Starting phenix.real_space_refine on Sat Mar 7 03:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqb_21347/03_2026/6vqb_21347.cif" } 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= 0.000 sd= 0.093 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: 5 Type Number sf(0) Gaussians P 2 5.49 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 189 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: 36113 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: 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: "R" 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: "S" 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.79, per 1000 atoms: 0.19 Number of scatterers: 36113 At special positions: 0 Unit cell: (173.84, 171.72, 145.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 203 16.00 P 2 15.00 O 6821 8.00 N 6223 7.00 C 22864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 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: 179 helices and 68 sheets defined 51.3% alpha, 115.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.955A pdb=" N MET A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.998A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (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 375 through 376 No H-bonds generated for 'chain 'A' and resid 375 through 376' Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.869A pdb=" N ARG A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.455A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 4.140A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.495A 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 557 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.592A pdb=" N ASP B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.644A 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 306 through 309 Processing helix chain 'B' and resid 319 through 339 removed outlier: 4.617A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.281A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.867A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 558 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.531A pdb=" N LEU B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.652A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 4.417A pdb=" N GLY C 255 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.532A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 319 through 339 removed outlier: 4.594A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.508A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 377 through 388 removed outlier: 3.725A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 4.121A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 471 through 489 Processing helix chain 'C' and resid 489 through 497 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 587 Processing helix chain 'C' and resid 593 through 614 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.601A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) 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: 4.057A pdb=" N TYR D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.667A pdb=" N HIS D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.511A pdb=" N ILE D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.343A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 445 through 462 removed outlier: 4.348A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) 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 removed outlier: 5.012A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 4.085A pdb=" N LEU E 128 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.814A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.853A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.627A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.781A pdb=" N ILE E 406 " --> pdb=" O MET E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 440 removed outlier: 4.031A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 removed outlier: 3.929A pdb=" N LEU E 444 " --> pdb=" O GLU E 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 441 through 444' 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 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 removed outlier: 3.549A pdb=" N ASN F 251 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 255 removed outlier: 4.119A pdb=" N ASP F 255 " --> pdb=" O GLY F 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 267 through 289 removed outlier: 3.580A pdb=" N ILE F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 319 through 323 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 371 Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 401 through 406 Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.691A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 462 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 486 through 487 No H-bonds generated for 'chain 'F' and resid 486 through 487' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'H' and resid 12 through 48 Processing helix chain 'H' and resid 155 through 175 Processing helix chain 'H' and resid 175 through 217 Processing helix chain 'I' and resid 67 through 107 Processing helix chain 'I' and resid 108 through 128 removed outlier: 4.628A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) 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 159 Proline residue: I 153 - end of helix removed outlier: 3.606A pdb=" N ILE I 157 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 217 removed outlier: 3.950A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix 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 196 through 205 Processing helix chain 'J' and resid 207 through 217 removed outlier: 3.613A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 107 Processing helix chain 'K' and resid 109 through 128 Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 removed outlier: 3.522A pdb=" N ALA K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 195 through 207 Processing helix chain 'K' and resid 207 through 217 removed outlier: 3.507A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 89 Processing helix chain 'M' and resid 91 through 105 Processing helix chain 'N' and resid 71 through 104 removed outlier: 3.648A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 4.276A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) 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 49 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 removed outlier: 3.907A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.524A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 Processing helix chain 'Q' and resid 192 through 205 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.561A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 48 Processing helix chain 'R' and resid 49 through 54 Processing helix chain 'R' and resid 61 through 71 Processing helix chain 'R' and resid 77 through 97 Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 120 through 123 Processing helix chain 'R' and resid 124 through 142 removed outlier: 3.949A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 187 Processing helix chain 'R' and resid 192 through 206 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'S' and resid 14 through 37 removed outlier: 3.506A pdb=" N HIS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 49 removed outlier: 3.679A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 62 through 72 Processing helix chain 'S' and resid 77 through 97 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 140 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 143 No H-bonds generated for 'chain 'S' and resid 141 through 143' Processing helix chain 'S' and resid 146 through 167 removed outlier: 3.541A pdb=" N GLN S 165 " --> pdb=" O MET S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 187 Processing helix chain 'S' and resid 193 through 207 Processing sheet with id=AA1, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AE2, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.207A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.207A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 164 through 167 removed outlier: 4.039A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.548A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.119A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.455A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 246 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AF3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AF4, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.306A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 344 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.982A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.409A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 409 through 410 removed outlier: 7.445A pdb=" N VAL C 410 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 248 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AF9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AG1, first strand: chain 'D' and resid 131 through 133 removed outlier: 6.698A pdb=" N PHE D 132 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU D 263 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.394A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.392A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 192 through 193 Processing sheet with id=AG5, first strand: chain 'D' and resid 375 through 376 Processing sheet with id=AG6, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AG7, first strand: chain 'E' and resid 130 through 133 removed outlier: 6.696A pdb=" N ARG E 130 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 261 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE E 132 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU E 263 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA E 228 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE E 296 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL E 230 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.010A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.595A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 191 through 193 removed outlier: 6.500A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AH3, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.751A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AH5, first strand: chain 'F' and resid 191 through 194 removed outlier: 6.202A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET F 356 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER F 193 " --> pdb=" O MET F 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 4861 hydrogen bonds defined for protein. 