Starting phenix.real_space_refine on Sat Feb 7 00:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vaj_31843/02_2026/7vaj_31843.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Time building chain proxies: 6.73, per 1000 atoms: 0.23 Number of scatterers: 29462 At special positions: 0 Unit cell: (147.84, 145.2, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5538 8.00 N 5116 7.00 C 18705 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: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 29 sheets defined 46.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.701A pdb=" N THR A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.120A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.801A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.705A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.112A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.992A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 removed outlier: 4.254A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.791A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 4.029A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.040A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.826A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.012A pdb=" N GLU B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 5.120A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.561A pdb=" N LEU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.874A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.651A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 3.828A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.731A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.792A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 578 removed outlier: 3.850A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.642A pdb=" N GLY C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.118A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.381A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.626A pdb=" N ARG C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.727A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.958A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.081A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.756A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.577A pdb=" N ALA C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.612A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.504A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.539A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.021A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.815A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.555A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.548A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.956A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 366' Processing helix chain 'D' and resid 374 through 400 removed outlier: 4.017A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.747A pdb=" N LEU D 404 " --> pdb=" O GLU D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.076A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.596A pdb=" N ARG E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.445A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.789A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.729A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.584A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.584A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 4.064A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 396 removed outlier: 3.553A pdb=" N ASN E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.579A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 4.045A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.803A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.642A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.583A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.893A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.703A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.123A pdb=" N VAL F 366 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.943A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.773A pdb=" N ARG F 409 " --> pdb=" O THR F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 4.039A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.820A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 121 through 209 removed outlier: 3.980A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.471A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.911A pdb=" N GLU H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 76 through 83 removed outlier: 4.075A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.650A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 105 Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.058A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 94 Processing helix chain 'J' and resid 99 through 115 removed outlier: 4.579A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 166 through 187 removed outlier: 5.376A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 4.295A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 130 Proline residue: L 129 - end of helix Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.502A pdb=" N ALA L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 131 through 136' Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.016A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.689A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.616A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 35 through 43 removed outlier: 6.280A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 43 " --> pdb=" O THR B 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.801A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 43 " --> pdb=" O THR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 6.073A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 5.752A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.730A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.831A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.792A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.839A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.631A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.834A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.639A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.760A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.540A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.759A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.531A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.916A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 219 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.517A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.644A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.696A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 313 through 315 Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AD2, first strand: chain 'H' and resid 44 through 48 removed outlier: 6.506A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 1235 hydrogen bonds defined for protein. 