85) REVERT: N 89 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8555 (tp-100) REVERT: N 105 ASP cc_start: 0.6939 (m-30) cc_final: 0.6620 (p0) REVERT: Q 61 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7233 (mtp85) REVERT: Q 195 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: Q 232 TYR cc_start: 0.8188 (t80) cc_final: 0.7948 (t80) REVERT: R 112 TYR cc_start: 0.8528 (t80) cc_final: 0.8243 (t80) REVERT: R 139 TYR cc_start: 0.8648 (t80) cc_final: 0.8106 (t80) REVERT: R 166 TYR cc_start: 0.8114 (m-80) cc_final: 0.7913 (m-80) REVERT: S 101 PHE cc_start: 0.8040 (m-80) cc_final: 0.7191 (m-10) outliers start: 116 outliers final: 69 residues processed: 807 average time/residue: 0.2167 time to fit residues: 287.8010 Evaluate side-chains 754 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 674 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 175 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 150 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 449 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN H 206 GLN I 194 ASN I 221 ASN M 75 GLN N 82 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097077 restraints weight = 67292.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100275 restraints weight = 30272.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102366 restraints weight = 17826.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103707 restraints weight = 12496.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104568 restraints weight = 9873.871| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36765 Z= 0.136 Angle : 0.601 11.734 49676 Z= 0.304 Chirality : 0.044 0.221 5575 Planarity : 0.004 0.055 6440 Dihedral : 4.779 112.750 5022 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 16.57 % Favored : 80.60 % 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: 1.06 (0.13), residues: 4538 helix: 2.03 (0.11), residues: 2111 sheet: -0.33 (0.21), residues: 537 loop : -0.47 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 78 TYR 0.041 0.002 TYR Q 197 PHE 0.022 0.001 PHE F 231 TRP 0.012 0.001 TRP C 567 HIS 0.015 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00306 (36765) covalent geometry : angle 0.60109 (49676) hydrogen bonds : bond 0.04014 ( 1955) hydrogen bonds : angle 2.83271 (13857) *********************** 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 834 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 722 time to evaluate : 1.512 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 61 MET cc_start: 0.7538 (mtp) cc_final: 0.7117 (ttm) REVERT: A 74 SER cc_start: 0.8893 (m) cc_final: 0.8681 (p) REVERT: A 141 LEU cc_start: 0.9133 (mt) cc_final: 0.8883 (mt) REVERT: A 142 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7310 (mmt180) REVERT: A 296 MET cc_start: 0.8684 (ptm) cc_final: 0.8185 (ptt) REVERT: A 308 ARG cc_start: 0.8397 (ptp-110) cc_final: 0.8069 (ptt-90) REVERT: A 438 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8415 (tptp) REVERT: A 450 TRP cc_start: 0.9097 (p90) cc_final: 0.8868 (p90) REVERT: A 500 SER cc_start: 0.8513 (m) cc_final: 0.8056 (p) REVERT: B 30 THR cc_start: 0.9067 (m) cc_final: 0.8853 (p) REVERT: B 84 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8110 (ptpp) REVERT: B 117 TYR cc_start: 0.8902 (m-80) cc_final: 0.8499 (m-80) REVERT: B 197 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7375 (tm-30) REVERT: B 324 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 334 SER cc_start: 0.9480 (t) cc_final: 0.9237 (t) REVERT: B 346 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7857 (ttt) REVERT: B 387 GLU cc_start: 0.8230 (tp30) cc_final: 0.7874 (tm-30) REVERT: B 466 ASP cc_start: 0.8516 (t70) cc_final: 0.8243 (t0) REVERT: B 571 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7298 (ptp90) REVERT: B 584 MET cc_start: 0.8468 (mtm) cc_final: 0.7779 (ttm) REVERT: B 601 TYR cc_start: 0.7467 (m-80) cc_final: 0.7199 (m-80) REVERT: B 613 ARG cc_start: 0.8982 (mtp-110) cc_final: 0.8568 (mtm180) REVERT: C 193 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6879 (tt0) REVERT: C 254 CYS cc_start: 0.7763 (m) cc_final: 0.7552 (m) REVERT: C 279 GLU cc_start: 0.6571 (tp30) cc_final: 0.5954 (tp30) REVERT: C 318 MET cc_start: 0.8782 (mtt) cc_final: 0.8100 (mtt) REVERT: C 445 PHE cc_start: 0.9264 (m-80) cc_final: 0.9026 (m-80) REVERT: C 448 VAL cc_start: 0.9291 (t) cc_final: 0.9082 (m) REVERT: C 518 ASP cc_start: 0.8460 (t0) cc_final: 0.8251 (t0) REVERT: C 603 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8038 (tm-30) REVERT: D 39 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.6048 (p90) REVERT: D 161 GLN cc_start: 0.9043 (tp40) cc_final: 0.8731 (tm-30) REVERT: D 201 GLU cc_start: 0.7503 (tp30) cc_final: 