13794 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: 21.83 Time building geometry restraints manager: 3.35 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: 7012 1.32 - 1.44: 8198 1.44 - 1.57: 21194 1.57 - 1.69: 3 1.69 - 1.81: 358 Bond restraints: 36765 Sorted by residual: bond pdb=" C ASP B 290 " pdb=" N PHE B 291 " ideal model delta sigma weight residual 1.334 1.217 0.118 1.26e-02 6.30e+03 8.73e+01 bond pdb=" N PRO F 391 " pdb=" CA PRO F 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.20e+01 bond pdb=" C TYR E 504 " pdb=" N PRO E 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.34e+01 bond pdb=" N PRO E 352 " pdb=" CA PRO E 352 " ideal model delta sigma weight residual 1.466 1.538 -0.071 1.24e-02 6.50e+03 3.32e+01 bond pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 1.469 1.540 -0.071 1.25e-02 6.40e+03 3.19e+01 ... (remaining 36760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 47770 2.13 - 4.26: 1754 4.26 - 6.39: 119 6.39 - 8.53: 23 8.53 - 10.66: 10 Bond angle restraints: 49676 Sorted by residual: angle pdb=" C ILE F 189 " pdb=" N PRO F 190 " pdb=" CA PRO F 190 " ideal model delta sigma weight residual 119.85 129.34 -9.49 1.01e+00 9.80e-01 8.83e+01 angle pdb=" C ARG A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.76 129.31 -9.55 1.03e+00 9.43e-01 8.61e+01 angle pdb=" C SER B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 120.38 129.06 -8.68 1.03e+00 9.43e-01 7.11e+01 angle pdb=" C LEU F 395 " pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 120.04 128.53 -8.49 1.08e+00 8.57e-01 6.18e+01 angle pdb=" C ASN A 397 " pdb=" N PRO A 398 " pdb=" CA PRO A 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: 22034 23.68 - 47.35: 399 47.35 - 71.03: 111 71.03 - 94.71: 34 94.71 - 118.38: 2 Dihedral angle restraints: 22580 sinusoidal: 9309 harmonic: 13271 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.38 118.38 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.49 -98.49 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA VAL A 392 " pdb=" C VAL A 392 " pdb=" N LYS A 393 " pdb=" CA LYS A 393 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 22577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3842 0.053 - 0.107: 1180 0.107 - 0.160: 459 0.160 - 0.214: 71 0.214 - 0.267: 23 Chirality restraints: 5575 Sorted by residual: chirality pdb=" CA VAL F 379 " pdb=" N VAL F 379 " pdb=" C VAL F 379 " pdb=" CB VAL F 379 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL B 404 " pdb=" N VAL B 404 " pdb=" C VAL B 404 " pdb=" CB VAL B 404 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA VAL B 448 " pdb=" N VAL B 448 " pdb=" C VAL B 448 " pdb=" CB VAL B 448 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5572 not shown) Planarity restraints: 6440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 390 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO F 390 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO F 390 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO F 391 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 584 " 0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C MET A 584 " -0.058 2.00e-02 2.50e+03 pdb=" O MET A 584 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 585 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 189 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ILE F 189 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE F 189 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO F 190 " -0.018 2.00e-02 2.50e+03 ... (remaining 6437 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5094 2.76 - 3.29: 36591 3.29 - 3.83: 59985 3.83 - 4.36: 73727 4.36 - 4.90: 124360 Nonbonded interactions: 299757 Sorted by model distance: nonbonded pdb=" OH TYR Q 126 " pdb=" OG1 THR Q 169 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP D 266 " pdb=" NZ LYS S 9 " model vdw 2.304 3.120 nonbonded pdb=" OD2 ASP F 360 " pdb=" NZ LYS H 20 " model vdw 2.362 3.120 nonbonded pdb=" NE ARG J 135 " pdb=" O ALA J 171 " model vdw 2.364 3.120 nonbonded pdb=" OG SER C 128 " pdb=" OD1 ASP C 130 " model vdw 2.370 3.040 ... (remaining 299752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 51.220 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.118 36765 Z= 0.585 Angle : 0.894 10.658 49676 Z= 0.631 Chirality : 0.062 0.267 5575 Planarity : 0.004 0.038 6440 Dihedral : 10.798 118.383 14048 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.39 % 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: 0.59 (0.10), residues: 2089 sheet: -0.21 (0.20), residues: 616 loop : -0.01 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 208 TYR 0.016 0.000 TYR D 389 PHE 0.011 0.000 PHE A 252 TRP 0.010 0.001 TRP Q 55 HIS 0.002 0.000 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00990 (36765) covalent geometry : angle 0.89396 (49676) hydrogen bonds : bond 0.18208 ( 1954) hydrogen bonds : angle 8.79874 (13794) *********************** 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 1506 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1504 time to evaluate : 1.373 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 60 ASP cc_start: 0.7728 (p0) cc_final: 0.7298 (p0) REVERT: A 73 VAL cc_start: 0.9189 (t) cc_final: 0.8888 (m) REVERT: A 84 LYS cc_start: 0.8491 (mttt) cc_final: 0.8180 (mtmt) REVERT: A 95 MET cc_start: 0.8765 (mmm) cc_final: 0.8099 (mmm) REVERT: A 173 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8235 (ptp90) REVERT: A 254 CYS cc_start: 0.8512 (m) cc_final: 0.7913 (m) REVERT: A 284 MET cc_start: 0.8484 (mmm) cc_final: 0.8210 (mpp) REVERT: A 290 ASP cc_start: 0.8252 (t70) cc_final: 0.7683 (t0) REVERT: A 302 VAL cc_start: 0.9046 (t) cc_final: 0.8582 (p) REVERT: A 360 GLU cc_start: 0.8052 (tt0) cc_final: 0.7750 (mt-10) REVERT: A 399 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7399 (mp0) REVERT: A 436 ASP cc_start: 0.7120 (t0) cc_final: 0.6873 (t0) REVERT: A 510 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 51 VAL cc_start: 0.8019 (t) cc_final: 0.7245 (t) REVERT: B 57 LEU cc_start: 0.8188 (mt) cc_final: 0.7938 (mt) REVERT: B 61 MET cc_start: 0.8012 (mtp) cc_final: 0.7782 (mtp) REVERT: B 65 GLN cc_start: 0.8260 (tp40) cc_final: 0.8050 (tt0) REVERT: B 74 SER cc_start: 0.8371 (m) cc_final: 0.7222 (p) REVERT: B 77 ASP cc_start: 0.7661 (m-30) cc_final: 0.6989 (m-30) REVERT: B 84 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7344 (mmtt) REVERT: B 115 SER cc_start: 0.8512 (t) cc_final: 0.8298 (p) REVERT: B 116 ILE cc_start: 0.8641 (pt) cc_final: 0.8359 (pt) REVERT: B 147 ILE cc_start: 0.8792 (pt) cc_final: 0.8580 (tt) REVERT: B 148 THR cc_start: 0.8204 (t) cc_final: 0.7618 (t) REVERT: B 151 ASP cc_start: 0.6340 (m-30) cc_final: 0.6108 (m-30) REVERT: B 257 THR cc_start: 0.8639 (p) cc_final: 0.8142 (t) REVERT: B 266 TYR cc_start: 0.7617 (m-80) cc_final: 0.6569 (m-80) REVERT: B 284 MET cc_start: 0.8965 (tpt) cc_final: 0.8709 (mmm) REVERT: B 296 MET cc_start: 0.7245 (ptm) cc_final: 0.6740 (ptm) REVERT: B 306 MET cc_start: 0.8253 (ptm) cc_final: 0.8013 (ptp) REVERT: B 308 ARG cc_start: 0.7138 (ptp-110) cc_final: 0.6660 (ptt180) REVERT: B 454 TYR cc_start: 0.8680 (p90) cc_final: 0.8428 (p90) REVERT: B 485 GLU cc_start: 0.8154 (tp30) cc_final: 0.7530 (tp30) REVERT: B 486 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 488 ASP cc_start: 0.8707 (m-30) cc_final: 0.8051 (t0) REVERT: C 55 ILE cc_start: 0.7823 (mt) cc_final: 0.7439 (pt) REVERT: C 82 THR cc_start: 0.7994 (m) cc_final: 0.7580 (p) REVERT: C 84 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7301 (pttm) REVERT: C 140 ASN cc_start: 0.8633 (m-40) cc_final: 0.8062 (m110) REVERT: C 248 ILE cc_start: 0.8512 (mp) cc_final: 0.8084 (pt) REVERT: C 262 SER cc_start: 0.8810 (m) cc_final: 0.8599 (p) REVERT: C 299 ASP cc_start: 0.7376 (m-30) cc_final: 0.6632 (p0) REVERT: C 327 ILE cc_start: 0.8871 (tp) cc_final: 0.8531 (tp) REVERT: C 345 SER cc_start: 0.9012 (t) cc_final: 0.8729 (m) REVERT: C 371 ASP cc_start: 0.8324 (m-30) cc_final: 0.7995 (m-30) REVERT: C 447 SER cc_start: 0.7927 (m) cc_final: 0.7532 (p) REVERT: C 449 ASN cc_start: 0.8687 (t0) cc_final: 0.8394 (t0) REVERT: C 466 ASP cc_start: 0.8964 (t70) cc_final: 0.8746 (t0) REVERT: C 484 GLN cc_start: 0.8464 (tp40) cc_final: 0.7358 (tp-100) REVERT: C 487 GLU cc_start: 0.9135 (tp30) cc_final: 0.8666 (tm-30) REVERT: C 522 GLN cc_start: 0.8273 (tt0) cc_final: 0.6864 (tt0) REVERT: C 574 MET cc_start: 0.7603 (ptp) cc_final: 0.7193 (mtm) REVERT: D 40 LEU cc_start: 0.8185 (mt) cc_final: 0.7977 (mt) REVERT: D 87 LEU cc_start: 0.8489 (mt) cc_final: 0.8232 (mt) REVERT: D 97 GLN cc_start: 0.7753 (tt0) cc_final: 0.7546 (pt0) REVERT: D 123 VAL cc_start: 0.9129 (m) cc_final: 0.8800 (p) REVERT: D 268 THR cc_start: 0.8132 (p) cc_final: 0.7831 (t) REVERT: D 328 TYR cc_start: 0.8810 (t80) cc_final: 0.8367 (t80) REVERT: D 360 ASP cc_start: 0.8298 (t0) cc_final: 0.8022 (t0) REVERT: D 406 ILE cc_start: 0.8758 (pt) cc_final: 0.8303 (pt) REVERT: D 410 MET cc_start: 0.8277 (mmm) cc_final: 0.7984 (mpp) REVERT: D 445 THR cc_start: 0.8416 (t) cc_final: 0.8198 (p) REVERT: E 49 THR cc_start: 0.8902 (p) cc_final: 0.8688 (p) REVERT: E 158 ILE cc_start: 0.8623 (mt) cc_final: 0.8158 (tp) REVERT: E 159 ASN cc_start: 0.6785 (t0) cc_final: 0.6242 (t0) REVERT: E 161 GLN cc_start: 0.8354 (tp40) cc_final: 0.7994 (tm-30) REVERT: E 187 GLN cc_start: 0.8618 (tt0) cc_final: 0.8366 (tt0) REVERT: E 355 THR cc_start: 0.8654 (m) cc_final: 0.8273 (p) REVERT: E 356 MET cc_start: 0.8424 (mtm) cc_final: 0.8128 (mtm) REVERT: E 382 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7914 (mm-40) REVERT: E 491 MET cc_start: 0.8663 (mtp) cc_final: 0.8308 (mtp) REVERT: F 63 VAL cc_start: 0.9474 (t) cc_final: 0.9211 (p) REVERT: F 164 ILE cc_start: 0.7865 (mm) cc_final: 0.7462 (mm) REVERT: F 180 MET cc_start: 0.8797 (mmm) cc_final: 0.8063 (mpp) REVERT: F 238 MET cc_start: 0.7977 (tpt) cc_final: 0.7739 (tpp) REVERT: F 298 THR cc_start: 0.8233 (m) cc_final: 0.7615 (p) REVERT: F 299 ASP cc_start: 0.8236 (m-30) cc_final: 0.7724 (m-30) REVERT: F 309 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7842 (tt0) REVERT: F 315 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 317 VAL cc_start: 0.9099 (t) cc_final: 0.8824 (p) REVERT: F 342 GLU cc_start: 0.8508 (tt0) cc_final: 0.7936 (tp30) REVERT: F 351 ILE cc_start: 0.8878 (mt) cc_final: 0.8637 (mm) REVERT: F 355 THR cc_start: 0.8565 (m) cc_final: 0.8344 (p) REVERT: F 441 GLU cc_start: 0.8731 (tt0) cc_final: 0.8472 (tm-30) REVERT: H 16 GLN cc_start: 0.7762 (tt0) cc_final: 0.7537 (tt0) REVERT: H 46 GLN cc_start: 0.7684 (mt0) cc_final: 0.7465 (mt0) REVERT: H 154 SER cc_start: 0.6618 (m) cc_final: 0.6253 (t) REVERT: H 173 GLU cc_start: 0.8383 (tt0) cc_final: 0.8054 (tt0) REVERT: H 192 ASP cc_start: 0.8751 (m-30) cc_final: 0.8509 (t70) REVERT: H 198 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7697 (mm-30) REVERT: H 210 LYS cc_start: 0.9243 (tttm) cc_final: 0.8663 (ttmm) REVERT: I 78 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8736 (mm110) REVERT: I 88 ASP cc_start: 0.8735 (t70) cc_final: 0.8355 (t0) REVERT: I 104 LYS cc_start: 0.8775 (mttt) cc_final: 0.8468 (tppt) REVERT: I 121 LEU cc_start: 0.8888 (tp) cc_final: 0.8590 (mt) REVERT: I 129 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8031 (mm-30) REVERT: I 132 MET cc_start: 0.9278 (mmt) cc_final: 0.8741 (mmt) REVERT: I 167 ILE cc_start: 0.7979 (mt) cc_final: 0.7778 (mt) REVERT: I 183 ILE cc_start: 0.8888 (mt) cc_final: 0.8661 (mm) REVERT: I 221 ASN cc_start: 0.8847 (m-40) cc_final: 0.8325 (t0) REVERT: J 97 GLU cc_start: 0.8558 (tp30) cc_final: 0.8214 (tm-30) REVERT: J 100 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8807 (mp10) REVERT: J 108 ASP cc_start: 0.8350 (t0) cc_final: 0.7693 (m-30) REVERT: J 109 THR cc_start: 0.9176 (m) cc_final: 0.8785 (p) REVERT: J 110 THR cc_start: 0.9181 (m) cc_final: 0.8927 (p) REVERT: J 120 VAL cc_start: 0.8915 (t) cc_final: 0.8714 (p) REVERT: J 121 LEU cc_start: 0.8350 (tp) cc_final: 0.8089 (tp) REVERT: J 149 GLN cc_start: 0.8679 (mt0) cc_final: 0.8399 (tm-30) REVERT: J 154 MET cc_start: 0.8276 (mtp) cc_final: 0.7906 (ttm) REVERT: J 168 ASP cc_start: 0.8346 (t0) cc_final: 0.8029 (t0) REVERT: J 172 TYR cc_start: 0.8163 (m-80) cc_final: 0.7910 (m-80) REVERT: J 182 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7853 (mt-10) REVERT: J 184 TYR cc_start: 0.7916 (m-80) cc_final: 0.7682 (m-80) REVERT: J 191 LYS cc_start: 0.7675 (pttt) cc_final: 0.7390 (ptmt) REVERT: J 198 SER cc_start: 0.9126 (m) cc_final: 0.8907 (p) REVERT: J 208 MET cc_start: 0.8487 (mmt) cc_final: 0.8127 (mmp) REVERT: J 223 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8277 (mptt) REVERT: K 93 ASP cc_start: 0.8997 (m-30) cc_final: 0.8794 (t0) REVERT: K 96 ASN cc_start: 0.9331 (m-40) cc_final: 0.9036 (m-40) REVERT: K 103 SER cc_start: 0.9491 (t) cc_final: 0.9256 (p) REVERT: K 104 LYS cc_start: 0.9472 (mttt) cc_final: 0.9213 (tppt) REVERT: K 129 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7733 (mm-30) REVERT: K 190 ILE cc_start: 0.8646 (mt) cc_final: 0.8388 (mt) REVERT: K 210 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8160 (tt0) REVERT: K 226 ASP cc_start: 0.6299 (t70) cc_final: 0.6020 (m-30) REVERT: M 78 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8206 (ttp-110) REVERT: M 85 GLN cc_start: 0.8624 (tt0) cc_final: 0.8279 (tm-30) REVERT: M 91 ASN cc_start: 0.8413 (m-40) cc_final: 0.8037 (m-40) REVERT: M 97 THR cc_start: 0.8542 (m) cc_final: 0.8187 (t) REVERT: M 98 GLN cc_start: 0.7764 (tt0) cc_final: 0.7242 (tt0) REVERT: M 105 ASP cc_start: 0.7821 (t0) cc_final: 0.7617 (p0) REVERT: N 78 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7662 (ptp-110) REVERT: N 91 ASN cc_start: 0.7713 (m-40) cc_final: 0.7366 (m-40) REVERT: N 96 LEU cc_start: 0.8029 (tp) cc_final: 0.7634 (tt) REVERT: O 86 SER cc_start: 0.8648 (t) cc_final: 0.8319 (m) REVERT: O 97 THR cc_start: 0.8940 (m) cc_final: 0.8716 (p) REVERT: Q 33 MET cc_start: 0.7617 (mmm) cc_final: 0.7147 (tpp) REVERT: Q 48 ASP cc_start: 0.8307 (t70) cc_final: 0.7908 (t0) REVERT: Q 74 CYS cc_start: 0.8571 (p) cc_final: 0.8158 (p) REVERT: Q 113 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8367 (tp30) REVERT: Q 166 TYR cc_start: 0.8265 (m-80) cc_final: 0.8046 (m-80) REVERT: Q 170 GLU cc_start: 0.7416 (tt0) cc_final: 0.6975 (mp0) REVERT: Q 171 ASP cc_start: 0.8462 (m-30) cc_final: 0.7934 (t0) REVERT: Q 180 LYS cc_start: 0.8415 (tttt) cc_final: 0.8212 (tppt) REVERT: Q 199 LEU cc_start: 0.8588 (tp) cc_final: 0.8382 (tp) REVERT: Q 203 TYR cc_start: 0.7116 (t80) cc_final: 0.6812 (t80) REVERT: Q 221 ASP cc_start: 0.7727 (m-30) cc_final: 0.7354 (m-30) REVERT: R 60 TYR cc_start: 0.6556 (m-80) cc_final: 0.6115 (m-80) REVERT: R 77 ASP cc_start: 0.8249 (t0) cc_final: 0.8034 (t70) REVERT: R 79 ASP cc_start: 0.8498 (m-30) cc_final: 0.7826 (t0) REVERT: R 103 MET cc_start: 0.5664 (ttm) cc_final: 0.5161 (mtt) REVERT: R 125 ASP cc_start: 0.8618 (m-30) cc_final: 0.8390 (m-30) REVERT: R 139 TYR cc_start: 0.8500 (t80) cc_final: 0.8006 (t80) REVERT: R 165 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7822 (mt0) REVERT: R 172 ASN cc_start: 0.8235 (t0) cc_final: 0.7902 (t0) REVERT: R 200 PHE cc_start: 0.7717 (t80) cc_final: 0.7346 (t80) REVERT: S 37 ASP cc_start: 0.6952 (t0) cc_final: 0.5454 (t70) REVERT: S 55 TRP cc_start: 0.8332 (m100) cc_final: 0.8053 (m100) REVERT: S 61 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: S 106 ASP cc_start: 0.9289 (m-30) cc_final: 0.8955 (t70) REVERT: S 115 MET cc_start: 0.8968 (mtm) cc_final: 0.8641 (mtm) outliers start: 2 outliers final: 0 residues processed: 1505 average time/residue: 0.2386 time to fit residues: 564.4572 Evaluate side-chains 842 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 841 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 0.9980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 573 HIS C 609 GLN ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN J 66 GLN J 67 GLN N 80 GLN Q 134 ASN R 50 GLN R 118 HIS ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087279 restraints weight = 71205.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090556 restraints weight = 32080.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092697 restraints weight = 18410.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094101 restraints weight = 12434.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095049 restraints weight = 9464.131| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36765 Z= 0.185 Angle : 0.675 11.311 49676 Z= 0.349 Chirality : 0.046 0.218 5575 Planarity : 0.005 0.048 6440 Dihedral : 4.983 108.075 5022 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 10.98 % Favored : 86.42 % 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: 1.09 (0.12), residues: 4538 helix: 1.76 (0.11), residues: 2088 sheet: -0.28 (0.20), residues: 633 loop : -0.02 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 135 TYR 0.023 0.002 TYR H 186 PHE 0.030 0.002 PHE C 612 TRP 0.012 0.001 TRP B 450 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00416 (36765) covalent geometry : angle 0.67482 (49676) hydrogen bonds : bond 0.05448 ( 1954) hydrogen bonds : angle 3.32142 (13794) *********************** 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 1049 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 946 time to evaluate : 1.227 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 60 ASP cc_start: 0.7870 (p0) cc_final: 0.7642 (p0) REVERT: A 73 VAL cc_start: 0.9266 (t) cc_final: 0.9025 (m) REVERT: A 95 MET cc_start: 0.8739 (mmm) cc_final: 0.8509 (mmm) REVERT: A 131 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8728 (pt) REVERT: A 173 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8389 (ptp90) REVERT: A 235 ASP cc_start: 0.8281 (t70) cc_final: 0.8079 (t0) REVERT: A 254 CYS cc_start: 0.8606 (m) cc_final: 0.8253 (m) REVERT: A 284 MET cc_start: 0.8438 (mmm) cc_final: 0.8184 (mmp) REVERT: A 285 SER cc_start: 0.8618 (t) cc_final: 0.8379 (p) REVERT: A 290 ASP cc_start: 0.8610 (t70) cc_final: 0.8100 (t0) REVERT: A 302 VAL cc_start: 0.8950 (t) cc_final: 0.8458 (p) REVERT: A 487 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 510 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 74 SER cc_start: 0.8868 (m) cc_final: 0.7701 (p) REVERT: B 77 ASP cc_start: 0.8043 (m-30) cc_final: 0.7465 (m-30) REVERT: B 84 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7743 (mmtt) REVERT: B 115 SER cc_start: 0.8708 (t) cc_final: 0.8461 (p) REVERT: B 116 ILE cc_start: 0.9028 (pt) cc_final: 0.8667 (pt) REVERT: B 142 ARG cc_start: 0.8545 (mmm160) cc_final: 0.7965 (tpp80) REVERT: B 270 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: B 296 MET cc_start: 0.7486 (ptm) cc_final: 0.7251 (ptm) REVERT: B 308 ARG cc_start: 0.7096 (ptp-110) cc_final: 0.6862 (ptt180) REVERT: B 349 ASP cc_start: 0.7257 (p0) cc_final: 0.6673 (p0) REVERT: B 485 GLU cc_start: 0.8415 (tp30) cc_final: 0.7687 (tp30) REVERT: B 488 ASP cc_start: 0.8655 (m-30) cc_final: 0.7935 (t0) REVERT: B 550 MET cc_start: 0.8815 (mtm) cc_final: 0.8557 (mtm) REVERT: C 30 THR cc_start: 0.8751 (m) cc_final: 0.8329 (p) REVERT: C 55 ILE cc_start: 0.8614 (mt) cc_final: 0.8249 (pt) REVERT: C 84 LYS cc_start: 0.8722 (mmtt) cc_final: 0.7977 (pttm) REVERT: C 140 ASN cc_start: 0.8094 (m-40) cc_final: 0.7811 (m110) REVERT: C 155 ILE cc_start: 0.8818 (mm) cc_final: 0.8515 (mm) REVERT: C 283 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 447 SER cc_start: 0.8450 (m) cc_final: 0.8063 (p) REVERT: C 466 ASP cc_start: 0.8729 (t70) cc_final: 0.8422 (t0) REVERT: C 484 GLN cc_start: 0.8370 (tp40) cc_final: 0.8096 (tp-100) REVERT: C 487 GLU cc_start: 0.8822 (tp30) cc_final: 0.8303 (tp30) REVERT: C 604 LEU cc_start: 0.9034 (mp) cc_final: 0.8764 (tt) REVERT: C 606 GLU cc_start: 0.8599 (tt0) cc_final: 0.7933 (tp30) REVERT: D 247 ASP cc_start: 0.8437 (t0) cc_final: 0.8003 (t0) REVERT: D 328 TYR cc_start: 0.9034 (t80) cc_final: 0.8427 (t80) REVERT: D 360 ASP cc_start: 0.8290 (t0) cc_final: 0.7812 (t0) REVERT: E 70 GLU cc_start: 0.7557 (tt0) cc_final: 0.7348 (tt0) REVERT: E 158 ILE cc_start: 0.8792 (mt) cc_final: 0.8499 (tp) REVERT: E 270 GLU cc_start: 0.8272 (tt0) cc_final: 0.7583 (tm-30) REVERT: E 355 THR cc_start: 0.8873 (m) cc_final: 0.8266 (p) REVERT: E 382 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7998 (mm-40) REVERT: E 410 MET cc_start: 0.8657 (mpp) cc_final: 0.7567 (mtp) REVERT: F 164 ILE cc_start: 0.8182 (mm) cc_final: 0.7841 (mm) REVERT: F 188 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8151 (pttm) REVERT: F 214 LYS cc_start: 0.9073 (pttt) cc_final: 0.8863 (tppt) REVERT: F 299 ASP cc_start: 0.8064 (m-30) cc_final: 0.7570 (m-30) REVERT: F 309 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7882 (tt0) REVERT: F 351 ILE cc_start: 0.9320 (mt) cc_final: 0.9077 (mt) REVERT: F 355 THR cc_start: 0.8986 (m) cc_final: 0.8573 (p) REVERT: F 368 LEU cc_start: 0.9219 (mm) cc_final: 0.8967 (mt) REVERT: H 46 GLN cc_start: 0.7977 (mt0) cc_final: 0.7776 (mt0) REVERT: H 154 SER cc_start: 0.6477 (m) cc_final: 0.6068 (t) REVERT: H 173 GLU cc_start: 0.8414 (tt0) cc_final: 0.8075 (tt0) REVERT: H 181 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8089 (pt0) REVERT: H 210 LYS cc_start: 0.8971 (tttm) cc_final: 0.8650 (ttmm) REVERT: I 78 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8608 (mm110) REVERT: I 129 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8229 (mm-30) REVERT: I 150 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8559 (ttpt) REVERT: I 167 ILE cc_start: 0.8294 (mt) cc_final: 0.7918 (mm) REVERT: I 182 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8140 (mt-10) REVERT: J 78 GLN cc_start: 0.7725 (tp40) cc_final: 0.7346 (tm-30) REVERT: J 108 ASP cc_start: 0.8340 (t0) cc_final: 0.7821 (m-30) REVERT: J 109 THR cc_start: 0.8658 (m) cc_final: 0.8344 (p) REVERT: J 154 MET cc_start: 0.8089 (mtp) cc_final: 0.7693 (ttm) REVERT: J 173 LEU cc_start: 0.9003 (mt) cc_final: 0.8748 (mt) REVERT: J 184 TYR cc_start: 0.8199 (m-80) cc_final: 0.7974 (m-80) REVERT: J 206 GLN cc_start: 0.8619 (mt0) cc_final: 0.8380 (mt0) REVERT: J 208 MET cc_start: 0.8831 (mmt) cc_final: 0.8592 (mmp) REVERT: J 223 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8387 (mptt) REVERT: K 96 ASN cc_start: 0.9327 (m-40) cc_final: 0.9044 (m-40) REVERT: K 103 SER cc_start: 0.9323 (t) cc_final: 0.9117 (p) REVERT: K 114 VAL cc_start: 0.9252 (t) cc_final: 0.8566 (p) REVERT: K 129 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7870 (mm-30) REVERT: K 141 PHE cc_start: 0.8385 (t80) cc_final: 0.7933 (t80) REVERT: K 226 ASP cc_start: 0.6218 (t70) cc_final: 0.5955 (m-30) REVERT: M 85 GLN cc_start: 0.8543 (tt0) cc_final: 0.8186 (tm-30) REVERT: M 91 ASN cc_start: 0.8331 (m-40) cc_final: 0.8116 (m-40) REVERT: M 93 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8506 (tm-30) REVERT: M 97 THR cc_start: 0.8476 (m) cc_final: 0.8129 (m) REVERT: M 107 ARG cc_start: 0.8350 (mmp80) cc_final: 0.7608 (mmm-85) REVERT: N 78 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: O 97 THR cc_start: 0.9288 (m) cc_final: 0.9040 (p) REVERT: Q 37 ASP cc_start: 0.8142 (t0) cc_final: 0.7171 (t0) REVERT: Q 48 ASP cc_start: 0.8797 (t70) cc_final: 0.8216 (t0) REVERT: Q 61 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7075 (mtp85) REVERT: Q 112 TYR cc_start: 0.8698 (t80) cc_final: 0.8447 (t80) REVERT: Q 221 ASP cc_start: 0.7430 (m-30) cc_final: 0.7119 (m-30) REVERT: R 33 MET cc_start: 0.8129 (mmm) cc_final: 0.7857 (mmm) REVERT: R 77 ASP cc_start: 0.8486 (t0) cc_final: 0.8256 (t70) REVERT: R 79 ASP cc_start: 0.8289 (m-30) cc_final: 0.7673 (t0) REVERT: R 165 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7969 (mt0) REVERT: R 200 PHE cc_start: 0.8018 (t80) cc_final: 0.7747 (t80) REVERT: S 37 ASP cc_start: 0.7440 (t0) cc_final: 0.6562 (t0) REVERT: S 40 ASN cc_start: 0.7915 (m-40) cc_final: 0.7652 (m-40) REVERT: S 48 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7746 (t0) outliers start: 103 outliers final: 58 residues processed: 1009 average time/residue: 0.2131 time to fit residues: 353.4533 Evaluate side-chains 793 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 730 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 156 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 386 optimal weight: 0.7980 chunk 406 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 448 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN I 221 ASN J 66 GLN J 67 GLN Q 135 GLN R 118 HIS ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083690 restraints weight = 71885.