3558 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: 5.66 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9659 1.33 - 1.45: 3809 1.45 - 1.57: 16353 1.57 - 1.69: 0 1.69 - 1.81: 194 Bond restraints: 30015 Sorted by residual: bond pdb=" C THR E 107 " pdb=" N PRO E 108 " ideal model delta sigma weight residual 1.335 1.309 0.026 8.70e-03 1.32e+04 9.09e+00 bond pdb=" C ARG B 89 " pdb=" N PRO B 90 " ideal model delta sigma weight residual 1.333 1.313 0.021 1.01e-02 9.80e+03 4.14e+00 bond pdb=" C ALA L 123 " pdb=" N ASN L 124 " ideal model delta sigma weight residual 1.331 1.289 0.042 2.07e-02 2.33e+03 4.05e+00 bond pdb=" C LEU L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CA THR F 107 " pdb=" CB THR F 107 " ideal model delta sigma weight residual 1.531 1.506 0.025 1.36e-02 5.41e+03 3.49e+00 ... (remaining 30010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 39985 2.44 - 4.88: 614 4.88 - 7.32: 50 7.32 - 9.76: 6 9.76 - 12.20: 3 Bond angle restraints: 40658 Sorted by residual: angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 123.16 117.86 5.30 1.06e+00 8.90e-01 2.50e+01 angle pdb=" C ILE F 352 " pdb=" N ASP F 353 " pdb=" CA ASP F 353 " ideal model delta sigma weight residual 122.31 111.64 10.67 2.34e+00 1.83e-01 2.08e+01 angle pdb=" N ILE E 96 " pdb=" CA ILE E 96 " pdb=" C ILE E 96 " ideal model delta sigma weight residual 111.77 107.91 3.86 1.04e+00 9.25e-01 1.38e+01 angle pdb=" N ILE D 96 " pdb=" CA ILE D 96 " pdb=" C ILE D 96 " ideal model delta sigma weight residual 112.43 109.05 3.38 9.20e-01 1.18e+00 1.35e+01 angle pdb=" N TRP J 100 " pdb=" CA TRP J 100 " pdb=" C TRP J 100 " ideal model delta sigma weight residual 109.81 116.59 -6.78 2.21e+00 2.05e-01 9.41e+00 ... (remaining 40653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16452 17.90 - 35.81: 1562 35.81 - 53.71: 226 53.71 - 71.62: 40 71.62 - 89.52: 24 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N ASN E 23 " pdb=" CA ASN E 23 " ideal model delta harmonic sigma weight residual -180.00 -123.83 -56.17 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ALA B 16 " pdb=" C ALA B 16 " pdb=" N LYS B 17 " pdb=" CA LYS B 17 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2600 0.038 - 0.077: 1349 0.077 - 0.115: 495 0.115 - 0.154: 109 0.154 - 0.192: 7 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA PRO C 420 " pdb=" N PRO C 420 " pdb=" C PRO C 420 " pdb=" CB PRO C 420 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL G 89 " pdb=" CA VAL G 89 " pdb=" CG1 VAL G 89 " pdb=" CG2 VAL G 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY G 72 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO G 73 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 73 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 73 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 262 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C MET B 262 " -0.040 2.00e-02 2.50e+03 pdb=" O MET B 262 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 263 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 344 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO C 345 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.027 5.00e-02 4.00e+02 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 352 2.64 - 3.21: 27788 3.21 - 3.77: 43705 3.77 - 4.34: 61599 4.34 - 4.90: 103621 Nonbonded interactions: 237065 Sorted by model distance: nonbonded pdb=" O PRO E 354 " pdb=" OH TYR E 383 " model vdw 2.081 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.098 3.040 nonbonded pdb=" O GLY E 464 " pdb=" NZ LYS E 466 " model vdw 2.114 3.120 nonbonded pdb=" OG1 THR F 197 " pdb=" OE1 GLU F 200 " model vdw 2.124 3.040 nonbonded pdb=" OE1 GLU F 109 " pdb=" OH TYR F 244 " model vdw 2.135 3.040 ... (remaining 237060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.230 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 0.071 30015 Z= 0.416 Angle : 0.788 12.200 40658 Z= 0.441 Chirality : 0.051 0.192 4560 Planarity : 0.005 0.058 5330 Dihedral : 14.014 89.523 11386 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.12), residues: 3764 helix: -1.02 (0.12), residues: 1478 sheet: -1.52 (0.21), residues: 530 loop : -2.20 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 417 TYR 0.020 0.002 TYR G 61 PHE 0.023 0.002 PHE A 230 TRP 0.009 0.002 TRP B 330 HIS 0.006 0.001 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00973 (30015) covalent geometry : angle 0.78817 (40658) hydrogen bonds : bond 0.15706 ( 1235) hydrogen bonds : angle 6.43162 ( 3558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5849 (mmm) cc_final: 0.5495 (pmm) REVERT: A 3 GLN cc_start: 0.8249 (pt0) cc_final: 0.7997 (pt0) REVERT: A 62 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 179 THR cc_start: 0.7144 (m) cc_final: 0.6561 (p) REVERT: A 230 PHE cc_start: 0.7455 (p90) cc_final: 0.7123 (p90) REVERT: A 239 GLN cc_start: 0.7321 (mt0) cc_final: 0.7050 (mt0) REVERT: A 268 GLU cc_start: 0.7794 (tp30) cc_final: 0.7538 (tt0) REVERT: A 456 GLU cc_start: 0.6974 (tt0) cc_final: 0.6718 (mt-10) REVERT: A 509 MET cc_start: 0.7832 (ttm) cc_final: 0.7222 (ttt) REVERT: B 95 ARG cc_start: 0.7437 (ttt180) cc_final: 0.7179 (ttt-90) REVERT: B 109 HIS cc_start: 0.7838 (m-70) cc_final: 0.7625 (m90) REVERT: B 262 MET cc_start: 0.7172 (pmm) cc_final: 0.6969 (pmm) REVERT: B 348 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 397 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7506 (mm110) REVERT: B 459 GLN cc_start: 0.7637 (tp40) cc_final: 0.7436 (mt0) REVERT: B 480 GLU cc_start: 0.7502 (mp0) cc_final: 