0.7253 (tp30) REVERT: D 316 GLU cc_start: 0.8528 (tp30) cc_final: 0.8123 (tt0) REVERT: D 402 MET cc_start: 0.8738 (tpt) cc_final: 0.8425 (ttp) REVERT: D 419 SER cc_start: 0.8997 (t) cc_final: 0.8744 (m) REVERT: D 456 GLN cc_start: 0.8316 (tp40) cc_final: 0.7991 (tp-100) REVERT: E 83 SER cc_start: 0.8917 (m) cc_final: 0.8383 (p) REVERT: E 168 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: E 187 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8813 (tt0) REVERT: E 254 MET cc_start: 0.8294 (tpp) cc_final: 0.7836 (tpp) REVERT: E 500 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8548 (mm) REVERT: F 74 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8788 (mt) REVERT: F 87 LEU cc_start: 0.8797 (mt) cc_final: 0.8584 (mp) REVERT: F 189 ILE cc_start: 0.8814 (mm) cc_final: 0.8452 (tt) REVERT: F 238 MET cc_start: 0.7856 (tpt) cc_final: 0.7652 (tmm) REVERT: F 246 SER cc_start: 0.8951 (t) cc_final: 0.8589 (m) REVERT: F 266 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: F 336 GLU cc_start: 0.7889 (tp30) cc_final: 0.7652 (tp30) REVERT: H 46 GLN cc_start: 0.8672 (mt0) cc_final: 0.8216 (mp10) REVERT: H 160 GLU cc_start: 0.8548 (tp30) cc_final: 0.8083 (tp30) REVERT: H 190 GLU cc_start: 0.8037 (tp30) cc_final: 0.7701 (tp30) REVERT: H 193 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8116 (tm-30) REVERT: H 197 GLU cc_start: 0.8160 (tt0) cc_final: 0.7778 (tt0) REVERT: I 88 ASP cc_start: 0.8452 (t70) cc_final: 0.8083 (t0) REVERT: I 97 GLU cc_start: 0.8363 (tt0) cc_final: 0.7597 (tp30) REVERT: I 129 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7829 (mm-30) REVERT: I 132 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7078 (mpp) REVERT: I 163 VAL cc_start: 0.8994 (p) cc_final: 0.7832 (p) REVERT: J 89 ASP cc_start: 0.8814 (m-30) cc_final: 0.8558 (m-30) REVERT: J 131 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7586 (mtt-85) REVERT: J 162 ASP cc_start: 0.7538 (t0) cc_final: 0.7116 (m-30) REVERT: J 164 ASP cc_start: 0.8295 (t0) cc_final: 0.7794 (t0) REVERT: J 168 ASP cc_start: 0.8577 (t0) cc_final: 0.8262 (t0) REVERT: J 182 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8010 (mm-30) REVERT: J 185 ASN cc_start: 0.8245 (p0) cc_final: 0.7825 (p0) REVERT: K 182 GLU cc_start: 0.6459 (mt-10) cc_final: 0.6228 (mt-10) REVERT: M 93 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7949 (mm-30) REVERT: M 107 ARG cc_start: 0.8215 (tpp80) cc_final: 0.7932 (mtm-85) REVERT: M 114 TYR cc_start: 0.8706 (t80) cc_final: 0.8484 (t80) REVERT: N 89 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8531 (tp-100) REVERT: N 105 ASP cc_start: 0.6975 (m-30) cc_final: 0.6716 (p0) REVERT: O 79 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8063 (ptp90) REVERT: Q 61 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7314 (mtp85) REVERT: Q 195 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: Q 213 PHE cc_start: 0.8047 (m-80) cc_final: 0.7770 (m-80) REVERT: Q 232 TYR cc_start: 0.8196 (t80) cc_final: 0.7689 (t80) REVERT: R 139 TYR cc_start: 0.8646 (t80) cc_final: 0.8356 (t80) REVERT: S 101 PHE cc_start: 0.8090 (m-80) cc_final: 0.7406 (m-10) REVERT: S 175 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7382 (mp) outliers start: 112 outliers final: 78 residues processed: 785 average time/residue: 0.2196 time to fit residues: 282.8027 Evaluate side-chains 743 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 655 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 175 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 156 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 414 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 417 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN M 75 GLN M 82 GLN N 82 GLN O 85 GLN Q 19 HIS ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092640 restraints weight = 67551.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095820 restraints weight = 30588.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097866 restraints weight = 18023.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099177 restraints weight = 12688.