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086800 restraints weight = 32475.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088856 restraints weight = 18756.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090222 restraints weight = 12747.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091112 restraints weight = 9742.108| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36765 Z= 0.193 Angle : 0.643 10.056 49676 Z= 0.329 Chirality : 0.046 0.193 5575 Planarity : 0.005 0.060 6440 Dihedral : 4.892 113.390 5022 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 3.62 % Allowed : 13.18 % Favored : 83.21 % 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: 1.16 (0.13), residues: 4538 helix: 1.94 (0.11), residues: 2092 sheet: -0.28 (0.20), residues: 627 loop : -0.15 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 79 TYR 0.024 0.002 TYR S 139 PHE 0.023 0.002 PHE C 337 TRP 0.014 0.002 TRP B 450 HIS 0.012 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00431 (36765) covalent geometry : angle 0.64289 (49676) hydrogen bonds : bond 0.04725 ( 1954) hydrogen bonds : angle 3.04277 (13794) *********************** 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 915 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 772 time to evaluate : 1.062 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 60 ASP cc_start: 0.7976 (p0) cc_final: 0.7677 (p0) REVERT: A 73 VAL cc_start: 0.9258 (t) cc_final: 0.9025 (m) REVERT: A 173 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8354 (ptp90) REVERT: A 254 CYS cc_start: 0.8711 (m) cc_final: 0.8328 (m) REVERT: A 279 GLU cc_start: 0.6292 (tp30) cc_final: 0.6051 (tp30) REVERT: A 290 ASP cc_start: 0.8634 (t70) cc_final: 0.8159 (t0) REVERT: A 485 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7952 (mp0) REVERT: A 510 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 61 MET cc_start: 0.7697 (mtp) cc_final: 0.7393 (ttm) REVERT: B 74 SER cc_start: 0.8657 (m) cc_final: 0.7488 (p) REVERT: B 77 ASP cc_start: 0.8207 (m-30) cc_final: 0.7571 (m-30) REVERT: B 84 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7632 (mmtt) REVERT: B 115 SER cc_start: 0.8846 (t) cc_final: 0.8589 (p) REVERT: B 116 ILE cc_start: 0.9150 (pt) cc_final: 0.8894 (pt) REVERT: B 272 ILE cc_start: 0.9008 (mm) cc_final: 0.8749 (mt) REVERT: B 308 ARG cc_start: 0.7358 (ptp-110) cc_final: 0.7032 (ptt180) REVERT: B 349 ASP cc_start: 0.7356 (p0) cc_final: 0.6776 (p0) REVERT: B 419 ASP cc_start: 0.7341 (t0) cc_final: 0.7115 (t0) REVERT: B 429 VAL cc_start: 0.9632 (m) cc_final: 0.9393 (p) REVERT: B 485 GLU cc_start: 0.8361 (tp30) cc_final: 0.7623 (tp30) REVERT: B 486 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 488 ASP cc_start: 0.8585 (m-30) cc_final: 0.7866 (t0) REVERT: B 540 MET cc_start: 0.7668 (mtp) cc_final: 0.7461 (mtp) REVERT: C 55 ILE cc_start: 0.8693 (mt) cc_final: 0.8280 (pt) REVERT: C 77 ASP cc_start: 0.7966 (m-30) cc_final: 0.7691 (m-30) REVERT: C 84 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8062 (pttm) REVERT: C 140 ASN cc_start: 0.8003 (m-40) cc_final: 0.7706 (m110) REVERT: C 155 ILE cc_start: 0.9039 (mm) cc_final: 0.8738 (mm) REVERT: C 299 ASP cc_start: 0.8030 (m-30) cc_final: 0.7663 (p0) REVERT: C 411 SER cc_start: 0.8166 (p) cc_final: 0.7951 (m) REVERT: C 447 SER cc_start: 0.8426 (m) cc_final: 0.8155 (p) REVERT: C 466 ASP cc_start: 0.8762 (t70) cc_final: 0.8479 (t0) REVERT: C 484 GLN cc_start: 0.8505 (tp40) cc_final: 0.8230 (tp-100) REVERT: C 606 GLU cc_start: 0.8607 (tt0) cc_final: 0.7827 (tp30) REVERT: D 54 ASN cc_start: 0.7907 (t0) cc_final: 0.7578 (t0) REVERT: D 127 MET cc_start: 0.8480 (mtp) cc_final: 0.8229 (mtp) REVERT: D 141 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7209 (ttm-80) REVERT: D 242 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.8091 (ttm170) REVERT: D 247 ASP cc_start: 0.8535 (t0) cc_final: 0.8059 (t0) REVERT: D 356 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8771 (mtp) REVERT: D 360 ASP cc_start: 0.8395 (t0) cc_final: 0.8041 (t0) REVERT: E 270 GLU cc_start: 0.8313 (tt0) cc_final: 0.7654 (tm-30) REVERT: E 330 ASP cc_start: 0.8763 (m-30) cc_final: 0.8491 (t0) REVERT: E 355 THR cc_start: 0.8792 (m) cc_final: 0.7970 (p) REVERT: E 382 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8120 (mm-40) REVERT: E 410 MET cc_start: 0.8755 (mpp) cc_final: 0.7586 (mtp) REVERT: F 299 ASP cc_start: 0.8153 (m-30) cc_final: 0.7614 (m-30) REVERT: F 309 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7842 (tt0) REVERT: F 368 LEU cc_start: 0.9251 (mm) cc_final: 0.8996 (mt) REVERT: H 154 SER cc_start: 0.6540 (m) cc_final: 0.6160 (t) REVERT: H 159 ASP cc_start: 0.8986 (t70) cc_final: 0.8744 (t70) REVERT: H 173 GLU cc_start: 0.8401 (tt0) cc_final: 0.8084 (tt0) REVERT: H 181 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8065 (pt0) REVERT: H 193 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8178 (tm-30) REVERT: H 210 LYS cc_start: 0.8992 (tttm) cc_final: 0.8706 (ttmm) REVERT: I 74 ASN cc_start: 0.9094 (t0) cc_final: 0.8871 (t0) REVERT: I 78 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8565 (mm110) REVERT: I 150 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8477 (ttpt) REVERT: I 221 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7956 (t0) REVERT: J 78 GLN cc_start: 0.7816 (tp40) cc_final: 0.7382 (tm-30) REVERT: J 154 MET cc_start: 0.8299 (mtp) cc_final: 0.7948 (ttm) REVERT: J 185 ASN cc_start: 0.8031 (p0) cc_final: 0.7827 (p0) REVERT: J 190 ILE cc_start: 0.9175 (mt) cc_final: 0.8923 (mt) REVERT: J 208 MET cc_start: 0.8823 (mmt) cc_final: 0.8613 (mmp) REVERT: K 75 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8868 (mm) REVERT: K 96 ASN cc_start: 0.9315 (m-40) cc_final: 0.9091 (m-40) REVERT: K 103 SER cc_start: 0.9369 (t) cc_final: 0.9137 (p) REVERT: K 132 MET cc_start: 0.9167 (mpp) cc_final: 0.8865 (mmm) REVERT: K 141 PHE cc_start: 0.8598 (t80) cc_final: 0.8289 (t80) REVERT: K 194 ASN cc_start: 0.8738 (t0) cc_final: 0.8497 (t0) REVERT: K 226 ASP cc_start: 0.6394 (t70) cc_final: 0.5913 (m-30) REVERT: M 85 GLN cc_start: 0.8588 (tt0) cc_final: 0.8257 (tm-30) REVERT: N 78 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7353 (mtm-85) REVERT: O 74 GLU cc_start: 0.8196 (pp20) cc_final: 0.7973 (pp20) REVERT: O 78 ARG cc_start: 0.8746 (tpt90) cc_final: 0.8417 (tpt90) REVERT: O 97 THR cc_start: 0.9341 (m) cc_final: 0.9100 (p) REVERT: Q 153 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7285 (ttm110) REVERT: Q 166 TYR cc_start: 0.8619 (m-80) cc_final: 0.7856 (m-10) REVERT: Q 170 GLU cc_start: 0.6845 (pm20) cc_final: 0.6617 (mp0) REVERT: R 33 MET cc_start: 0.8087 (mmm) cc_final: 0.7807 (mmm) REVERT: R 77 ASP cc_start: 0.8483 (t0) cc_final: 0.8245 (t70) REVERT: R 79 ASP cc_start: 0.8294 (m-30) cc_final: 0.7688 (t0) REVERT: R 188 MET cc_start: 0.8072 (tpp) cc_final: 0.7853 (ttm) REVERT: S 48 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7721 (t0) outliers start: 143 outliers final: 92 residues processed: 863 average time/residue: 0.2044 time to fit residues: 292.7764 Evaluate side-chains 777 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 680 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 67 GLN Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 439 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 288 optimal weight: 0.1980 chunk 299 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 441 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** B 268 ASN E 262 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN J 66 GLN M 91 ASN N 75 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 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 = 0.3390 r_free = 0.3390 target = 0.103106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086044 restraints weight = 72016.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089059 restraints weight = 32564.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091049 restraints weight = 18825.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092364 restraints weight = 12806.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093122 restraints weight = 9802.164| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36765 Z= 0.147 Angle : 0.600 11.626 49676 Z= 0.303 Chirality : 0.044 0.190 5575 Planarity : 0.004 0.050 6440 Dihedral : 4.785 112.713 5022 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.27 % Favored : 97.71 % Rotamer: Outliers : 3.14 % Allowed : 14.67 % Favored : 82.20 % 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: 1.20 (0.13), residues: 4538 helix: 2.05 (0.11), residues: 2101 sheet: -0.45 (0.20), residues: 640 loop : -0.16 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 61 TYR 0.022 0.001 TYR S 139 PHE 0.033 0.002 PHE R 200 TRP 0.010 0.001 TRP B 450 HIS 0.020 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00327 (36765) covalent geometry : angle 0.60036 (49676) hydrogen bonds : bond 0.04296 ( 1954) hydrogen bonds : angle 2.90368 (13794) *********************** 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 889 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 765 time to evaluate : 1.501 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 60 ASP cc_start: 0.7980 (p0) cc_final: 0.7723 (p0) REVERT: A 173 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8163 (ptp90) REVERT: A 254 CYS cc_start: 0.8660 (m) cc_final: 0.8268 (m) REVERT: A 290 ASP cc_start: 0.8647 (t70) cc_final: 0.8224 (t0) REVERT: A 349 ASP cc_start: 0.8201 (t0) cc_final: 0.7645 (t0) REVERT: A 485 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7926 (mp0) REVERT: A 487 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 510 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 544 MET cc_start: 0.8280 (mtt) cc_final: 0.8051 (mtt) REVERT: B 74 SER cc_start: 0.8722 (m) cc_final: 0.7631 (p) REVERT: B 77 ASP cc_start: 0.8244 (m-30) cc_final: 0.7615 (m-30) REVERT: B 84 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7666 (mmtt) REVERT: B 98 ILE cc_start: 0.8888 (mp) cc_final: 0.8302 (tt) REVERT: B 115 SER cc_start: 0.8862 (t) cc_final: 0.8584 (p) REVERT: B 116 ILE cc_start: 0.9197 (pt) cc_final: 0.8928 (pt) REVERT: B 142 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8309 (tpp80) REVERT: B 272 ILE cc_start: 0.8990 (mm) cc_final: 0.8736 (mt) REVERT: B 429 VAL cc_start: 0.9633 (m) cc_final: 0.9380 (p) REVERT: B 436 ASP cc_start: 0.7502 (t70) cc_final: 0.7271 (t70) REVERT: B 485 GLU cc_start: 0.8346 (tp30) cc_final: 0.7607 (tp30) REVERT: B 486 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 488 ASP cc_start: 0.8398 (m-30) cc_final: 0.7727 (t0) REVERT: B 565 ILE cc_start: 0.8570 (mt) cc_final: 0.8354 (mp) REVERT: C 55 ILE cc_start: 0.8803 (mt) cc_final: 0.8388 (pt) REVERT: C 84 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8078 (pttm) REVERT: C 155 ILE cc_start: 0.9083 (mm) cc_final: 0.8823 (mm) REVERT: C 299 ASP cc_start: 0.7894 (m-30) cc_final: 0.7669 (p0) REVERT: C 447 SER cc_start: 0.8495 (m) cc_final: 0.8288 (p) REVERT: C 466 ASP cc_start: 0.8660 (t70) cc_final: 0.8359 (t0) REVERT: C 484 GLN cc_start: 0.8474 (tp40) cc_final: 0.8180 (tp-100) REVERT: C 606 GLU cc_start: 0.8602 (tt0) cc_final: 0.7777 (tp30) REVERT: D 127 MET cc_start: 0.8451 (mtp) cc_final: 0.8148 (mtp) REVERT: D 242 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: D 247 ASP cc_start: 0.8532 (t0) cc_final: 0.8086 (t0) REVERT: D 360 ASP cc_start: 0.8355 (t0) cc_final: 0.7962 (t0) REVERT: D 433 