0.7024 (mt-10) REVERT: B 481 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.7215 (tpt90) REVERT: B 488 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6443 (ttp-170) REVERT: B 489 ILE cc_start: 0.7834 (mt) cc_final: 0.7610 (tt) REVERT: B 571 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6589 (mp10) REVERT: C 93 ARG cc_start: 0.7497 (mmt-90) cc_final: 0.7284 (mmt90) REVERT: C 124 LYS cc_start: 0.7969 (mttp) cc_final: 0.7550 (mtmt) REVERT: C 261 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6975 (mt-10) REVERT: C 268 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6515 (mt-10) REVERT: C 416 ARG cc_start: 0.8044 (ptp-110) cc_final: 0.7716 (ptp-170) REVERT: C 469 GLN cc_start: 0.7632 (tp40) cc_final: 0.7403 (mm-40) REVERT: D 296 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 301 VAL cc_start: 0.8993 (m) cc_final: 0.8684 (t) REVERT: D 331 TYR cc_start: 0.6937 (m-10) cc_final: 0.6610 (m-10) REVERT: D 368 LYS cc_start: 0.6974 (ptmm) cc_final: 0.6465 (pttm) REVERT: D 388 ASN cc_start: 0.7951 (m-40) cc_final: 0.7623 (m-40) REVERT: D 391 ASP cc_start: 0.7632 (t0) cc_final: 0.7160 (t0) REVERT: D 411 TYR cc_start: 0.7833 (m-80) cc_final: 0.7587 (m-80) REVERT: E 6 LYS cc_start: 0.7691 (tttt) cc_final: 0.7172 (ptpt) REVERT: E 53 GLU cc_start: 0.6718 (tt0) cc_final: 0.6301 (tt0) REVERT: E 117 LEU cc_start: 0.8641 (mt) cc_final: 0.8242 (mp) REVERT: E 345 ARG cc_start: 0.7435 (mmt90) cc_final: 0.7197 (mtt90) REVERT: E 393 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.8184 (ttp-170) REVERT: E 420 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7127 (ttm-80) REVERT: E 466 LYS cc_start: 0.6471 (mmtm) cc_final: 0.5070 (tppp) REVERT: F 6 LYS cc_start: 0.7540 (tttt) cc_final: 0.7016 (mttt) REVERT: F 7 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7126 (tt0) REVERT: F 25 LYS cc_start: 0.7807 (ptpt) cc_final: 0.7270 (pptt) REVERT: F 162 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6763 (tt0) REVERT: G 30 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7480 (mttm) REVERT: G 47 MET cc_start: 0.6805 (ptm) cc_final: 0.6153 (ptt) REVERT: G 180 GLN cc_start: 0.8228 (tt0) cc_final: 0.7921 (mt0) REVERT: H 63 MET cc_start: 0.3808 (mmm) cc_final: 0.2860 (mtm) REVERT: J 61 GLU cc_start: 0.2371 (pm20) cc_final: 0.2025 (mt-10) REVERT: J 65 GLU cc_start: 0.5832 (mp0) cc_final: 0.5544 (mp0) REVERT: J 78 GLU cc_start: 0.4491 (mt-10) cc_final: 0.4249 (mt-10) REVERT: J 82 GLU cc_start: 0.4884 (mm-30) cc_final: 0.4669 (mm-30) REVERT: J 136 ARG cc_start: 0.3979 (mmp80) cc_final: 0.3689 (ttm170) REVERT: J 150 LEU cc_start: 0.5532 (pp) cc_final: 0.4743 (tp) REVERT: J 160 LYS cc_start: 0.7072 (mttm) cc_final: 0.6063 (mmtt) REVERT: J 164 GLU cc_start: 0.6989 (tt0) cc_final: 0.6722 (tt0) REVERT: J 165 ASN cc_start: 0.6806 (t0) cc_final: 0.6272 (t0) REVERT: L 85 ARG cc_start: 0.5667 (tmm160) cc_final: 0.5199 (ttm-80) REVERT: L 86 ARG cc_start: 0.6231 (tpp80) cc_final: 0.5715 (mtt-85) outliers start: 2 outliers final: 1 residues processed: 519 average time/residue: 0.2532 time to fit residues: 189.6833 Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 457 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN B 316 GLN B 397 GLN B 477 GLN D 310 GLN E 58 GLN E 170 GLN E 249 HIS E 252 HIS E 407 ASN F 413 GLN F 448 GLN G 13 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098932 restraints weight = 46260.169| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.52 r_work: 0.3080 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30015 Z= 0.135 Angle : 0.583 9.535 40658 Z= 0.299 Chirality : 0.045 0.152 4560 Planarity : 0.005 0.045 5330 Dihedral : 4.569 51.723 4182 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.33 % Allowed : 11.16 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3764 helix: 0.53 (0.14), residues: 1519 sheet: -1.04 (0.22), residues: 527 loop : -1.47 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 88 TYR 0.012 0.001 TYR G 61 PHE 0.026 0.001 PHE B 143 TRP 0.009 0.001 TRP C 119 HIS 0.005 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00290 (30015) covalent geometry : angle 0.58313 (40658) hydrogen bonds : bond 0.05138 ( 1235) hydrogen bonds : angle 4.88627 ( 3558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6353 (mmm) cc_final: 0.5773 (pmm) REVERT: A 179 THR cc_start: 0.7090 (m) cc_final: 0.6593 (p) REVERT: A 268 GLU cc_start: 0.8193 (tp30) cc_final: 0.7865 (tt0) REVERT: A 456 GLU cc_start: 0.7840 (tt0) cc_final: 0.7598 (mt-10) REVERT: A 540 LEU cc_start: 0.7910 (mt) cc_final: 0.7516 (mp) REVERT: B 15 ILE cc_start: 0.8140 (mm) cc_final: 0.7662 (mm) REVERT: B 54 ASP cc_start: 0.7650 (p0) cc_final: 0.7165 (p0) REVERT: B 344 MET cc_start: 0.8588 (mmm) cc_final: 0.8266 (tmm) REVERT: B 468 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8044 (m) REVERT: B 480 GLU cc_start: 0.7792 (mp0) cc_final: 0.7542 (mt-10) REVERT: B 481 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.6939 (ttp-110) REVERT: B 525 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 264 ASP cc_start: 0.7620 (m-30) cc_final: 0.7415 (m-30) REVERT: C 268 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 416 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.8041 (ptp-170) REVERT: C 469 GLN cc_start: 0.7649 (tp40) cc_final: 0.7443 (mm-40) REVERT: C 547 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7577 (mmm160) REVERT: D 258 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6096 (m) REVERT: D 388 ASN cc_start: 0.8572 (m-40) cc_final: 0.8357 (m-40) REVERT: D 391 ASP cc_start: 0.8307 (t0) cc_final: 0.8100 (t70) REVERT: D 411 TYR cc_start: 0.8307 (m-80) cc_final: 0.8076 (m-80) REVERT: E 53 GLU cc_start: 0.7351 (tt0) cc_final: 0.7086 (tt0) REVERT: E 183 LYS cc_start: 0.5435 (mmtt) cc_final: 0.5122 (mmmt) REVERT: E 420 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7541 (mtp85) REVERT: E 466 LYS cc_start: 0.6169 (mmtm) cc_final: 0.5184 (tppt) REVERT: F 25 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7584 (pptt) REVERT: F 230 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7957 (mt-10) REVERT: F 318 ASP cc_start: 0.7818 (t0) cc_final: 0.7453 (t70) REVERT: F 394 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7558 (tptp) REVERT: F 434 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7396 (mt-10) REVERT: G 47 MET cc_start: 0.7423 (ptm) cc_final: 0.6897 (ptt) REVERT: G 58 