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099966 restraints weight = 10063.392| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 36765 Z= 0.245 Angle : 0.674 11.333 49676 Z= 0.343 Chirality : 0.047 0.201 5575 Planarity : 0.005 0.059 6440 Dihedral : 4.910 111.695 5022 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.44 % Allowed : 16.72 % Favored : 79.84 % 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: 0.92 (0.13), residues: 4538 helix: 1.94 (0.11), residues: 2112 sheet: -0.50 (0.21), residues: 568 loop : -0.54 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 115 TYR 0.027 0.002 TYR Q 112 PHE 0.022 0.002 PHE H 44 TRP 0.015 0.002 TRP Q 122 HIS 0.006 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00565 (36765) covalent geometry : angle 0.67376 (49676) hydrogen bonds : bond 0.04287 ( 1955) hydrogen bonds : angle 2.92689 (13857) *********************** 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 813 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 677 time to evaluate : 1.345 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 74 SER cc_start: 0.8936 (m) cc_final: 0.8614 (m) REVERT: A 141 LEU cc_start: 0.9243 (mt) cc_final: 0.8946 (mt) REVERT: A 142 ARG cc_start: 0.7897 (mmt180) cc_final: 0.7454 (mmt180) REVERT: A 296 MET cc_start: 0.8775 (ptm) cc_final: 0.8187 (ptt) REVERT: A 308 ARG cc_start: 0.8469 (ptp-110) cc_final: 0.8085 (ptt-90) REVERT: A 438 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8487 (tptp) REVERT: A 500 SER cc_start: 0.8640 (m) cc_final: 0.8262 (p) REVERT: A 576 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: A 607 ASP cc_start: 0.8816 (m-30) cc_final: 0.8456 (m-30) REVERT: B 30 THR cc_start: 0.9138 (m) cc_final: 0.8884 (p) REVERT: B 81 ARG cc_start: 0.7365 (ptt180) cc_final: 0.7165 (mtm180) REVERT: B 84 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8297 (pttm) REVERT: B 151 ASP cc_start: 0.8260 (t70) cc_final: 0.7851 (t0) REVERT: B 197 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7439 (tm-30) REVERT: B 324 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8800 (tm-30) REVERT: B 334 SER cc_start: 0.9565 (t) cc_final: 0.9335 (t) REVERT: B 346 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7837 (ttt) REVERT: B 349 ASP cc_start: 0.7619 (m-30) cc_final: 0.7342 (m-30) REVERT: B 387 GLU cc_start: 0.8308 (tp30) cc_final: 0.7782 (tm-30) REVERT: B 466 ASP cc_start: 0.8624 (t70) cc_final: 0.8334 (t0) REVERT: B 571 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7161 (ptp90) REVERT: B 613 ARG cc_start: 0.9047 (mtp-110) cc_final: 0.8574 (mtm180) REVERT: C 100 ASP cc_start: 0.8503 (p0) cc_final: 0.8192 (p0) REVERT: C 254 CYS cc_start: 0.7787 (m) cc_final: 0.7455 (m) REVERT: C 364 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8386 (mmm-85) REVERT: C 445 PHE cc_start: 0.9317 (m-80) cc_final: 0.9067 (m-80) REVERT: C 603 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8084 (tm-30) REVERT: D 314 ARG cc_start: 0.8794 (ttp-110) cc_final: 0.8562 (ttp80) REVERT: D 316 GLU cc_start: 0.8590 (tp30) cc_final: 0.8268 (tt0) REVERT: D 402 MET cc_start: 0.8903 (tpt) cc_final: 0.8496 (tpt) REVERT: D 419 SER cc_start: 0.9058 (t) cc_final: 0.8794 (m) REVERT: E 83 SER cc_start: 0.8965 (m) cc_final: 0.8437 (p) REVERT: E 168 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: E 180 MET cc_start: 0.8928 (mmp) cc_final: 0.8668 (mmt) REVERT: E 182 SER cc_start: 0.8702 (p) cc_final: 0.8475 (t) REVERT: E 254 MET cc_start: 0.8192 (tpp) cc_final: 0.7786 (tpp) REVERT: E 398 LEU cc_start: 0.8652 (mt) cc_final: 0.8310 (mt) REVERT: E 500 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8691 (mm) REVERT: F 74 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8831 (mt) REVERT: F 189 ILE cc_start: 0.8903 (mm) cc_final: 0.8591 (tt) REVERT: F 238 MET cc_start: 0.7927 (tpt) cc_final: 0.7681 (tmm) REVERT: F 246 SER cc_start: 0.9003 (t) cc_final: 0.8632 (m) REVERT: F 266 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: F 336 GLU cc_start: 0.8025 (tp30) cc_final: 0.7750 (tp30) REVERT: H 46 GLN cc_start: 0.8697 (mt0) cc_final: 0.8200 (mp10) REVERT: H 160 GLU cc_start: 0.8531 (tp30) cc_final: 0.8053 (tp30) REVERT: I 88 ASP cc_start: 0.8495 (t70) cc_final: 0.8128 (t0) REVERT: I 97 GLU cc_start: 0.8356 (tt0) cc_final: 0.7640 (tp30) REVERT: I 129 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7811 (mm-30) REVERT: I 132 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: I 163 VAL cc_start: 0.8839 (p) cc_final: 0.7846 (p) REVERT: J 89 ASP cc_start: 0.8825 (m-30) cc_final: 0.8603 (m-30) REVERT: J 131 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7748 (mtt-85) REVERT: J 164 ASP cc_start: 0.8328 (t0) cc_final: 0.7907 (t0) REVERT: J 168 ASP cc_start: 0.8531 (t0) cc_final: 0.8249 (t0) REVERT: J 172 TYR cc_start: 0.8392 (m-10) cc_final: 0.8077 (m-10) REVERT: J 182 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8016 (mm-30) REVERT: J 185 ASN cc_start: 0.8352 (p0) cc_final: 0.7915 (p0) REVERT: K 121 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8632 (mm) REVERT: K 182 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6455 (mt-10) REVERT: M 75 GLN cc_start: 0.8849 (pt0) cc_final: 0.8619 (pt0) REVERT: M 93 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7987 (mm-30) REVERT: N 82 GLN cc_start: 0.8646 (pt0) cc_final: 0.8349 (tm-30) REVERT: N 89 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8574 (tp-100) REVERT: N 105 ASP cc_start: 0.6988 (m-30) cc_final: 0.6614 (p0) REVERT: Q 195 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: Q 232 TYR cc_start: 0.8173 (t80) cc_final: 0.7758 (t80) REVERT: R 139 TYR cc_start: 0.8703 (t80) cc_final: 0.8434 (t80) REVERT: R 161 MET cc_start: 0.8550 (tmm) cc_final: 0.7693 (tmm) REVERT: S 101 PHE cc_start: 0.8248 (m-80) cc_final: 0.7490 (m-10) REVERT: S 161 MET cc_start: 0.8295 (tmm) cc_final: 0.7905 (tmm) REVERT: S 188 MET cc_start: 0.7644 (tmm) cc_final: 0.7311 (tmm) outliers start: 136 outliers final: 100 residues processed: 755 average time/residue: 0.2215 time to fit residues: 275.2482 Evaluate side-chains 764 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 654 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 464 THR Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 175 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 411 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 301 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN I 221 ASN M 82 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097345 restraints weight = 66781.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100593 restraints weight = 29792.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102669 restraints weight = 17373.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103957 restraints weight = 12125.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104832 restraints weight = 9601.903| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36765 Z= 0.128 Angle : 0.616 11.535 49676 Z= 0.312 Chirality : 0.044 0.217 5575 Planarity : 0.004 0.054 6440 Dihedral : 4.778 111.902 5022 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.55 % Allowed : 18.21 % Favored : 79.24 % 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: 1.04 (0.13), residues: 4538 helix: 2.07 (0.11), residues: 2113 sheet: -0.41 (0.21), residues: 564 loop : -0.55 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 78 TYR 0.028 0.001 TYR Q 112 PHE 0.027 0.001 PHE H 155 TRP 0.012 0.001 TRP C 567 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00284 (36765) covalent geometry : angle 0.61646 (49676) hydrogen bonds : bond 0.03905 ( 1955) hydrogen bonds : angle 2.80085 (13857) *********************** 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 822 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 721 time to evaluate : 1.462 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 61 MET cc_start: 0.7441 (mtp) cc_final: 0.7128 (ttm) REVERT: A 141 LEU cc_start: 0.9045 (mt) cc_final: 0.8809 (mt) REVERT: A 142 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7319 (mmt180) REVERT: A 296 MET cc_start: 0.8692 (ptm) cc_final: 0.8290 (ptt) REVERT: A 308 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8076 (ptt180) REVERT: A 438 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8443 (tptp) REVERT: A 450 TRP cc_start: 0.9086 (p90) cc_final: 0.8848 (p90) REVERT: A 500 SER cc_start: 0.8604 (m) cc_final: 0.8128 (p) REVERT: A 576 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 607 ASP cc_start: 0.8803 (m-30) cc_final: 0.8438 (m-30) REVERT: B 84 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8249 (pttm) REVERT: B 117 TYR cc_start: 0.8936 (m-80) cc_final: 0.8524 (m-80) REVERT: B 151 ASP cc_start: 0.8229 (t70) cc_final: 0.7711 (t0) REVERT: B 197 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7387 (tm-30) REVERT: B 324 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8783 (tm-30) REVERT: B 334 SER cc_start: 0.9511 (t) cc_final: 0.9273 (t) REVERT: B 346 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7742 (ttt) REVERT: B 387 GLU cc_start: 0.8252 (tp30) cc_final: 0.7903 (tm-30) REVERT: B 466 ASP cc_start: 0.8510 (t70) cc_final: 0.8241 (t0) REVERT: B 584 MET cc_start: 0.8555 (mtm) cc_final: 0.6687 (ttm) REVERT: B 601 TYR cc_start: 0.6757 (m-80) cc_final: 0.5378 (m-80) REVERT: B 613 ARG cc_start: 0.9064 (mtp-110) cc_final: 0.8660 (mtm180) REVERT: C 100 ASP cc_start: 0.8512 (p0) cc_final: 0.8181 (p0) REVERT: C 254 CYS cc_start: 0.7915 (m) cc_final: 0.7582 (m) REVERT: C 445 PHE cc_start: 0.9322 (m-80) cc_final: 0.9040 (m-80) REVERT: C 603 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8097 (tm-30) REVERT: D 316 GLU cc_start: 0.8534 (tp30) cc_final: 0.8207 (tt0) REVERT: D 402 MET cc_start: 0.8825 (tpt) cc_final: 0.8165 (tmm) REVERT: E 83 SER cc_start: 0.8938 (m) cc_final: 0.8386 (p) REVERT: E 187 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8947 (tt0) REVERT: E 254 MET cc_start: 0.8092 (tpp) cc_final: 0.7625 (tpp) REVERT: E 398 LEU cc_start: 0.8575 (mt) cc_final: 0.8252 (mt) REVERT: E 500 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8477 (mm) REVERT: F 74 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8742 (mt) REVERT: F 189 ILE cc_start: 0.8806 (mm) cc_final: 0.8502 (tt) REVERT: F 246 SER cc_start: 0.8942 (t) cc_final: 0.8563 (m) REVERT: F 266 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: F 300 MET cc_start: 0.8961 (mmm) cc_final: 0.8544 (mmt) REVERT: F 336 GLU cc_start: 0.8036 (tp30) cc_final: 0.7722 (tp30) REVERT: F 367 ASP cc_start: 0.8546 (t0) cc_final: 0.8332 (t0) REVERT: H 46 GLN cc_start: 0.8699 (mt0) cc_final: 0.8252 (mp10) REVERT: H 160 GLU cc_start: 0.8542 (tp30) cc_final: 0.8080 (tp30) REVERT: H 190 GLU cc_start: 0.8084 (tp30) cc_final: 0.7758 (tp30) REVERT: H 193 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8133 (tm-30) REVERT: I 88 ASP cc_start: 0.8472 (t70) cc_final: 0.8153 (t0) REVERT: I 97 GLU cc_start: 0.8350 (tt0) cc_final: 0.7612 (tp30) REVERT: I 132 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8047 (mmt) REVERT: J 89 ASP cc_start: 0.8807 (m-30) cc_final: 0.8554 (m-30) REVERT: J 131 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7734 (mtt-85) REVERT: J 132 MET cc_start: 0.7917 (mmm) cc_final: 0.7396 (mmt) REVERT: J 162 ASP cc_start: 0.7662 (t0) cc_final: 0.7200 (m-30) REVERT: J 164 ASP cc_start: 0.8350 (t0) cc_final: 0.7972 (t0) REVERT: J 168 ASP cc_start: 0.8494 (t0) cc_final: 0.8184 (t0) REVERT: J 172 TYR cc_start: 0.8353 (m-10) cc_final: 0.8076 (m-10) REVERT: J 185 ASN cc_start: 0.8216 (p0) cc_final: 0.7872 (p0) REVERT: K 121 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8604 (mm) REVERT: K 182 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6364 (mt-10) REVERT: M 84 MET cc_start: 0.8129 (mtp) cc_final: 0.7882 (ttm) REVERT: M 114 TYR cc_start: 0.8754 (t80) cc_final: 0.8530 (t80) REVERT: N 82 GLN cc_start: 0.8633 (pt0) cc_final: 0.8263 (pp30) REVERT: N 89 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8460 (tp-100) REVERT: N 102 MET cc_start: 0.8161 (mtm) cc_final: 0.7814 (mtp) REVERT: N 105 ASP cc_start: 0.6927 (m-30) cc_final: 0.6648 (p0) REVERT: O 79 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8088 (ptp90) REVERT: Q 61 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7323 (mtp85) REVERT: Q 153 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7955 (tpp80) REVERT: Q 195 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: Q 232 TYR cc_start: 0.8142 (t80) cc_final: 0.7770 (t80) REVERT: R 10 MET cc_start: 0.5746 (mpp) cc_final: 0.5419 (mpp) REVERT: R 115 MET cc_start: 0.8582 (tpp) cc_final: 0.7453 (mmm) REVERT: R 139 TYR cc_start: 0.8646 (t80) cc_final: 0.8412 (t80) REVERT: R 161 MET cc_start: 0.8572 (tmm) cc_final: 0.7780 (tmm) REVERT: R 188 MET cc_start: 0.8081 (tpp) cc_final: 0.7679 (tpp) REVERT: S 101 PHE cc_start: 0.8186 (m-80) cc_final: 0.7411 (m-10) REVERT: S 161 MET cc_start: 0.8225 (tmm) cc_final: 0.7804 (tmm) REVERT: S 175 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7530 (mp) outliers start: 101 outliers final: 73 residues processed: 779 average time/residue: 0.2136 time to fit residues: 274.1274 Evaluate side-chains 738 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 655 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 175 ILE Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 445 optimal weight: 0.9990 chunk 290 optimal weight: 8.9990 chunk 381 optimal weight: 6.9990 chunk 433 optimal weight: 0.0170 chunk 356 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 560 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN M 82 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN R 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098125 restraints weight = 67387.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101384 restraints weight = 30206.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103487 restraints weight = 17641.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104842 restraints weight = 12266.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105611 restraints weight = 9632.203| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36765 Z= 0.130 Angle : 0.626 12.173 49676 Z= 0.315 Chirality : 0.044 0.263 5575 Planarity : 0.004 0.078 6440 Dihedral : 4.712 111.510 5022 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 2.20 % Allowed : 18.92 % Favored : 78.88 % 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: 1.07 (0.13), residues: 4538 helix: 2.12 (0.11), residues: 2112 sheet: -0.45 (0.21), residues: 558 loop : -0.54 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 78 TYR 0.027 0.001 TYR Q 112 PHE 0.026 0.001 PHE F 114 TRP 0.014 0.001 TRP C 567 HIS 0.004 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00291 (36765) covalent geometry : angle 0.62605 (49676) hydrogen bonds : bond 0.03818 ( 1955) hydrogen bonds : angle 2.77168 (13857) *********************** 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 791 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 704 time to evaluate : 1.287 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 61 MET cc_start: 0.7480 (mtp) cc_final: 0.7123 (ttm) REVERT: A 68 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6346 (mt-10) REVERT: A 141 LEU cc_start: 0.9002 (mt) cc_final: 0.8757 (mt) REVERT: A 142 ARG cc_start: 0.7892 (mmt180) cc_final: 0.7334 (mmt180) REVERT: A 296 MET cc_start: 0.8638 (ptm) cc_final: 0.8279 (ptt) REVERT: A 308 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (ptt180) REVERT: A 438 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8471 (tptp) REVERT: A 450 TRP cc_start: 0.9066 (p90) cc_final: 0.8820 (p90) REVERT: A 500 SER cc_start: 0.8555 (m) cc_final: 0.8108 (p) REVERT: A 530 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7542 (ptm-80) REVERT: A 576 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: A 607 ASP cc_start: 0.8819 (m-30) cc_final: 0.8456 (m-30) REVERT: B 84 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8245 (pttm) REVERT: B 117 TYR cc_start: 0.8912 (m-80) cc_final: 0.8517 (m-80) REVERT: B 151 ASP cc_start: 0.8196 (t70) cc_final: 0.7889 (t0) REVERT: B 197 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7382 (tm-30) REVERT: B 306 MET cc_start: 0.7794 (tpp) cc_final: 0.6976 (mmm) REVERT: B 324 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8757 (tm-30) REVERT: B 334 SER cc_start: 0.9477 (t) cc_final: 0.9248 (t) REVERT: B 346 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7721 (ttt) REVERT: B 387 GLU cc_start: 0.8248 (tp30) cc_final: 0.7864 (tm-30) REVERT: B 466 ASP cc_start: 0.8486 (t70) cc_final: 0.8231 (t0) REVERT: B 571 ARG cc_start: 0.7868 (ttp80) cc_final: 0.6974 (ptp90) REVERT: B 584 MET cc_start: 0.8528 (mtm) cc_final: 0.6751 (ttm) REVERT: B 601 TYR cc_start: 0.6769 (m-80) cc_final: 0.5507 (m-80) REVERT: B 613 ARG cc_start: 0.9068 (mtp-110) cc_final: 0.8645 (mtm110) REVERT: C 100 ASP cc_start: 0.8568 (p0) cc_final: 0.8275 (p0) REVERT: C 108 ASP cc_start: 0.8120 (m-30) cc_final: 0.7814 (t0) REVERT: C 254 CYS cc_start: 0.7920 (m) cc_final: 0.7563 (m) REVERT: C 445 PHE cc_start: 0.9326 (m-80) cc_final: 0.9051 (m-80) REVERT: C 603 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8072 (tm-30) REVERT: D 39 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5893 (p90) REVERT: D 47 TYR cc_start: 0.8769 (m-80) cc_final: 0.8391 (m-80) REVERT: D 161 GLN cc_start: 0.9028 (tp40) cc_final: 0.8722 (tm-30) REVERT: D 316 GLU cc_start: 0.8603 (tp30) cc_final: 0.8397 (tp30) REVERT: D 402 MET cc_start: 0.8862 (tpt) cc_final: 0.8458 (tpt) REVERT: E 83 SER cc_start: 0.8908 (m) cc_final: 0.8374 (p) REVERT: E 180 MET cc_start: 0.8862 (mmm) cc_final: 0.8639 (mmt) REVERT: E 187 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8913 (tt0) REVERT: E 254 MET cc_start: 0.8104 (tpp) cc_final: 0.7625 (tpp) REVERT: E 398 LEU cc_start: 0.8567 (mt) cc_final: 0.8246 (mt) REVERT: E 500 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8446 (mm) REVERT: F 74 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (mt) REVERT: F 189 ILE cc_start: 0.8880 (mm) cc_final: 0.8550 (tt) REVERT: F 246 SER cc_start: 0.8903 (t) cc_final: 0.8531 (m) REVERT: F 266 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: F 336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7722 (tp30) REVERT: H 46 GLN cc_start: 0.8674 (mt0) cc_final: 0.8220 (mp10) REVERT: H 160 GLU cc_start: 0.8539 (tp30) cc_final: 0.8067 (tp30) REVERT: H 193 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8164 (tm-30) REVERT: I 88 ASP cc_start: 0.8482 (t70) cc_final: 0.8135 (t0) REVERT: I 97 GLU cc_start: 0.8384 (tt0) cc_final: 0.7820 (tp30) REVERT: I 132 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7398 (mpp) REVERT: J 89 ASP cc_start: 0.8658 (m-30) cc_final: 0.8407 (m-30) REVERT: J 131 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7748 (mtt-85) REVERT: J 162 ASP cc_start: 0.7720 (t0) cc_final: 0.7236 (m-30) REVERT: J 164 ASP cc_start: 0.8357 (t0) cc_final: 0.7957 (t0) REVERT: J 168 ASP cc_start: 0.8498 (t0) cc_final: 0.8176 (t0) REVERT: J 172 TYR cc_start: 0.8339 (m-10) cc_final: 0.8066 (m-10) REVERT: J 182 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7976 (mm-30) REVERT: J 185 ASN cc_start: 0.8162 (p0) cc_final: 0.7847 (p0) REVERT: K 121 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8615 (mm) REVERT: K 182 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6340 (mt-10) REVERT: K 190 ILE cc_start: 0.8797 (mt) cc_final: 0.8518 (mm) REVERT: K 210 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7700 (tm-30) REVERT: M 75 GLN cc_start: 0.8801 (pt0) cc_final: 