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: D 497 GLN cc_start: 0.8052 (pp30) cc_final: 0.7797 (pp30) REVERT: E 270 GLU cc_start: 0.8341 (tt0) cc_final: 0.7673 (tm-30) REVERT: E 330 ASP cc_start: 0.8700 (m-30) cc_final: 0.8470 (t0) REVERT: E 382 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8128 (tp40) REVERT: E 410 MET cc_start: 0.8750 (mpp) cc_final: 0.7840 (mtp) REVERT: F 299 ASP cc_start: 0.8053 (m-30) cc_final: 0.7647 (m-30) REVERT: F 309 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7820 (tt0) REVERT: H 154 SER cc_start: 0.6715 (m) cc_final: 0.6320 (t) REVERT: H 173 GLU cc_start: 0.8409 (tt0) cc_final: 0.8109 (tt0) REVERT: H 181 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8064 (pt0) REVERT: H 193 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8136 (tm-30) REVERT: H 210 LYS cc_start: 0.9084 (tttm) cc_final: 0.8785 (ttmm) REVERT: I 74 ASN cc_start: 0.9091 (t0) cc_final: 0.8879 (t0) REVERT: I 78 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8514 (mm110) REVERT: I 221 ASN cc_start: 0.8353 (t0) cc_final: 0.7865 (t0) REVERT: J 97 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8279 (tm-30) REVERT: J 121 LEU cc_start: 0.8751 (mt) cc_final: 0.8543 (mt) REVERT: J 154 MET cc_start: 0.8353 (mtp) cc_final: 0.7968 (ttm) REVERT: J 172 TYR cc_start: 0.8259 (m-80) cc_final: 0.7883 (m-10) REVERT: K 75 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8761 (mm) REVERT: K 96 ASN cc_start: 0.9302 (m-40) cc_final: 0.8985 (m-40) REVERT: K 103 SER cc_start: 0.9344 (t) cc_final: 0.9123 (p) REVERT: K 129 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7902 (mm-30) REVERT: K 132 MET cc_start: 0.9125 (mpp) cc_final: 0.8822 (mmm) REVERT: K 141 PHE cc_start: 0.8646 (t80) cc_final: 0.8337 (t80) REVERT: K 194 ASN cc_start: 0.8851 (t0) cc_final: 0.8512 (t0) REVERT: M 85 GLN cc_start: 0.8566 (tt0) cc_final: 0.8266 (tm-30) REVERT: O 78 ARG cc_start: 0.8754 (tpt90) cc_final: 0.8332 (tpt90) REVERT: Q 33 MET cc_start: 0.8456 (tpt) cc_final: 0.8135 (tpp) REVERT: Q 37 ASP cc_start: 0.8144 (t0) cc_final: 0.7260 (t0) REVERT: Q 48 ASP cc_start: 0.8735 (t70) cc_final: 0.8239 (t0) REVERT: Q 101 PHE cc_start: 0.7285 (m-80) cc_final: 0.7052 (m-10) REVERT: Q 153 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7089 (ttp-170) REVERT: Q 166 TYR cc_start: 0.8616 (m-80) cc_final: 0.8157 (m-10) REVERT: Q 170 GLU cc_start: 0.6843 (pm20) cc_final: 0.6627 (mp0) REVERT: Q 221 ASP cc_start: 0.7553 (m-30) cc_final: 0.7224 (m-30) REVERT: R 63 GLU cc_start: 0.7659 (mp0) cc_final: 0.7275 (mp0) REVERT: R 77 ASP cc_start: 0.8414 (t0) cc_final: 0.8183 (t70) REVERT: R 79 ASP cc_start: 0.8190 (m-30) cc_final: 0.7645 (t0) REVERT: R 188 MET cc_start: 0.8170 (tpp) cc_final: 0.7913 (ttm) REVERT: S 48 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7938 (t0) REVERT: S 196 GLN cc_start: 0.8207 (pt0) cc_final: 0.7949 (pt0) outliers start: 124 outliers final: 89 residues processed: 838 average time/residue: 0.2031 time to fit residues: 283.1472 Evaluate side-chains 790 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 697 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 314 ARG Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 142 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 150 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 301 optimal weight: 0.0030 chunk 42 optimal weight: 0.5980 chunk 310 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 339 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 262 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN I 113 GLN J 66 GLN J 67 GLN M 82 GLN N 75 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN S 198 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085471 restraints weight = 71952.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088550 restraints weight = 32354.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090572 restraints weight = 18602.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091918 restraints weight = 12627.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.092792 restraints weight = 9628.900| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36765 Z= 0.133 Angle : 0.594 10.232 49676 Z= 0.296 Chirality : 0.044 0.196 5575 Planarity : 0.004 0.055 6440 Dihedral : 4.699 114.960 5022 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 3.36 % Allowed : 15.81 % Favored : 80.83 % 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: 1.22 (0.13), residues: 4538 helix: 2.09 (0.11), residues: 2110 sheet: -0.40 (0.20), residues: 609 loop : -0.22 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 115 TYR 0.026 0.001 TYR B 266 PHE 0.020 0.001 PHE H 44 TRP 0.013 0.001 TRP Q 55 HIS 0.014 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00295 (36765) covalent geometry : angle 0.59362 (49676) hydrogen bonds : bond 0.04073 ( 1954) hydrogen bonds : angle 2.83430 (13794) *********************** 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 870 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 737 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: A 173 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7742 (pmt100) REVERT: A 254 CYS cc_start: 0.8669 (m) cc_final: 0.8253 (m) REVERT: A 279 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6200 (mm-30) REVERT: A 290 ASP cc_start: 0.8620 (t70) cc_final: 0.8171 (t0) REVERT: A 318 MET cc_start: 0.9115 (mtt) cc_final: 0.8750 (mmm) REVERT: A 346 MET cc_start: 0.7925 (ttt) cc_final: 0.7485 (ttt) REVERT: A 365 LEU cc_start: 0.9138 (tp) cc_final: 0.8936 (tp) REVERT: A 485 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7933 (mp0) REVERT: A 510 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 61 MET cc_start: 0.7775 (mtp) cc_final: 0.7388 (ttm) REVERT: B 74 SER cc_start: 0.8630 (m) cc_final: 0.7580 (p) REVERT: B 77 ASP cc_start: 0.8297 (m-30) cc_final: 0.7627 (m-30) REVERT: B 84 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7600 (mmtt) REVERT: B 115 SER cc_start: 0.8933 (t) cc_final: 0.8654 (p) REVERT: B 116 ILE cc_start: 0.9232 (pt) cc_final: 0.8970 (pt) REVERT: B 272 ILE cc_start: 0.8964 (mm) cc_final: 0.8717 (mp) REVERT: B 318 MET cc_start: 0.8651 (tpp) cc_final: 0.8016 (mpp) REVERT: B 399 GLU cc_start: 0.8476 (tp30) cc_final: 0.8199 (mm-30) REVERT: B 429 VAL cc_start: 0.9600 (m) cc_final: 0.9306 (p) REVERT: B 485 GLU cc_start: 0.8337 (tp30) cc_final: 0.7594 (tp30) REVERT: B 486 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 488 ASP cc_start: 0.8349 (m-30) cc_final: 0.7674 (t0) REVERT: B 565 ILE cc_start: 0.8535 (mt) cc_final: 0.8286 (mp) REVERT: C 30 THR cc_start: 0.8643 (m) cc_final: 0.8220 (p) REVERT: C 55 ILE cc_start: 0.8823 (mt) cc_final: 0.8208 (pt) REVERT: C 84 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8038 (pttm) REVERT: C 155 ILE cc_start: 0.9060 (mm) cc_final: 0.8791 (mm) REVERT: C 466 ASP cc_start: 0.8670 (t70) cc_final: 0.8379 (t0) REVERT: C 484 GLN cc_start: 0.8506 (tp40) cc_final: 0.8177 (tp-100) REVERT: C 606 GLU cc_start: 0.8622 (tt0) cc_final: 0.7777 (tp30) REVERT: D 127 MET cc_start: 0.8437 (mtp) cc_final: 0.8094 (mtp) REVERT: D 247 ASP cc_start: 0.8547 (t0) cc_final: 0.8295 (t0) REVERT: D 360 ASP cc_start: 0.8406 (t0) cc_final: 0.7984 (t0) REVERT: D 497 GLN cc_start: 0.8112 (pp30) cc_final: 0.7821 (pp30) REVERT: E 93 LYS cc_start: 0.8150 (mttp) cc_final: 0.7871 (ttpp) REVERT: E 270 GLU cc_start: 0.8353 (tt0) cc_final: 0.7583 (tm-30) REVERT: E 330 ASP cc_start: 0.8732 (m-30) cc_final: 0.8501 (t0) REVERT: E 382 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8122 (tp40) REVERT: E 410 MET cc_start: 0.8739 (mpp) cc_final: 0.7897 (mtp) REVERT: F 299 ASP cc_start: 0.8036 (m-30) cc_final: 0.7549 (m-30) REVERT: F 309 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7815 (tt0) REVERT: F 351 ILE cc_start: 0.9285 (mt) cc_final: 0.8965 (mm) REVERT: H 181 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8124 (pt0) REVERT: H 193 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8143 (tm-30) REVERT: H 210 LYS cc_start: 0.9215 (tttm) cc_final: 0.8803 (ttmm) REVERT: I 74 ASN cc_start: 0.9054 (t0) cc_final: 0.8797 (t0) REVERT: I 78 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8524 (mm110) REVERT: I 221 ASN cc_start: 0.8355 (t0) cc_final: 0.7506 (t0) REVERT: J 97 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8444 (tm-30) REVERT: J 154 MET cc_start: 0.8383 (mtp) cc_final: 0.7981 (ttm) REVERT: J 172 TYR cc_start: 0.8265 (m-80) cc_final: 0.7886 (m-10) REVERT: K 75 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8784 (mm) REVERT: K 96 ASN cc_start: 0.9300 (m-40) cc_final: 0.8984 (m-40) REVERT: K 129 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7937 (mm-30) REVERT: K 132 MET cc_start: 0.9212 (mpp) cc_final: 0.8922 (mmm) REVERT: K 141 PHE cc_start: 0.8564 (t80) cc_final: 0.8250 (t80) REVERT: K 143 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8223 (tp) REVERT: K 184 TYR cc_start: 0.8654 (m-80) cc_final: 0.8366 (m-80) REVERT: K 194 ASN cc_start: 0.8853 (t0) cc_final: 0.8568 (t0) REVERT: M 78 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7783 (ttp-110) REVERT: M 85 GLN cc_start: 0.8586 (tt0) cc_final: 0.8313 (tm-30) REVERT: N 75 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7915 (mm-40) REVERT: O 78 ARG cc_start: 0.8774 (tpt90) cc_final: 0.8379 (tpt90) REVERT: O 97 THR cc_start: 0.9369 (m) cc_final: 0.9061 (p) REVERT: Q 33 MET cc_start: 0.8415 (tpt) cc_final: 0.8143 (tpp) REVERT: Q 37 ASP cc_start: 0.8086 (t0) cc_final: 0.7209 (t0) REVERT: Q 48 ASP cc_start: 0.8755 (t70) cc_final: 0.8266 (t0) REVERT: Q 153 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7204 (ttm110) REVERT: Q 166 TYR cc_start: 0.8643 (m-80) cc_final: 0.8315 (m-10) REVERT: Q 170 GLU cc_start: 0.6775 (pm20) cc_final: 0.6537 (mp0) REVERT: Q 188 MET cc_start: 0.7790 (ttm) cc_final: 0.7266 (ttt) REVERT: Q 221 ASP cc_start: 0.7510 (m-30) cc_final: 0.7152 (m-30) REVERT: R 33 MET cc_start: 0.8292 (mmm) cc_final: 0.7973 (mmm) REVERT: R 77 ASP cc_start: 0.8437 (t0) cc_final: 0.8166 (t70) REVERT: R 79 ASP cc_start: 0.8160 (m-30) cc_final: 0.7621 (t0) REVERT: R 188 MET cc_start: 0.8114 (tpp) cc_final: 0.7859 (ttm) REVERT: R 200 PHE cc_start: 0.7279 (t80) cc_final: 0.7026 (t80) REVERT: S 37 ASP cc_start: 0.7365 (t0) cc_final: 0.6630 (t70) REVERT: S 45 ILE cc_start: 0.8610 (pt) cc_final: 0.8405 (pt) REVERT: S 48 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7608 (t0) REVERT: S 196 GLN cc_start: 0.8254 (pt0) cc_final: 0.7995 (pt0) outliers start: 133 outliers final: 98 residues processed: 817 average time/residue: 0.2081 time to fit residues: 281.5618 Evaluate side-chains 780 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 677 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 127 optimal weight: 2.9990 chunk 396 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 449 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 314 ASN A 444 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN N 75 GLN Q 111 GLN R 19 HIS R 21 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN ** S 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078568 restraints weight = 73805.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081443 restraints weight = 33703.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.083342 restraints weight = 19710.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084604 restraints weight = 13527.