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5916 (mtpp) REVERT: G 103 ARG cc_start: 0.6962 (ttt90) cc_final: 0.6734 (ttm-80) REVERT: G 152 GLU cc_start: 0.7656 (tp30) cc_final: 0.7399 (tp30) REVERT: G 169 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7780 (mp) REVERT: G 180 GLN cc_start: 0.8672 (tt0) cc_final: 0.8442 (mt0) REVERT: G 195 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8047 (tptt) REVERT: H 63 MET cc_start: 0.3860 (mmm) cc_final: 0.2964 (mtm) REVERT: H 104 LEU cc_start: 0.4169 (mp) cc_final: 0.3847 (tp) REVERT: J 61 GLU cc_start: 0.2707 (pm20) cc_final: 0.2280 (mt-10) REVERT: J 82 GLU cc_start: 0.5454 (mm-30) cc_final: 0.5097 (mm-30) REVERT: J 119 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7127 (tttt) REVERT: J 136 ARG cc_start: 0.3947 (mmp80) cc_final: 0.3507 (tpp80) REVERT: J 150 LEU cc_start: 0.6040 (pp) cc_final: 0.5164 (tp) REVERT: J 160 LYS cc_start: 0.7695 (mttm) cc_final: 0.6867 (mmtt) REVERT: J 165 ASN cc_start: 0.6673 (t0) cc_final: 0.6290 (t0) REVERT: L 85 ARG cc_start: 0.6058 (tmm160) cc_final: 0.5664 (ttm-80) REVERT: L 88 ARG cc_start: 0.6939 (ttp80) cc_final: 0.6301 (ttp80) REVERT: L 105 ARG cc_start: 0.6408 (mtm-85) cc_final: 0.6014 (ttp-110) outliers start: 41 outliers final: 17 residues processed: 405 average time/residue: 0.2422 time to fit residues: 146.4113 Evaluate side-chains 335 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 461 LYS Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain L residue 74 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 40 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 0.0570 chunk 169 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 235 optimal weight: 0.2980 chunk 3 optimal weight: 8.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN F 413 GLN G 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100934 restraints weight = 46321.078| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.47 r_work: 0.3096 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30015 Z= 0.116 Angle : 0.530 10.146 40658 Z= 0.270 Chirality : 0.044 0.144 4560 Planarity : 0.004 0.043 5330 Dihedral : 4.263 49.246 4180 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.65 % Allowed : 12.91 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.29 (0.14), residues: 3764 helix: 1.06 (0.14), residues: 1523 sheet: -0.75 (0.23), residues: 526 loop : -1.14 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 156 TYR 0.010 0.001 TYR F 203 PHE 0.027 0.001 PHE B 143 TRP 0.009 0.001 TRP B 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00259 (30015) covalent geometry : angle 0.53023 (40658) hydrogen bonds : bond 0.04411 ( 1235) hydrogen bonds : angle 4.54285 ( 3558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6299 (mmm) cc_final: 0.5705 (pmm) REVERT: A 179 THR cc_start: 0.7046 (m) cc_final: 0.6607 (p) REVERT: A 268 GLU cc_start: 0.8094 (tp30) cc_final: 0.7820 (tt0) REVERT: A 492 GLU cc_start: 0.7781 (pt0) cc_final: 0.7428 (pt0) REVERT: B 38 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 54 ASP cc_start: 0.7589 (p0) cc_final: 0.7096 (p0) REVERT: B 344 MET cc_start: 0.8560 (mmm) cc_final: 0.8213 (tmm) REVERT: B 480 GLU cc_start: 0.7719 (mp0) cc_final: 0.7465 (mt-10) REVERT: B 481 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7581 (tpt-90) REVERT: B 488 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7265 (ttt-90) REVERT: C 268 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7438 (mt-10) REVERT: C 416 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.7964 (ptp-170) REVERT: C 547 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7676 (mmm160) REVERT: D 258 THR cc_start: 0.6312 (OUTLIER) cc_final: 0.5873 (m) REVERT: D 388 ASN cc_start: 0.8519 (m-40) cc_final: 0.8305 (m-40) REVERT: D 411 TYR cc_start: 0.8295 (m-80) cc_final: 0.8070 (m-80) REVERT: E 53 GLU cc_start: 0.7350 (tt0) cc_final: 0.7130 (tt0) REVERT: E 183 LYS cc_start: 0.5407 (mmtt) cc_final: 0.4995 (mmmt) REVERT: E 302 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: E 420 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7496 (mtp85) REVERT: E 466 LYS cc_start: 0.6052 (mmtm) cc_final: 0.5175 (tppt) REVERT: F 25 LYS cc_start: 0.7825 (ptpt) cc_final: 0.7595 (pptt) REVERT: F 230 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7842 (mt-10) REVERT: F 318 ASP cc_start: 0.7650 (t0) cc_final: 0.7321 (t70) REVERT: F 394 LYS cc_start: 0.7855 (mmmt) cc_final: 0.7556 (tptp) REVERT: F 434 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7474 (mt-10) REVERT: G 47 MET cc_start: 0.7428 (ptm) cc_final: 0.6913 (ptt) REVERT: G 58 LYS cc_start: 0.6363 (mmtt) cc_final: 0.5970 (mtpp) REVERT: G 152 GLU cc_start: 0.7696 (tp30) cc_final: 0.7413 (tp30) REVERT: G 169 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7672 (mp) REVERT: G 180 GLN cc_start: 0.8643 (tt0) cc_final: 0.8387 (mt0) REVERT: G 195 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8091 (tptt) REVERT: H 63 MET cc_start: 0.3860 (mmm) cc_final: 0.3075 (mtm) REVERT: H 104 LEU cc_start: 0.4051 (mp) cc_final: 0.3786 (tp) REVERT: J 61 GLU cc_start: 0.2680 (pm20) cc_final: 0.2169 (mt-10) REVERT: J 82 GLU cc_start: 0.5557 (mm-30) cc_final: 0.5267 (mm-30) REVERT: J 119 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7292 (tttt) REVERT: J 136 ARG cc_start: 0.4045 (mmp80) cc_final: 0.3604 (tpp80) REVERT: J 150 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5161 (tp) REVERT: J 160 LYS cc_start: 0.7620 (mttm) cc_final: 0.6926 (mmtt) REVERT: J 165 ASN cc_start: 0.6619 (t0) cc_final: 0.6242 (t0) REVERT: L 81 GLU cc_start: 0.7745 (tt0) cc_final: 0.7089 (mt-10) REVERT: L 85 ARG cc_start: 0.6027 (tmm160) cc_final: 0.5381 (ttm-80) REVERT: L 88 ARG cc_start: 0.6807 (ttp80) cc_final: 0.6200 (ttp80) REVERT: L 89 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: L 105 ARG cc_start: 0.6460 (mtm-85) cc_final: 0.6136 (ttp-110) REVERT: L 130 HIS cc_start: 0.5403 (m-70) cc_final: 0.4954 (m-70) outliers start: 51 outliers final: 23 residues processed: 377 average time/residue: 0.2198 time to fit residues: 126.2140 Evaluate side-chains 335 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 10 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098607 restraints weight = 46065.362| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.51 r_work: 0.3077 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30015 