0.8571 (pt0) REVERT: M 107 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7995 (mtm-85) REVERT: M 115 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: N 82 GLN cc_start: 0.8634 (pt0) cc_final: 0.8320 (tm-30) REVERT: N 89 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8431 (tp-100) REVERT: O 78 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8130 (mtm-85) REVERT: O 79 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8089 (ptp90) REVERT: Q 61 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7348 (mtp85) REVERT: Q 195 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: Q 232 TYR cc_start: 0.8066 (t80) cc_final: 0.7811 (t80) REVERT: R 10 MET cc_start: 0.5847 (mpp) cc_final: 0.5531 (mpp) REVERT: R 13 LEU cc_start: 0.8715 (mp) cc_final: 0.8454 (mt) REVERT: R 115 MET cc_start: 0.8572 (tpp) cc_final: 0.7453 (mmm) REVERT: R 188 MET cc_start: 0.8066 (tpp) cc_final: 0.7663 (tpp) REVERT: S 101 PHE cc_start: 0.8184 (m-80) cc_final: 0.7438 (m-10) REVERT: S 161 MET cc_start: 0.8201 (tmm) cc_final: 0.7779 (tmm) REVERT: S 213 PHE cc_start: 0.8441 (m-10) cc_final: 0.8117 (m-80) outliers start: 87 outliers final: 59 residues processed: 754 average time/residue: 0.2136 time to fit residues: 265.8415 Evaluate side-chains 725 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 655 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 194 ASN Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 197 optimal weight: 7.9990 chunk 395 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 338 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN M 82 GLN M 91 ASN O 82 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095833 restraints weight = 68497.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099012 restraints weight = 30818.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101058 restraints weight = 18083.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102341 restraints weight = 12660.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103167 restraints weight = 10035.947| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36765 Z= 0.201 Angle : 0.669 12.491 49676 Z= 0.340 Chirality : 0.046 0.362 5575 Planarity : 0.005 0.072 6440 Dihedral : 4.812 111.007 5022 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 2.02 % Allowed : 19.40 % Favored : 78.58 % 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: 0.97 (0.13), residues: 4538 helix: 2.06 (0.11), residues: 2107 sheet: -0.47 (0.21), residues: 545 loop : -0.63 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 78 TYR 0.029 0.002 TYR Q 112 PHE 0.026 0.002 PHE R 62 TRP 0.013 0.001 TRP Q 122 HIS 0.005 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00468 (36765) covalent geometry : angle 0.66922 (49676) hydrogen bonds : bond 0.04036 ( 1955) hydrogen bonds : angle 2.85057 (13857) ********************** 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 749 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 669 time to evaluate : 1.425 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 68 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6576 (mt-10) REVERT: A 141 LEU cc_start: 0.9187 (mt) cc_final: 0.8895 (mt) REVERT: A 142 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7442 (mmt180) REVERT: A 296 MET cc_start: 0.8720 (ptm) cc_final: 0.8215 (ptt) REVERT: A 308 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8113 (ptt-90) REVERT: A 438 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8512 (tptp) REVERT: A 500 SER cc_start: 0.8668 (m) cc_final: 0.8243 (p) REVERT: A 530 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7647 (ptm-80) REVERT: A 576 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: A 607 ASP cc_start: 0.8815 (m-30) cc_final: 0.8455 (m-30) REVERT: B 84 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8320 (pttm) REVERT: B 117 TYR cc_start: 0.8979 (m-80) cc_final: 0.8520 (m-80) REVERT: B 151 ASP cc_start: 0.8204 (t70) cc_final: 0.7715 (t0) REVERT: B 324 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 334 SER cc_start: 0.9517 (t) cc_final: 0.9274 (t) REVERT: B 346 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7789 (ttt) REVERT: B 387 GLU cc_start: 0.8292 (tp30) cc_final: 0.7763 (tm-30) REVERT: B 571 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7059 (ptp90) REVERT: B 584 MET cc_start: 0.8616 (mtm) cc_final: 0.6945 (ttm) REVERT: B 601 TYR cc_start: 0.6705 (m-80) cc_final: 0.5596 (m-80) REVERT: B 613 ARG cc_start: 0.9029 (mtp-110) cc_final: 0.8611 (mtm180) REVERT: C 254 CYS cc_start: 0.8036 (m) cc_final: 0.7652 (m) REVERT: C 387 GLU cc_start: 0.7950 (tp30) cc_final: 0.7734 (tp30) REVERT: C 445 PHE cc_start: 0.9324 (m-80) cc_final: 0.9052 (m-80) REVERT: C 603 