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085477 restraints weight = 10424.208| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 36765 Z= 0.318 Angle : 0.734 10.350 49676 Z= 0.374 Chirality : 0.049 0.203 5575 Planarity : 0.005 0.049 6440 Dihedral : 5.010 111.737 5022 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 4.68 % Allowed : 15.28 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4538 helix: 1.83 (0.11), residues: 2117 sheet: -0.78 (0.20), residues: 643 loop : -0.38 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 61 TYR 0.030 0.002 TYR B 266 PHE 0.023 0.003 PHE B 472 TRP 0.020 0.002 TRP S 122 HIS 0.018 0.002 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00728 (36765) covalent geometry : angle 0.73378 (49676) hydrogen bonds : bond 0.04622 ( 1954) hydrogen bonds : angle 3.00546 (13794) *********************** 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 877 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 692 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8351 (ptp90) REVERT: A 254 CYS cc_start: 0.8792 (m) cc_final: 0.8345 (m) REVERT: A 290 ASP cc_start: 0.8733 (t70) cc_final: 0.8350 (t0) REVERT: A 346 MET cc_start: 0.8173 (ttt) cc_final: 0.7619 (ttt) REVERT: A 485 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7922 (mp0) REVERT: A 510 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 74 SER cc_start: 0.8576 (m) cc_final: 0.7457 (p) REVERT: B 77 ASP cc_start: 0.8334 (m-30) cc_final: 0.7529 (m-30) REVERT: B 84 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7816 (mmtt) REVERT: B 98 ILE cc_start: 0.8837 (mp) cc_final: 0.8366 (tt) REVERT: B 115 SER cc_start: 0.9082 (t) cc_final: 0.8780 (p) REVERT: B 116 ILE cc_start: 0.9331 (pt) cc_final: 0.8957 (pt) REVERT: B 201 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 270 ASP cc_start: 0.7841 (m-30) cc_final: 0.7609 (m-30) REVERT: B 340 MET cc_start: 0.8769 (mtm) cc_final: 0.8563 (ttp) REVERT: B 429 VAL cc_start: 0.9663 (m) cc_final: 0.9453 (p) REVERT: B 485 GLU cc_start: 0.8387 (tp30) cc_final: 0.7685 (tp30) REVERT: B 486 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 488 ASP cc_start: 0.8466 (m-30) cc_final: 0.7798 (t0) REVERT: B 565 ILE cc_start: 0.8507 (mt) cc_final: 0.8247 (mp) REVERT: C 30 THR cc_start: 0.8802 (m) cc_final: 0.8315 (p) REVERT: C 84 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8176 (pttm) REVERT: C 155 ILE cc_start: 0.9203 (mm) cc_final: 0.8883 (mm) REVERT: C 299 ASP cc_start: 0.7303 (p0) cc_final: 0.7099 (p0) REVERT: C 306 MET cc_start: 0.9037 (tpp) cc_final: 0.8639 (tpp) REVERT: C 466 ASP cc_start: 0.8753 (t70) cc_final: 0.8471 (t0) REVERT: C 484 GLN cc_start: 0.8594 (tp40) cc_final: 0.8310 (tp-100) REVERT: C 606 GLU cc_start: 0.8631 (tt0) cc_final: 0.7804 (tp30) REVERT: D 127 MET cc_start: 0.8588 (mtp) cc_final: 0.8250 (mtp) REVERT: D 238 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7344 (tmm) REVERT: D 247 ASP cc_start: 0.8615 (t0) cc_final: 0.8392 (t0) REVERT: D 257 VAL cc_start: 0.9220 (t) cc_final: 0.8915 (p) REVERT: D 360 ASP cc_start: 0.8538 (t0) cc_final: 0.8141 (t0) REVERT: E 256 ASN cc_start: 0.8203 (m-40) cc_final: 0.7731 (p0) REVERT: E 262 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8476 (t0) REVERT: E 268 THR cc_start: 0.8823 (p) cc_final: 0.8519 (t) REVERT: E 270 GLU cc_start: 0.8412 (tt0) cc_final: 0.7743 (tm-30) REVERT: E 330 ASP cc_start: 0.8758 (m-30) cc_final: 0.8556 (t70) REVERT: E 382 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8434 (tp40) REVERT: E 410 MET cc_start: 0.8784 (mpp) cc_final: 0.8250 (mtp) REVERT: F 299 ASP cc_start: 0.8366 (m-30) cc_final: 0.7902 (m-30) REVERT: F 309 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7974 (tt0) REVERT: F 464 THR cc_start: 0.8905 (m) cc_final: 0.8541 (p) REVERT: H 181 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7937 (pt0) REVERT: H 193 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8218 (tm-30) REVERT: H 210 LYS cc_start: 0.9200 (tttm) cc_final: 0.8909 (ttmm) REVERT: I 74 ASN cc_start: 0.9062 (t0) cc_final: 0.8771 (t0) REVERT: I 78 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8621 (mm110) REVERT: I 133 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8842 (tt) REVERT: J 78 GLN cc_start: 0.7891 (tp40) cc_final: 0.7411 (tm-30) REVERT: J 133 ILE cc_start: 0.9099 (mp) cc_final: 0.8897 (mt) REVERT: J 135 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8193 (mtp-110) REVERT: J 206 GLN cc_start: 0.8723 (mt0) cc_final: 0.8437 (mt0) REVERT: J 210 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7858 (tt0) REVERT: J 223 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8359 (mptt) REVERT: K 96 ASN cc_start: 0.9348 (m-40) cc_final: 0.9123 (m-40) REVERT: K 129 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7908 (mm-30) REVERT: K 132 MET cc_start: 0.9078 (mpp) cc_final: 0.8713 (mmm) REVERT: K 143 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (tp) REVERT: K 184 TYR cc_start: 0.8756 (m-80) cc_final: 0.8417 (m-80) REVERT: M 85 GLN cc_start: 0.8643 (tt0) cc_final: 0.8384 (tm-30) REVERT: M 107 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8262 (mmp80) REVERT: N 75 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: N 78 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: O 74 GLU cc_start: 0.8153 (pp20) cc_final: 0.7909 (pp20) REVERT: O 78 ARG cc_start: 0.8802 (tpt90) cc_final: 0.8384 (tpt90) REVERT: Q 33 MET cc_start: 0.8517 (tpt) cc_final: 0.8242 (tpp) REVERT: Q 37 ASP cc_start: 0.8195 (t0) cc_final: 0.7308 (t0) REVERT: Q 48 ASP cc_start: 0.8900 (t70) cc_final: 0.8387 (t0) REVERT: Q 61 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7606 (mtm110) REVERT: Q 153 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7293 (ttm110) REVERT: Q 166 TYR cc_start: 0.8725 (m-80) cc_final: 0.8436 (m-10) REVERT: Q 188 MET cc_start: 0.8119 (ttm) cc_final: 0.7686 (ttm) REVERT: Q 221 ASP cc_start: 0.7741 (m-30) cc_final: 0.7400 (m-30) REVERT: R 77 ASP cc_start: 0.8615 (t0) cc_final: 0.8363 (t70) REVERT: R 79 ASP cc_start: 0.8304 (m-30) cc_final: 0.7694 (t0) REVERT: R 188 MET cc_start: 0.8161 (tpp) cc_final: 0.7839 (ttm) REVERT: R 200 PHE cc_start: 0.7607 (t80) cc_final: 0.7350 (t80) REVERT: S 37 ASP cc_start: 0.7353 (t0) cc_final: 0.6469 (t0) REVERT: S 48 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7672 (t0) outliers start: 185 outliers final: 132 residues processed: 799 average time/residue: 0.2098 time to fit residues: 277.1092 Evaluate side-chains 790 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 650 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 326 TYR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 135 ARG Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 142 ASN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 158 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 211 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 274 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 342 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 414 optimal weight: 0.0970 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN D 209 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN J 66 GLN ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.082244 restraints weight = 73038.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085187 restraints weight = 32840.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087119 restraints weight = 18888.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088402 restraints weight = 12815.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089195 restraints weight = 9788.760| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36765 Z= 0.155 Angle : 0.627 10.970 49676 Z= 0.314 Chirality : 0.045 0.214 5575 Planarity : 0.004 0.048 6440 Dihedral : 4.826 112.315 5022 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 3.59 % Allowed : 17.32 % Favored : 79.08 % 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: 0.98 (0.13), residues: 4538 helix: 1.97 (0.11), residues: 2119 sheet: -0.80 (0.20), residues: 645 loop : -0.34 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 61 TYR 0.030 0.001 TYR B 266 PHE 0.019 0.002 PHE S 213 TRP 0.015 0.001 TRP Q 55 HIS 0.016 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00351 (36765) covalent geometry : angle 0.62700 (49676) hydrogen bonds : bond 0.04128 ( 1954) hydrogen bonds : angle 2.85117 (13794) *********************** 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 829 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 687 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8229 (ptp90) REVERT: A 254 CYS cc_start: 0.8826 (m) cc_final: 0.8328 (m) REVERT: A 290 ASP cc_start: 0.8758 (t70) cc_final: 0.8368 (t0) REVERT: A 318 MET cc_start: 0.9116 (mtt) cc_final: 0.8800 (mmm) REVERT: A 346 MET cc_start: 0.8113 (ttt) cc_final: 0.7590 (ttt) REVERT: A 458 MET cc_start: 0.8371 (mmm) cc_final: 0.8111 (mmt) REVERT: A 487 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 510 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 544 MET cc_start: 0.8339 (mtt) cc_final: 0.8085 (mtt) REVERT: B 61 MET cc_start: 0.7816 (mtp) cc_final: 0.7509 (ttm) REVERT: B 74 SER cc_start: 0.8592 (m) cc_final: 0.7487 (p) REVERT: B 77 ASP cc_start: 0.8345 (m-30) cc_final: 0.7594 (m-30) REVERT: B 84 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7793 (mmtt) REVERT: B 98 ILE cc_start: 0.8760 (mp) cc_final: 0.8303 (tt) REVERT: B 115 SER cc_start: 0.8996 (t) cc_final: 0.8663 (p) REVERT: B 116 ILE cc_start: 0.9260 (pt) cc_final: 0.8990 (pt) REVERT: B 201 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 238 PHE cc_start: 0.8985 (m-80) cc_final: 0.8636 (m-80) REVERT: B 429 VAL cc_start: 0.9633 (m) cc_final: 0.9403 (p) REVERT: B 485 GLU cc_start: 0.8335 (tp30) cc_final: 0.7628 (tp30) REVERT: B 486 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 488 ASP cc_start: 0.8389 (m-30) cc_final: 0.7733 (t0) REVERT: B 565 ILE cc_start: 0.8503 (mt) cc_final: 0.8254 (mp) REVERT: C 30 THR cc_start: 0.8745 (m) cc_final: 0.8276 (p) REVERT: C 84 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8105 (pttm) REVERT: C 123 ASN cc_start: 0.9036 (t0) cc_final: 0.8821 (t0) REVERT: C 155 ILE cc_start: 0.9122 (mm) cc_final: 0.8916 (mm) REVERT: C 299 ASP cc_start: 0.7403 (p0) cc_final: 0.7153 (p0) REVERT: C 449 ASN cc_start: 0.8169 (t0) cc_final: 0.7947 (t0) REVERT: C 466 ASP cc_start: 0.8707 (t70) cc_final: 0.8440 (t0) REVERT: C 484 GLN cc_start: 0.8537 (tp40) cc_final: 0.8263 (tp40) REVERT: C 606 GLU cc_start: 0.8595 (tt0) cc_final: 0.7714 (tp30) REVERT: D 127 MET cc_start: 0.8514 (mtp) cc_final: 0.8167 (mtp) REVERT: D 247 ASP cc_start: 0.8558 (t0) cc_final: 0.8107 (t0) REVERT: D 358 ASN cc_start: 0.8485 (t0) cc_final: 0.8274 (t0) REVERT: D 360 ASP cc_start: 0.8530 (t0) cc_final: 0.8138 (t0) REVERT: D 497 GLN cc_start: 0.8178 (pm20) cc_final: 0.7943 (tt0) REVERT: E 256 ASN cc_start: 0.8093 (m-40) cc_final: 0.7626 (p0) REVERT: E 270 GLU cc_start: 0.8245 (tt0) cc_final: 0.7411 (tm-30) REVERT: E 382 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8318 (tp40) REVERT: E 410 MET cc_start: 0.8702 (mpp) cc_final: 0.8282 (mtp) REVERT: F 299 ASP cc_start: 0.8136 (m-30) cc_final: 0.7633 (m-30) REVERT: F 309 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7881 (tt0) REVERT: F 464 THR cc_start: 0.8869 (m) cc_final: 0.8475 (p) REVERT: H 193 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 210 LYS cc_start: 0.9278 (tttm) cc_final: 0.8859 (ttmm) REVERT: I 74 ASN cc_start: 0.9014 (t0) cc_final: 0.8737 (t0) REVERT: I 78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8580 (mm110) REVERT: I 133 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8795 (tt) REVERT: J 210 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7841 (tt0) REVERT: J 223 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8349 (mptt) REVERT: K 96 ASN cc_start: 0.9278 (m-40) cc_final: 0.8966 (m-40) REVERT: K 129 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8017 (mm-30) REVERT: K 132 MET cc_start: 0.9102 (mpp) cc_final: 0.8732 (mmm) REVERT: K 143 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (tp) REVERT: K 184 TYR cc_start: 0.8641 (m-80) cc_final: 0.8358 (m-80) REVERT: M 85 GLN cc_start: 0.8617 (tt0) cc_final: 0.8383 (tm-30) REVERT: M 107 ARG cc_start: 0.8502 (mmp80) cc_final: 0.8273 (mmp80) REVERT: N 75 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7918 (mm-40) REVERT: N 78 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: O 74 GLU cc_start: 0.8131 (pp20) cc_final: 0.7847 (pp20) REVERT: O 78 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8356 (tpt90) REVERT: Q 33 MET cc_start: 0.8453 (tpt) cc_final: 0.8190 (tpp) REVERT: Q 37 ASP cc_start: 0.8086 (t0) cc_final: 0.7196 (t0) REVERT: Q 48 ASP cc_start: 0.8808 (t70) cc_final: 0.8314 (t0) REVERT: Q 153 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7235 (ttm110) REVERT: Q 166 TYR cc_start: 0.8631 (m-80) cc_final: 0.8330 (m-10) REVERT: Q 170 GLU cc_start: 0.6530 (pm20) cc_final: 0.6247 (mp0) REVERT: Q 188 MET cc_start: 0.8001 (ttm) cc_final: 0.7652 (ttm) REVERT: Q 221 ASP cc_start: 0.7710 (m-30) cc_final: 0.7380 (m-30) REVERT: R 33 MET cc_start: 0.8146 (mmm) cc_final: 0.7913 (mmm) REVERT: R 77 ASP cc_start: 0.8495 (t0) cc_final: 0.8254 (t70) REVERT: R 79 ASP cc_start: 0.8225 (m-30) cc_final: 0.7682 (t0) REVERT: R 188 MET cc_start: 0.8135 (tpp) cc_final: 0.7852 (ttm) REVERT: R 200 PHE cc_start: 0.7407 (t80) cc_final: 0.7163 (t80) REVERT: S 37 ASP cc_start: 0.7288 (t0) cc_final: 0.6441 (t0) REVERT: S 48 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7588 (t0) outliers start: 142 outliers final: 109 residues processed: 774 average time/residue: 0.2068 time to fit residues: 265.2966 Evaluate side-chains 759 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 645 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 142 ASN Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 325 optimal weight: 0.6980 chunk 391 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 356 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 239 optimal weight: 0.0470 chunk 187 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 411 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN J 66 GLN ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN S 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083762 restraints weight = 72046.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086801 restraints weight = 32490.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088803 restraints weight = 18722.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090123 restraints weight = 12694.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090953 restraints weight = 9691.244| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36765 Z= 0.128 Angle : 0.616 11.916 49676 Z= 0.305 Chirality : 0.044 0.219 5575 Planarity : 0.004 0.064 6440 Dihedral : 4.671 113.381 5022 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.96 % Allowed : 18.51 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4538 helix: 2.05 (0.11), residues: 2117 sheet: -0.72 (0.20), residues: 624 loop : -0.36 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 61 TYR 0.029 0.001 TYR B 266 PHE 0.016 0.001 PHE D 487 TRP 0.012 0.001 TRP Q 55 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00286 (36765) covalent geometry : angle 0.61642 (49676) hydrogen bonds : bond 0.03851 ( 1954) hydrogen bonds : angle 2.76126 (13794) *********************** 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 813 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 696 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8532 (mtpp) REVERT: A 254 CYS cc_start: 0.8775 (m) cc_final: 0.8366 (m) REVERT: A 290 ASP cc_start: 0.8736 (t70) cc_final: 0.8341 (t0) REVERT: A 346 MET cc_start: 0.8104 (ttt) cc_final: 0.7518 (ttt) REVERT: A 485 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7913 (mp0) REVERT: A 510 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 61 MET cc_start: 0.7861 (mtp) cc_final: 0.7483 (ttm) REVERT: B 74 SER cc_start: 0.8584 (m) cc_final: 0.7554 (p) REVERT: B 77 ASP cc_start: 0.8386 (m-30) cc_final: 0.7777 (m-30) REVERT: B 84 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7691 (mmtt) REVERT: B 115 SER cc_start: 0.8992 (t) cc_final: 0.8656 (p) REVERT: B 116 ILE cc_start: 0.9232 (pt) cc_final: 0.9019 (pt) REVERT: B 201 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 429 VAL cc_start: 0.9594 (m) cc_final: 0.9355 (p) REVERT: B 485 GLU cc_start: 0.8266 (tp30) cc_final: 0.7524 (tp30) REVERT: B 486 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 488 ASP cc_start: 0.8306 (m-30) cc_final: 0.7651 (t0) REVERT: B 565 ILE cc_start: 0.8487 (mt) cc_final: 0.8123 (pt) REVERT: C 30 THR cc_start: 0.8657 (m) cc_final: 0.8248 (p) REVERT: C 84 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8127 (pttm) REVERT: C 123 ASN cc_start: 0.9010 (t0) cc_final: 0.8785 (t0) REVERT: C 299 ASP cc_start: 0.7291 (p0) cc_final: 0.7013 (p0) REVERT: C 449 ASN cc_start: 0.8261 (t0) cc_final: 0.8045 (t0) REVERT: C 466 ASP cc_start: 0.8612 (t70) cc_final: 0.8340 (t0) REVERT: C 484 GLN cc_start: 0.8566 (tp40) cc_final: 0.8300 (tp40) REVERT: C 606 GLU cc_start: 0.8586 (tt0) cc_final: 0.7694 (tp30) REVERT: D 127 MET cc_start: 0.8508 (mtp) cc_final: 0.8146 (mtp) REVERT: D 247 ASP cc_start: 0.8521 (t0) cc_final: 0.8272 (t0) REVERT: D 358 ASN cc_start: 0.8505 (t0) cc_final: 0.8255 (t0) REVERT: D 360 ASP cc_start: 0.8548 (t0) cc_final: 0.8146 (t70) REVERT: D 497 GLN cc_start: 0.8200 (pm20) cc_final: 0.7888 (tt0) REVERT: E 148 GLU cc_start: 0.8043 (tt0) cc_final: 0.7660 (mt-10) REVERT: E 256 ASN cc_start: 0.8077 (m-40) cc_final: 0.7618 (p0) REVERT: E 262 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8335 (t0) REVERT: E 270 GLU cc_start: 0.8134 (tt0) cc_final: 0.7504 (tm-30) REVERT: E 330 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.7491 (t0) REVERT: E 382 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8248 (tp40) REVERT: E 410 MET cc_start: 0.8709 (mpp) cc_final: 0.8481 (mtp) REVERT: F 238 MET cc_start: 0.7739 (tpp) cc_final: 0.7503 (ptp) REVERT: F 254 MET cc_start: 0.7995 (tpp) cc_final: 0.7233 (mpp) REVERT: F 299 ASP cc_start: 0.7932 (m-30) cc_final: 0.7434 (m-30) REVERT: F 309 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7794 (tt0) REVERT: F 464 THR cc_start: 0.8843 (m) cc_final: 0.8412 (p) REVERT: H 193 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8122 (tm-30) REVERT: H 210 LYS cc_start: 0.9195 (tttm) cc_final: 0.8878 (ttmm) REVERT: I 74 ASN cc_start: 0.8983 (t0) cc_final: 0.8491 (t0) REVERT: I 78 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8420 (mm110) REVERT: J 210 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7878 (tt0) REVERT: J 223 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8339 (mptt) REVERT: K 75 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8776 (mm) REVERT: K 96 ASN cc_start: 0.9263 (m-40) cc_final: 0.8909 (m-40) REVERT: K 132 MET cc_start: 0.9150 (mpp) cc_final: 0.8782 (mmm) REVERT: K 143 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8219 (tp) REVERT: K 184 TYR cc_start: 0.8568 (m-80) cc_final: 0.8367 (m-80) REVERT: M 85 GLN cc_start: 0.8567 (tt0) cc_final: 0.8341 (tm-30) REVERT: N 74 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8009 (mm-30) REVERT: N 78 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7107 (mtm-85) REVERT: N 100 LEU cc_start: 0.8517 (tt) cc_final: 0.8273 (mt) REVERT: O 74 GLU cc_start: 0.8158 (pp20) cc_final: 0.7770 (pp20) REVERT: O 78 ARG cc_start: 0.8754 (tpt90) cc_final: 0.7572 (tpt90) REVERT: O 90 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7254 (ttm-80) REVERT: Q 33 MET cc_start: 0.8412 (tpt) cc_final: 0.8163 (tpp) REVERT: Q 37 ASP cc_start: 0.8024 (t0) cc_final: 0.7152 (t0) REVERT: Q 48 ASP cc_start: 0.8789 (t70) cc_final: 0.8329 (t0) REVERT: Q 153 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7190 (ttm110) REVERT: Q 161 MET cc_start: 0.8228 (tpp) cc_final: 0.7874 (tpp) REVERT: Q 166 TYR cc_start: 0.8581 (m-80) cc_final: 0.8327 (m-10) REVERT: Q 170 GLU cc_start: 0.6473 (pm20) cc_final: 0.6165 (mp0) REVERT: Q 221 ASP cc_start: 0.7756 (m-30) cc_final: 0.7385 (m-30) REVERT: R 33 MET cc_start: 0.8264 (mmm) cc_final: 0.7980 (mmm) REVERT: R 77 ASP cc_start: 0.8481 (t0) cc_final: 0.8211 (t70) REVERT: R 78 LEU cc_start: 0.8654 (tp) cc_final: 0.8370 (tp) REVERT: R 79 ASP cc_start: 0.8229 (m-30) cc_final: 0.7731 (t0) REVERT: R 188 MET cc_start: 0.8100 (tpp) cc_final: 0.7866 (ttm) REVERT: S 37 ASP cc_start: 0.7263 (t0) cc_final: 0.6393 (t0) REVERT: S 48 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7585 (t0) outliers start: 117 outliers final: 87 residues processed: 764 average time/residue: 0.2050 time to fit residues: 260.1763 Evaluate side-chains 749 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 656 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 75 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 155 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 445 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 381 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN J 66 GLN ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN N 75 GLN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN S 198 HIS ** S 207 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 = 0.3332 r_free = 0.3332 target = 0.099829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.082451 restraints weight = 72556.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085489 restraints weight = 32943.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087479 restraints weight = 19090.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088793 restraints weight = 13040.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089662 restraints weight = 10003.548| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36765 Z= 0.149 Angle : 0.639 12.166 49676 Z= 0.316 Chirality : 0.045 0.196 5575 Planarity : 0.004 0.112 6440 Dihedral : 4.655 112.611 5022 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.78 % Allowed : 19.09 % Favored : 78.12 % 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 (0.13), residues: 4538 helix: 2.07 (0.11), residues: 2111 sheet: -0.65 (0.21), residues: 613 loop : -0.39 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG O 115 TYR 0.064 0.001 TYR C 20 PHE 0.029 0.002 PHE R 200 TRP 0.016 0.001 TRP Q 55 HIS 0.009 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00339 (36765) covalent geometry : angle 0.63867 (49676) hydrogen bonds : bond 0.03875 ( 1954) hydrogen bonds : angle 2.75863 (13794) *********************** 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 768 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 658 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: A 254 CYS cc_start: 0.8778 (m) cc_final: 0.8379 (m) REVERT: A 290 ASP cc_start: 0.8751 (t70) cc_final: 0.8390 (t0) REVERT: A 309 THR cc_start: 0.8735 (m) cc_final: 0.8496 (m) REVERT: A 346 MET cc_start: 0.8188 (ttt) cc_final: 0.7605 (ttt) REVERT: A 485 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7679 (mp0) REVERT: A 510 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 61 MET cc_start: 0.7896 (mtp) cc_final: 0.7451 (ttm) REVERT: B 74 SER cc_start: 0.8562 (m) cc_final: 0.7576 (p) REVERT: B 77 ASP cc_start: 0.8375 (m-30) cc_final: 0.7769 (m-30) REVERT: B 84 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7707 (mmtt) REVERT: B 115 SER cc_start: 0.9003 (t) cc_final: 0.8662 (p) REVERT: B 116 ILE cc_start: 0.9242 (pt) cc_final: 0.9030 (pt) REVERT: B 270 ASP cc_start: 0.7824 (m-30) cc_final: 0.7583 (m-30) REVERT: B 429 VAL cc_start: 0.9599 (m) cc_final: 0.9361 (p) REVERT: B 485 GLU cc_start: 0.8263 (tp30) cc_final: 0.7517 (tp30) REVERT: B 486 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 488 ASP cc_start: 0.8313 (m-30) cc_final: 0.7656 (t0) REVERT: B 565 ILE cc_start: 0.8521 (mt) cc_final: 0.8183 (pt) REVERT: C 30 THR cc_start: 0.8655 (m) cc_final: 0.8236 (p) REVERT: C 123 ASN cc_start: 0.9014 (t0) cc_final: 0.8784 (t0) REVERT: C 299 ASP cc_start: 0.7419 (p0) cc_final: 0.7112 (p0) REVERT: C 449 ASN cc_start: 0.8255 (t0) cc_final: 0.8050 (t0) REVERT: C 466 ASP cc_start: 0.8628 (t70) cc_final: 0.8402 (t0) REVERT: C 484 GLN cc_start: 0.8501 (tp40) cc_final: 0.8188 (tp40) REVERT: C 606 GLU cc_start: 0.8579 (tt0) cc_final: 0.7681 (tp30) REVERT: D 127 MET cc_start: 0.8499 (mtp) cc_final: 0.8146 (mtp) REVERT: D 358 ASN cc_start: 0.8531 (t0) cc_final: 0.8289 (t0) REVERT: D 360 ASP cc_start: 0.8520 (t0) cc_final: 0.8099 (t70) REVERT: D 497 GLN cc_start: 0.8205 (pm20) cc_final: 0.7924 (pp30) REVERT: E 127 MET cc_start: 0.7694 (mtp) cc_final: 0.7450 (mtp) REVERT: E 148 GLU cc_start: 0.8047 (tt0) cc_final: 0.7686 (mt-10) REVERT: E 262 ASN cc_start: 0.8503 (t0) cc_final: 0.8258 (t0) REVERT: E 270 GLU cc_start: 0.8149 (tt0) cc_final: 0.7371 (tm-30) REVERT: E 330 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7565 (t0) REVERT: E 382 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8330 (tp40) REVERT: E 410 MET cc_start: 0.8730 (mpp) cc_final: 0.8499 (mtp) REVERT: F 254 MET cc_start: 0.8123 (tpp) cc_final: 0.7537 (mpp) REVERT: F 299 ASP cc_start: 0.7975 (m-30) cc_final: 0.7480 (m-30) REVERT: F 309 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7869 (tt0) REVERT: F 464 THR cc_start: 0.8849 (m) cc_final: 0.8427 (p) REVERT: F 491 MET cc_start: 0.7803 (mtp) cc_final: 0.7600 (mtp) REVERT: H 193 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8125 (tm-30) REVERT: H 210 LYS cc_start: 0.9193 (tttm) cc_final: 0.8886 (ttmm) REVERT: I 74 ASN cc_start: 0.8979 (t0) cc_final: 0.8495 (t0) REVERT: I 78 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8427 (mm110) REVERT: J 210 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7841 (tt0) REVERT: K 75 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8801 (mm) REVERT: K 96 ASN cc_start: 0.9301 (m-40) cc_final: 0.8941 (m-40) REVERT: K 132 MET cc_start: 0.9235 (mpp) cc_final: 0.8952 (mmm) REVERT: K 143 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (tp) REVERT: K 184 TYR cc_start: 0.8575 (m-80) cc_final: 0.8364 (m-80) REVERT: M 85 GLN cc_start: 0.8543 (tt0) cc_final: 0.8325 (tm-30) REVERT: M 107 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8269 (mmp80) REVERT: N 100 LEU cc_start: 0.8520 (tt) cc_final: 0.8299 (mt) REVERT: O 74 GLU cc_start: 0.8147 (pp20) cc_final: 0.7751 (pp20) REVERT: Q 33 MET cc_start: 0.8394 (tpt) cc_final: 0.8138 (tpp) REVERT: Q 153 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7226 (ttm110) REVERT: Q 161 MET cc_start: 0.8284 (tpp) cc_final: 0.7254 (tpp) REVERT: Q 166 TYR cc_start: 0.8570 (m-80) cc_final: 0.8349 (m-10) REVERT: Q 170 GLU cc_start: 0.6478 (pm20) cc_final: 0.6142 (mp0) REVERT: R 77 ASP cc_start: 0.8531 (t0) cc_final: 0.8256 (t70) REVERT: R 79 ASP cc_start: 0.8236 (m-30) cc_final: 0.7754 (t0) REVERT: S 37 ASP cc_start: 0.7338 (t0) cc_final: 0.6453 (t0) REVERT: S 48 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7658 (t0) REVERT: S 188 MET cc_start: 0.7285 (ttm) cc_final: 0.6913 (ttp) outliers start: 110 outliers final: 91 residues processed: 727 average time/residue: 0.2110 time to fit residues: 254.4999 Evaluate side-chains 739 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 643 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 330 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 395 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN J 66 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 ASN ** N 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN S 198 HIS ** S 207 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 = 0.3264 r_free = 0.3264 target = 0.095535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078516 restraints weight = 73801.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081406 restraints weight = 33695.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083299 restraints weight = 19657.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084557 restraints weight = 13473.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085298 restraints weight = 10379.312| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 36765 Z= 0.284 Angle : 0.734 11.742 49676 Z= 0.371 Chirality : 0.048 0.215 5575 Planarity : 0.005 0.116 6440 Dihedral : 4.918 110.404 5022 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 3.14 % Allowed : 18.87 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4538 helix: 1.87 (0.11), residues: 2122 sheet: -0.89 (0.21), residues: 604 loop : -0.56 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 78 TYR 0.065 0.002 TYR C 20 PHE 0.021 0.002 PHE B 472 TRP 0.017 0.002 TRP S 122 HIS 0.055 0.002 HIS S 198 Details of bonding type rmsd covalent geometry : bond 0.00650 (36765) covalent geometry : angle 0.73371 (49676) hydrogen bonds : bond 0.04353 ( 1954) hydrogen bonds : angle 2.90144 (13794) ********************** 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 775 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 651 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8353 (ptp90) REVERT: A 254 CYS cc_start: 0.8827 (m) cc_final: 0.8389 (m) REVERT: A 290 ASP cc_start: 0.8787 (t70) cc_final: 0.8406 (t0) REVERT: A 346 MET cc_start: 0.8253 (ttt) cc_final: 0.7707 (ttt) REVERT: A 485 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7705 (mp0) REVERT: A 510 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 74 SER cc_start: 0.8629 (m) cc_final: 0.7497 (p) REVERT: B 77 ASP cc_start: 0.8360 (m-30) cc_final: 0.7587 (m-30) REVERT: B 115 SER cc_start: 0.9065 (t) cc_final: 0.8754 (p) REVERT: B 116 ILE cc_start: 0.9305 (pt) cc_final: 0.9031 (pt) REVERT: B 201 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 270 ASP cc_start: 0.8032 (m-30) cc_final: 0.7794 (m-30) REVERT: B 429 VAL cc_start: 0.9663 (m) cc_final: 0.9440 (p) REVERT: B 485 GLU cc_start: 0.8324 (tp30) cc_final: 0.7629 (tp30) REVERT: B 486 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 488 ASP cc_start: 0.8423 (m-30) cc_final: 0.7756 (t0) REVERT: B 565 ILE cc_start: 0.8523 (mt) cc_final: 0.8231 (mp) REVERT: C 84 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8171 (pttm) REVERT: C 284 MET cc_start: 0.8671 (tpp) cc_final: 0.7732 (mpp) REVERT: C 299 ASP cc_start: 0.7557 (p0) cc_final: 0.7273 (p0) REVERT: C 449 ASN cc_start: 0.8210 (t0) cc_final: 0.7985 (t0) REVERT: C 466 ASP cc_start: 0.8736 (t70) cc_final: 0.8469 (t0) REVERT: C 484 GLN cc_start: 0.8496 (tp40) cc_final: 0.8234 (tp-100) REVERT: C 606 GLU cc_start: 0.8591 (tt0) cc_final: 0.7698 (tp30) REVERT: D 127 MET cc_start: 0.8645 (mtp) cc_final: 0.8291 (mtp) REVERT: D 257 VAL cc_start: 0.9200 (t) cc_final: 0.8935 (p) REVERT: D 262 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8385 (t0) REVERT: D 358 ASN cc_start: 0.8619 (t0) cc_final: 0.8358 (t0) REVERT: D 360 ASP cc_start: 0.8661 (t0) cc_final: 0.8270 (t0) REVERT: D 497 GLN cc_start: 0.8271 (pm20) cc_final: 0.8005 (pp30) REVERT: E 256 ASN cc_start: 0.8203 (m-40) cc_final: 0.7728 (p0) REVERT: E 270 GLU cc_start: 0.8250 (tt0) cc_final: 0.7735 (tm-30) REVERT: E 330 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.7723 (t0) REVERT: E 410 MET cc_start: 0.8829 (mpp) cc_final: 0.8547 (mtp) REVERT: F 254 MET cc_start: 0.8308 (tpp) cc_final: 0.7676 (mpp) REVERT: F 299 ASP cc_start: 0.8270 (m-30) cc_final: 0.7767 (m-30) REVERT: F 309 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7968 (tt0) REVERT: F 464 THR cc_start: 0.8905 (m) cc_final: 0.8566 (p) REVERT: F 491 MET cc_start: 0.7913 (mtp) cc_final: 0.7710 (mtp) REVERT: H 193 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8152 (tm-30) REVERT: H 210 LYS cc_start: 0.9188 (tttm) cc_final: 0.8869 (ttmm) REVERT: I 74 ASN cc_start: 0.9014 (t0) cc_final: 0.8554 (t0) REVERT: I 78 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8553 (mm110) REVERT: J 210 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7964 (tt0) REVERT: J 223 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8360 (mptt) REVERT: K 96 ASN cc_start: 0.9322 (m-40) cc_final: 0.8972 (m-40) REVERT: K 132 MET cc_start: 0.9093 (mpp) cc_final: 0.8748 (mmm) REVERT: K 143 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8299 (tp) REVERT: K 184 TYR cc_start: 0.8670 (m-80) cc_final: 0.8303 (m-80) REVERT: M 75 GLN cc_start: 0.9046 (pp30) cc_final: 0.8756 (pp30) REVERT: M 85 GLN cc_start: 0.8605 (tt0) cc_final: 0.8350 (tm-30) REVERT: M 107 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8296 (mmp80) REVERT: N 100 LEU cc_start: 0.8540 (tt) cc_final: 0.8312 (mt) REVERT: O 74 GLU cc_start: 0.8302 (pp20) cc_final: 0.7829 (pp20) REVERT: Q 33 MET cc_start: 0.8455 (tpt) cc_final: 0.8184 (tpp) REVERT: Q 37 ASP cc_start: 0.8078 (t0) cc_final: 0.7216 (t0) REVERT: Q 48 ASP cc_start: 0.8878 (t70) cc_final: 0.8376 (t0) REVERT: Q 151 PHE cc_start: 0.8251 (m-10) cc_final: 0.7725 (m-80) REVERT: Q 153 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7289 (ttm110) REVERT: Q 221 ASP cc_start: 0.7881 (m-30) cc_final: 0.7496 (m-30) REVERT: R 77 ASP cc_start: 0.8620 (t0) cc_final: 0.8350 (t70) REVERT: R 79 ASP cc_start: 0.8283 (m-30) cc_final: 0.7721 (t0) REVERT: S 37 ASP cc_start: 0.7291 (t0) cc_final: 0.6415 (t0) REVERT: S 48 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7710 (t0) REVERT: S 57 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: S 188 MET cc_start: 0.7166 (ttm) cc_final: 0.6963 (ttp) outliers start: 124 outliers final: 103 residues processed: 727 average time/residue: 0.2062 time to fit residues: 249.3669 Evaluate side-chains 740 residues out of total 3955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 631 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain M residue 91 ASN Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 230 ILE Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 57 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 271 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 290 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN ** N 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN ** S 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.078660 restraints weight = 73091.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.081558 restraints weight = 33587.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083452 restraints weight = 19660.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.084706 restraints weight = 13531.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085528 restraints weight = 10474.654| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.209 36765 Z= 0.263 Angle : 0.891 59.199 49676 Z= 0.490 Chirality : 0.047 0.227 5575 Planarity : 0.005 0.115 6440 Dihedral : 4.921 110.263 5022 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.11 % Allowed : 19.35 % Favored : 77.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4538 helix: 1.88 (0.11), residues: 2122 sheet: -0.91 (0.21), residues: 604 loop : -0.56 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 115 TYR 0.053 0.002 TYR C 20 PHE 0.020 0.002 PHE B 472 TRP 0.016 0.002 TRP S 122 HIS 0.034 0.001 HIS S 198 Details of bonding type rmsd covalent geometry : bond 0.00609 (36765) covalent geometry : angle 0.89084 (49676) hydrogen bonds : bond 0.04314 ( 1954) hydrogen bonds : angle 2.89902 (13794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6978.84 seconds wall clock time: 120 minutes 49.72 seconds (7249.72 seconds total)