Z= 0.168 Angle : 0.577 9.093 40658 Z= 0.293 Chirality : 0.046 0.166 4560 Planarity : 0.005 0.042 5330 Dihedral : 4.446 50.954 4180 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.50 % Allowed : 13.46 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.21 (0.14), residues: 3764 helix: 1.11 (0.14), residues: 1530 sheet: -0.64 (0.22), residues: 541 loop : -1.10 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 130 TYR 0.011 0.001 TYR C 25 PHE 0.031 0.002 PHE A 230 TRP 0.009 0.001 TRP B 119 HIS 0.005 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00408 (30015) covalent geometry : angle 0.57677 (40658) hydrogen bonds : bond 0.04961 ( 1235) hydrogen bonds : angle 4.55199 ( 3558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 309 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6304 (mmm) cc_final: 0.5686 (pmm) REVERT: A 122 MET cc_start: 0.7525 (ttm) cc_final: 0.7295 (ttt) REVERT: A 179 THR cc_start: 0.6959 (m) cc_final: 0.6542 (p) REVERT: A 268 GLU cc_start: 0.8125 (tp30) cc_final: 0.7841 (tt0) REVERT: A 492 GLU cc_start: 0.7887 (pt0) cc_final: 0.7685 (tt0) REVERT: A 540 LEU cc_start: 0.7873 (mt) cc_final: 0.7287 (mp) REVERT: A 558 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7036 (mt-10) REVERT: B 15 ILE cc_start: 0.8127 (mm) cc_final: 0.7748 (mm) REVERT: B 54 ASP cc_start: 0.7615 (p0) cc_final: 0.7138 (p0) REVERT: B 344 MET cc_start: 0.8553 (mmm) cc_final: 0.8221 (tmm) REVERT: B 467 ILE cc_start: 0.8528 (tt) cc_final: 0.8066 (mt) REVERT: B 480 GLU cc_start: 0.7705 (mp0) cc_final: 0.7439 (mt-10) REVERT: C 241 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (tt) REVERT: C 268 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 287 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 416 ARG cc_start: 0.8349 (ptp-110) cc_final: 0.7997 (ptp-170) REVERT: C 547 ARG cc_start: 0.8138 (tpp-160) cc_final: 0.7697 (mmm160) REVERT: D 388 ASN cc_start: 0.8514 (m-40) cc_final: 0.8286 (m-40) REVERT: E 53 GLU cc_start: 0.7295 (tt0) cc_final: 0.7056 (tt0) REVERT: E 275 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7628 (mt-10) REVERT: E 450 GLU cc_start: 0.6334 (mp0) cc_final: 0.5713 (mm-30) REVERT: E 466 LYS cc_start: 0.6107 (mmtm) cc_final: 0.5237 (tppt) REVERT: F 25 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7630 (pptt) REVERT: F 230 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7860 (mt-10) REVERT: F 318 ASP cc_start: 0.7762 (t0) cc_final: 0.7279 (t0) REVERT: F 394 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7597 (tptp) REVERT: F 434 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7552 (mt-10) REVERT: G 47 MET cc_start: 0.7448 (ptm) cc_final: 0.6925 (ptt) REVERT: G 58 LYS cc_start: 0.6376 (mmtt) cc_final: 0.5982 (mtpp) REVERT: G 71 ASP cc_start: 0.5584 (OUTLIER) cc_final: 0.5068 (m-30) REVERT: G 152 GLU cc_start: 0.7783 (tp30) cc_final: 0.7487 (tp30) REVERT: G 169 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7761 (mp) REVERT: G 180 GLN cc_start: 0.8729 (tt0) cc_final: 0.8469 (mt0) REVERT: G 195 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8082 (tptt) REVERT: H 18 LEU cc_start: 0.2843 (OUTLIER) cc_final: 0.2223 (mp) REVERT: H 63 MET cc_start: 0.3949 (mmm) cc_final: 0.3068 (mtm) REVERT: H 104 LEU cc_start: 0.4214 (mp) cc_final: 0.3903 (tp) REVERT: J 61 GLU cc_start: 0.2828 (pm20) cc_final: 0.2230 (mt-10) REVERT: J 82 GLU cc_start: 0.5673 (mm-30) cc_final: 0.5305 (mm-30) REVERT: J 119 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7223 (tttt) REVERT: J 136 ARG cc_start: 0.4151 (mmp80) cc_final: 0.3737 (tpp80) REVERT: J 150 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5267 (tp) REVERT: J 160 LYS cc_start: 0.7631 (mttm) cc_final: 0.6910 (mmtt) REVERT: J 165 ASN cc_start: 0.6745 (t0) cc_final: 0.6350 (t0) REVERT: L 85 ARG cc_start: 0.6000 (tmm160) cc_final: 0.5344 (ttm-80) REVERT: L 88 ARG cc_start: 0.6837 (ttp80) cc_final: 0.6585 (ttp80) REVERT: L 89 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: L 105 ARG cc_start: 0.6490 (mtm-85) cc_final: 0.6242 (ttp-110) REVERT: L 130 HIS cc_start: 0.5455 (m-70) cc_final: 0.5007 (m-70) outliers start: 77 outliers final: 50 residues processed: 369 average time/residue: 0.2061 time to fit residues: 117.8288 Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 139 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100394 restraints weight = 46087.687| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.50 r_work: 0.3102 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30015 Z= 0.117 Angle : 0.521 9.295 40658 Z= 0.265 Chirality : 0.043 0.168 4560 Planarity : 0.004 0.044 5330 Dihedral : 4.230 47.770 4180 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 14.27 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.00 (0.14), residues: 3764 helix: 1.29 (0.14), residues: 1526 sheet: -0.57 (0.22), residues: 552 loop : -0.98 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 130 TYR 0.009 0.001 TYR F 463 PHE 0.025 0.001 PHE B 143 TRP 0.009 0.001 TRP B 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00267 (30015) covalent geometry : angle 0.52060 (40658) hydrogen bonds : bond 0.04292 ( 1235) hydrogen bonds : angle 4.40253 ( 3558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6244 (mmm) cc_final: 0.5708 (pmm) REVERT: A 122 MET cc_start: 0.7474 (ttm) cc_final: 0.7244 (ttt) REVERT: A 179 THR cc_start: 0.6959 (m) cc_final: 0.6542 (p) REVERT: A 268 GLU cc_start: 0.8097 (tp30) cc_final: 0.7834 (tt0) REVERT: B 38 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6865 (mt-10) REVERT: B 54 ASP cc_start: 0.7625 (p0) cc_final: 0.7197 (p0) REVERT: B 344 MET cc_start: 0.8541 (mmm) cc_final: 0.8215 (tmm) REVERT: B 480 GLU cc_start: 0.7662 (mp0) cc_final: 0.7435 (mt-10) REVERT: C 241 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8265 (tt) REVERT: C 268 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7348 (mt-10) REVERT: C 416 ARG cc_start: 0.8316 (ptp-110) cc_final: 0.7976 (ptp-170) REVERT: C 547 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7808 (ttm110) REVERT: D 258 THR cc_start: 0.6334 (OUTLIER) cc_final: 0.5925 (m) REVERT: D 388 ASN cc_start: 0.8530 (m-40) cc_final: 0.8313 (m-40) REVERT: D 456 LYS cc_start: 0.6523 (mmmt) cc_final: 0.6260 (mtmt) REVERT: E 53 GLU cc_start: 0.7202 (tt0) cc_final: 0.7001 (tt0) REVERT: E 275 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7597 (mt-10) REVERT: E 450 GLU cc_start: 0.6317 (mp0) cc_final: 0.5764 (mm-30) REVERT: E 466 LYS cc_start: 0.5997 (mmtm) cc_final: 0.5170 (tppt) REVERT: F 25 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7629 (pptt) REVERT: F 230 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7809 (mt-10) REVERT: F 394 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7582 (tptp) REVERT: F 434 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7517 (mt-10) REVERT: G 47 MET cc_start: 0.7468 (ptm) cc_final: 0.6956 (ptt) REVERT: G 58 LYS cc_start: 0.6430 (mmtt) cc_final: 0.6039 (mtpp) REVERT: G 71 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.5166 (m-30) REVERT: G 152 GLU cc_start: 0.7772 (tp30) cc_final: 0.7473 (tp30) REVERT: G 169 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7743 (mp) REVERT: G 180 GLN cc_start: 0.8679 (tt0) cc_final: 0.8438 (mt0) REVERT: G 195 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8112 (tptt) REVERT: H 18 LEU cc_start: 0.2922 (OUTLIER) cc_final: 0.2289 (mp) REVERT: H 63 MET cc_start: 0.3854 (mmm) cc_final: 0.2997 (mtm) REVERT: H 104 LEU cc_start: 0.3973 (mp) cc_final: 0.3660 (tp) REVERT: J 61 GLU cc_start: 0.2821 (pm20) cc_final: 0.2247 (mt-10) REVERT: J 82 GLU cc_start: 0.5546 (mm-30) cc_final: 0.5226 (mm-30) REVERT: J 119 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7253 (tttt) REVERT: J 136 ARG cc_start: 0.4060 (mmp80) cc_final: 0.3651 (tpp80) REVERT: J 150 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5201 (tp) REVERT: J 160 LYS cc_start: 0.7582 (mttm) cc_final: 0.6943 (mmtt) REVERT: J 165 ASN cc_start: 0.6709 (t0) cc_final: 0.6476 (t0) REVERT: L 85 ARG cc_start: 0.5994 (tmm160) cc_final: 0.5401 (ttm-80) REVERT: L 89 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: L 105 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.6196 (ttp-110) REVERT: L 130 HIS cc_start: 0.5384 (m-70) cc_final: 0.4934 (m-70) outliers start: 65 outliers final: 39 residues processed: 368 average time/residue: 0.2213 time to fit residues: 125.4107 Evaluate side-chains 344 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 169 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098871 restraints weight = 46129.412| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.52 r_work: 0.3065 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30015 Z= 0.186 Angle : 0.591 8.927 40658 Z= 0.301 Chirality : 0.046 0.161 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.491 50.890 4180 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.92 % Allowed : 14.76 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1519 sheet: -0.61 (0.22), residues: 556 loop : -0.96 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 186 TYR 0.014 0.002 TYR F 383 PHE 0.024 0.002 PHE B 143 TRP 0.008 0.001 TRP B 119 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00456 (30015) covalent geometry : angle 0.59090 (40658) hydrogen bonds : bond 0.05113 ( 1235) hydrogen bonds : angle 4.53651 ( 3558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6372 (mmm) cc_final: 0.5700 (pmm) REVERT: A 179 THR cc_start: 0.7041 (m) cc_final: 0.6626 (p) REVERT: A 268 GLU cc_start: 0.8191 (tp30) cc_final: 0.7907 (tt0) REVERT: B 15 ILE cc_start: 0.8172 (mm) cc_final: 0.7820 (mm) REVERT: B 38 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 45 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: B 54 ASP cc_start: 0.7657 (p0) cc_final: 0.7254 (p0) REVERT: B 480 GLU cc_start: 0.7729 (mp0) cc_final: 0.7439 (mt-10) REVERT: C 241 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8220 (tt) REVERT: C 268 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 287 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8774 (mp) REVERT: C 416 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.7936 (ptp-170) REVERT: C 547 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7876 (ttm110) REVERT: D 128 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: D 130 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8796 (p90) REVERT: D 258 THR cc_start: 0.6679 (OUTLIER) cc_final: 0.6242 (m) REVERT: D 331 TYR cc_start: 0.7799 (m-10) cc_final: 0.7343 (m-10) REVERT: D 388 ASN cc_start: 0.8517 (m-40) cc_final: 0.8300 (m-40) REVERT: D 456 LYS cc_start: 0.6525 (mmmt) cc_final: 0.6246 (mtmt) REVERT: E 53 GLU cc_start: 0.7271 (tt0) cc_final: 0.7066 (tt0) REVERT: E 420 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7570 (mtp85) REVERT: E 450 GLU cc_start: 0.6493 (mp0) cc_final: 0.5978 (mm-30) REVERT: E 466 LYS cc_start: 0.6220 (mmtm) cc_final: 0.5443 (mmtp) REVERT: F 25 LYS cc_start: 0.7992 (ptpt) cc_final: 0.7702 (pptt) REVERT: F 230 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7850 (mt-10) REVERT: F 394 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7581 (tptp) REVERT: F 434 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7519 (mt-10) REVERT: G 47 MET cc_start: 0.7558 (ptm) cc_final: 0.7042 (ptt) REVERT: G 58 LYS cc_start: 0.6405 (mmtt) cc_final: 0.6004 (mtpp) REVERT: G 71 ASP cc_start: 0.5605 (OUTLIER) cc_final: 0.5116 (m-30) REVERT: G 137 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6803 (tt) REVERT: G 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7566 (tp30) REVERT: G 169 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7769 (mp) REVERT: G 180 GLN cc_start: 0.8761 (tt0) cc_final: 0.8504 (mt0) REVERT: G 195 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8120 (tptt) REVERT: H 18 LEU cc_start: 0.2849 (OUTLIER) cc_final: 0.2224 (mp) REVERT: H 63 MET cc_start: 0.3960 (mmm) cc_final: 0.3114 (mtm) REVERT: H 104 LEU cc_start: 0.4133 (mp) cc_final: 0.3781 (tp) REVERT: J 61 GLU cc_start: 0.2800 (pm20) cc_final: 0.2228 (mt-10) REVERT: J 82 GLU cc_start: 0.5720 (mm-30) cc_final: 0.5345 (mm-30) REVERT: J 119 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7313 (tttt) REVERT: J 136 ARG cc_start: 0.4124 (mmp80) cc_final: 0.3790 (tpp80) REVERT: J 145 GLU cc_start: 0.4555 (OUTLIER) cc_final: 0.2738 (mm-30) REVERT: J 149 ARG cc_start: 0.6527 (mtm-85) cc_final: 0.6261 (mtm-85) REVERT: J 150 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5260 (tp) REVERT: J 160 LYS cc_start: 0.7624 (mttm) cc_final: 0.6908 (mmtt) REVERT: J 165 ASN cc_start: 0.6714 (t0) cc_final: 0.6359 (t0) REVERT: L 85 ARG cc_start: 0.6076 (tmm160) cc_final: 0.5515 (ttm-80) REVERT: L 89 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: L 105 ARG