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8109 (tm-30) REVERT: D 316 GLU cc_start: 0.8586 (tp30) cc_final: 0.8369 (tp30) REVERT: D 402 MET cc_start: 0.8919 (tpt) cc_final: 0.8525 (tpt) REVERT: E 83 SER cc_start: 0.8915 (m) cc_final: 0.8395 (p) REVERT: E 180 MET cc_start: 0.8955 (mmm) cc_final: 0.8669 (mmt) REVERT: E 187 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8907 (tt0) REVERT: E 398 LEU cc_start: 0.8552 (mt) cc_final: 0.8201 (mt) REVERT: E 500 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8605 (mm) REVERT: F 74 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (mt) REVERT: F 246 SER cc_start: 0.8938 (t) cc_final: 0.8574 (m) REVERT: F 266 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: F 336 GLU cc_start: 0.8085 (tp30) cc_final: 0.7743 (tp30) REVERT: H 46 GLN cc_start: 0.8613 (mt0) cc_final: 0.8199 (mp10) REVERT: H 160 GLU cc_start: 0.8537 (tp30) cc_final: 0.8067 (tp30) REVERT: H 193 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8125 (tm-30) REVERT: I 88 ASP cc_start: 0.8445 (t70) cc_final: 0.8083 (t0) REVERT: I 97 GLU cc_start: 0.8435 (tt0) cc_final: 0.7810 (tp30) REVERT: I 132 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7473 (mpp) REVERT: J 89 ASP cc_start: 0.8661 (m-30) cc_final: 0.8423 (m-30) REVERT: J 112 TYR cc_start: 0.8339 (t80) cc_final: 0.8084 (t80) REVERT: J 131 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7778 (mtt-85) REVERT: J 162 ASP cc_start: 0.7674 (t0) cc_final: 0.7132 (m-30) REVERT: J 164 ASP cc_start: 0.8321 (t0) cc_final: 0.7970 (t0) REVERT: J 168 ASP cc_start: 0.8521 (t0) cc_final: 0.8200 (t0) REVERT: J 172 TYR cc_start: 0.8375 (m-10) cc_final: 0.8109 (m-10) REVERT: J 182 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8004 (mm-30) REVERT: J 185 ASN cc_start: 0.8289 (p0) cc_final: 0.7933 (p0) REVERT: K 121 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8663 (mm) REVERT: K 182 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6465 (mt-10) REVERT: K 190 ILE cc_start: 0.8858 (mt) cc_final: 0.8581 (mm) REVERT: K 210 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7690 (tm-30) REVERT: M 107 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7933 (ttm-80) REVERT: N 82 GLN cc_start: 0.8617 (pt0) cc_final: 0.8340 (tm-30) REVERT: N 89 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8488 (tp-100) REVERT: O 78 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: Q 195 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: R 115 MET cc_start: 0.8640 (tpp) cc_final: 0.7849 (mmm) REVERT: R 188 MET cc_start: 0.8157 (tpp) cc_final: 0.7770 (tpp) REVERT: S 101 PHE cc_start: 0.8206 (m-80) cc_final: 0.7451 (m-10) REVERT: S 161 MET cc_start: 0.8259 (tmm) cc_final: 0.7756 (tmm) REVERT: S 213 PHE cc_start: 0.8471 (m-10) cc_final: 0.8100 (m-80) outliers start: 80 outliers final: 64 residues processed: 718 average time/residue: 0.2192 time to fit residues: 259.7024 Evaluate side-chains 728 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 654 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 194 ASN Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 299 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 437 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 397 optimal weight: 8.9990 chunk 383 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN M 75 GLN M 82 GLN O 85 GLN ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN R 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095169 restraints weight = 67021.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098286 restraints weight = 30344.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100296 restraints weight = 17858.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101561 restraints weight = 12513.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102383 restraints weight = 9918.309| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36765 Z= 0.204 Angle : 0.683 12.141 49676 Z= 0.346 Chirality : 0.046 0.340 5575 Planarity : 0.005 0.062 6440 Dihedral : 4.855 111.671 5022 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 2.25 % Allowed : 19.55 % Favored : 78.20 % 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: 0.89 (0.13), residues: 4538 helix: 2.03 (0.11), residues: 2106 sheet: -0.53 (0.22), residues: 543 loop : -0.72 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 78 TYR 0.030 0.002 TYR Q 112 PHE 0.025 0.002 PHE F 114 TRP 0.013 0.001 TRP C 567 HIS 0.005 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00472 (36765) covalent geometry : angle 0.68333 (49676) hydrogen bonds : bond 0.04068 ( 1955) hydrogen bonds : angle 2.87240 (13857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7188.13 seconds wall clock time: 124 minutes 36.63 seconds (7476.63 seconds total)