cc_start: 0.6465 (mtm-85) cc_final: 0.6180 (ttp-110) outliers start: 90 outliers final: 66 residues processed: 379 average time/residue: 0.2054 time to fit residues: 120.8799 Evaluate side-chains 377 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 298 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 chunk 369 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 155 optimal weight: 0.0050 chunk 15 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 571 GLN F 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101035 restraints weight = 45969.061| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.52 r_work: 0.3097 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30015 Z= 0.114 Angle : 0.517 9.519 40658 Z= 0.264 Chirality : 0.043 0.159 4560 Planarity : 0.004 0.045 5330 Dihedral : 4.193 46.443 4180 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.30 % Allowed : 15.80 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.19 (0.14), residues: 3764 helix: 1.44 (0.14), residues: 1519 sheet: -0.46 (0.23), residues: 549 loop : -0.86 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 409 TYR 0.010 0.001 TYR F 463 PHE 0.025 0.001 PHE A 230 TRP 0.009 0.001 TRP B 119 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00261 (30015) covalent geometry : angle 0.51721 (40658) hydrogen bonds : bond 0.04143 ( 1235) hydrogen bonds : angle 4.34868 ( 3558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6250 (mmm) cc_final: 0.5600 (pmm) REVERT: A 179 THR cc_start: 0.7006 (m) cc_final: 0.6590 (p) REVERT: A 268 GLU cc_start: 0.8119 (tp30) cc_final: 0.7849 (tt0) REVERT: B 38 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6882 (mt-10) REVERT: B 54 ASP cc_start: 0.7670 (p0) cc_final: 0.7274 (p0) REVERT: B 436 ASP cc_start: 0.7914 (m-30) cc_final: 0.7705 (m-30) REVERT: B 480 GLU cc_start: 0.7700 (mp0) cc_final: 0.7360 (mt-10) REVERT: C 241 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8229 (tt) REVERT: C 268 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7375 (mt-10) REVERT: C 287 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8788 (mp) REVERT: C 547 ARG cc_start: 0.8165 (tpp-160) cc_final: 0.7913 (ttm110) REVERT: D 61 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: D 128 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: D 258 THR cc_start: 0.6338 (OUTLIER) cc_final: 0.5928 (m) REVERT: D 388 ASN cc_start: 0.8511 (m-40) cc_final: 0.8286 (m-40) REVERT: D 456 LYS cc_start: 0.6542 (mmmt) cc_final: 0.6237 (mtmt) REVERT: E 275 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7485 (mt-10) REVERT: E 420 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7528 (mtp85) REVERT: E 450 GLU cc_start: 0.6373 (mp0) cc_final: 0.5906 (mm-30) REVERT: E 466 LYS cc_start: 0.6055 (mmtm) cc_final: 0.5356 (mmtp) REVERT: F 25 LYS cc_start: 0.7980 (ptpt) cc_final: 0.7724 (pptt) REVERT: F 230 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7787 (mt-10) REVERT: F 265 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: F 394 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7578 (tptp) REVERT: F 434 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7583 (mt-10) REVERT: G 47 MET cc_start: 0.7493 (ptm) cc_final: 0.6981 (ptt) REVERT: G 152 GLU cc_start: 0.7830 (tp30) cc_final: 0.7547 (tp30) REVERT: G 169 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7743 (mp) REVERT: G 180 GLN cc_start: 0.8705 (tt0) cc_final: 0.8459 (mt0) REVERT: G 195 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8159 (tptt) REVERT: H 63 MET cc_start: 0.3913 (mmm) cc_final: 0.3060 (mtm) REVERT: H 91 ARG cc_start: 0.6710 (mtt180) cc_final: 0.6272 (tmm-80) REVERT: H 104 LEU cc_start: 0.3927 (mp) cc_final: 0.3716 (tp) REVERT: J 61 GLU cc_start: 0.2826 (pm20) cc_final: 0.2238 (mt-10) REVERT: J 82 GLU cc_start: 0.5697 (mm-30) cc_final: 0.5335 (mm-30) REVERT: J 119 LYS cc_start: 0.7526 (ttpt) cc_final: 0.7201 (tttt) REVERT: J 121 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.5120 (mt) REVERT: J 136 ARG cc_start: 0.3927 (mmp80) cc_final: 0.3587 (tpp80) REVERT: J 145 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.2697 (mm-30) REVERT: J 149 ARG cc_start: 0.6490 (mtm-85) cc_final: 0.6226 (mtm-85) REVERT: J 150 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5185 (tp) REVERT: J 160 LYS cc_start: 0.7577 (mttm) cc_final: 0.6973 (mmtt) REVERT: J 165 ASN cc_start: 0.6662 (t0) cc_final: 0.6312 (t0) REVERT: L 81 GLU cc_start: 0.7841 (tt0) cc_final: 0.7343 (mt-10) REVERT: L 85 ARG cc_start: 0.6019 (tmm160) cc_final: 0.5426 (ttm-80) REVERT: L 89 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: L 105 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.6190 (ttp-110) outliers start: 71 outliers final: 43 residues processed: 366 average time/residue: 0.2084 time to fit residues: 118.0952 Evaluate side-chains 343 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 227 optimal weight: 0.0970 chunk 238 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102447 restraints weight = 45984.732| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.54 r_work: 0.3124 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30015 Z= 0.098 Angle : 0.499 9.877 40658 Z= 0.253 Chirality : 0.043 0.152 4560 Planarity : 0.004 0.044 5330 Dihedral : 3.945 44.768 4180 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 16.12 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3764 helix: 1.61 (0.14), residues: 1517 sheet: -0.27 (0.23), residues: 551 loop : -0.71 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 372 TYR 0.009 0.001 TYR D 331 PHE 0.024 0.001 PHE B 143 TRP 0.009 0.001 TRP D 471 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00213 (30015) covalent geometry : angle 0.49851 (40658) hydrogen bonds : bond 0.03674 ( 1235) hydrogen bonds : angle 4.21250 ( 3558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6325 (mmm) cc_final: 0.5611 (pmm) REVERT: A 179 THR cc_start: 0.7026 (m) cc_final: 0.6614 (p) REVERT: A 268 GLU cc_start: 0.8135 (tp30) cc_final: 0.7860 (tt0) REVERT: A 567 MET cc_start: 0.8215 (mmm) cc_final: 0.7874 (mmm) REVERT: B 38 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6783 (mt-10) REVERT: B 54 ASP cc_start: 0.7633 (p0) cc_final: 0.7235 (p0) REVERT: B 344 MET cc_start: 0.8548 (mmm) cc_final: 0.8227 (tmm) REVERT: B 436 ASP cc_start: 0.7880 (m-30) cc_final: 0.7671 (m-30) REVERT: B 480 GLU cc_start: 0.7704 (mp0) cc_final: 0.7389 (mt-10) REVERT: C 241 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 268 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 547 ARG cc_start: 0.8109 (tpp-160) cc_final: 0.7885 (ttm110) REVERT: D 61 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: D 128 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6459 (pp20) REVERT: D 258 THR cc_start: 0.6212 (OUTLIER) cc_final: 0.5870 (m) REVERT: D 388 ASN cc_start: 0.8451 (m-40) cc_final: 0.8207 (m-40) REVERT: D 391 ASP cc_start: 0.8156 (t0) cc_final: 0.7519 (t0) REVERT: D 456 LYS cc_start: 0.6543 (mmmt) cc_final: 0.6218 (mtmt) REVERT: E 275 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7448 (mt-10) REVERT: E 302 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: E 450 GLU cc_start: 0.6298 (mp0) cc_final: 0.5875 (mm-30) REVERT: E 466 LYS cc_start: 0.5874 (mmtm) cc_final: 0.5186 (mmtp) REVERT: F 25 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7686 (pptt) REVERT: F 96 ILE cc_start: 0.8501 (pt) cc_final: 0.8211 (mm) REVERT: F 318 ASP cc_start: 0.7529 (t0) cc_final: 0.6995 (t0) REVERT: F 394 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7525 (tptp) REVERT: F 434 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7557 (mt-10) REVERT: G 47 MET cc_start: 0.7438 (ptm) cc_final: 0.6949 (ptt) REVERT: G 152 GLU cc_start: 0.7821 (tp30) cc_final: 0.7529 (tp30) REVERT: G 180 GLN cc_start: 0.8628 (tt0) cc_final: 0.8407 (mt0) REVERT: G 195 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8134 (tptt) REVERT: H 18 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2444 (mp) REVERT: H 63 MET cc_start: 0.3734 (mmm) cc_final: 0.2943 (mtm) REVERT: H 91 ARG cc_start: 0.6758 (mtt180) cc_final: 0.6294 (tmm-80) REVERT: H 104 LEU cc_start: 0.3884 (mp) cc_final: 0.3633 (tp) REVERT: J 61 GLU cc_start: 0.2726 (pm20) cc_final: 0.2147 (mt-10) REVERT: J 82 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5289 (mm-30) REVERT: J 119 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7245 (tttt) REVERT: J 121 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5147 (mt) REVERT: J 136 ARG cc_start: 0.3905 (mmp80) cc_final: 0.3593 (tpp80) REVERT: J 145 GLU cc_start: 0.4311 (OUTLIER) cc_final: 0.2687 (mm-30) REVERT: J 149 ARG cc_start: 0.6524 (mtm-85) cc_final: 0.6260 (mtm-85) REVERT: J 150 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5225 (tp) REVERT: J 160 LYS cc_start: 0.7441 (mttm) cc_final: 0.6998 (mmtt) REVERT: J 165 ASN cc_start: 0.6596 (t0) cc_final: 0.6205 (t0) REVERT: L 81 GLU cc_start: 0.7850 (tt0) cc_final: 0.7224 (mt-10) REVERT: L 85 ARG cc_start: 0.5953 (tmm160) cc_final: 0.5333 (ttm-80) REVERT: L 89 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: L 105 ARG cc_start: 0.6552 (mtm-85) cc_final: 0.6216 (ttp-110) outliers start: 62 outliers final: 40 residues processed: 351 average time/residue: 0.2094 time to fit residues: 114.2789 Evaluate side-chains 339 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 144 optimal weight: 0.9990 chunk 322 optimal weight: 0.0470 chunk 13 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 303 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 413 GLN G 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100422 restraints weight = 45953.943| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.50 r_work: 0.3099 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30015 Z= 0.143 Angle : 0.543 9.270 40658 Z= 0.276 Chirality : 0.044 0.196 4560 Planarity : 0.004 0.043 5330 Dihedral : 4.153 46.410 4180 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.40 % Allowed : 16.02 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.14), residues: 3764 helix: 1.51 (0.14), residues: 1520 sheet: -0.39 (0.22), residues: 558 loop : -0.72 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 130 TYR 0.011 0.001 TYR F 383 PHE 0.032 0.001 PHE A 230 TRP 0.007 0.001 TRP B 119 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00344 (30015) covalent geometry : angle 0.54259 (40658) hydrogen bonds : bond 0.04363 ( 1235) hydrogen bonds : angle 4.30776 ( 3558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6224 (mmm) cc_final: 0.5585 (pmm) REVERT: A 122 MET cc_start: 0.7448 (ttm) cc_final: 0.7219 (ttt) REVERT: A 179 THR cc_start: 0.7016 (m) cc_final: 0.6608 (p) REVERT: A 268 GLU cc_start: 0.8116 (tp30) cc_final: 0.7867 (tt0) REVERT: B 38 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6825 (tt0) REVERT: B 54 ASP cc_start: 0.7662 (p0) cc_final: 0.7296 (p0) REVERT: B 130 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.6586 (mtm110) REVERT: B 436 ASP cc_start: 0.7932 (m-30) cc_final: 0.7631 (m-30) REVERT: B 480 GLU cc_start: 0.7709 (mp0) cc_final: 0.7226 (mt-10) REVERT: C 241 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 268 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7331 (mt-10) REVERT: C 547 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7946 (ttm110) REVERT: D 61 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: D 258 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6013 (m) REVERT: D 388 ASN cc_start: 0.8454 (m-40) cc_final: 0.8200 (m-40) REVERT: D 456 LYS cc_start: 0.6549 (mmmt) cc_final: 0.6199 (mtmt) REVERT: E 275 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7466 (mt-10) REVERT: E 302 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: E 450 GLU cc_start: 0.6318 (mp0) cc_final: 0.5864 (mm-30) REVERT: F 25 LYS cc_start: 0.7888 (ptpt) cc_final: 0.7631 (pptt) REVERT: F 96 ILE cc_start: 0.8495 (pt) cc_final: 0.8238 (mm) REVERT: F 394 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7592 (tptp) REVERT: G 47 MET cc_start: 0.7421 (ptm) cc_final: 0.6931 (ptt) REVERT: G 137 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6655 (tt) REVERT: G 152 GLU cc_start: 0.7820 (tp30) cc_final: 0.7533 (tp30) REVERT: G 180 GLN cc_start: 0.8728 (tt0) cc_final: 0.8477 (mt0) REVERT: G 195 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8127 (tptt) REVERT: H 18 LEU cc_start: 0.3044 (OUTLIER) cc_final: 0.2471 (mp) REVERT: H 63 MET cc_start: 0.3921 (mmm) cc_final: 0.3074 (mtm) REVERT: H 91 ARG cc_start: 0.6605 (mtt180) cc_final: 0.6159 (ttp-110) REVERT: H 104 LEU cc_start: 0.3872 (mp) cc_final: 0.3627 (tp) REVERT: J 61 GLU cc_start: 0.2742 (pm20) cc_final: 0.2130 (mt-10) REVERT: J 82 GLU cc_start: 0.5553 (mm-30) cc_final: 0.5285 (mm-30) REVERT: J 119 LYS cc_start: 0.7582 (ttpt) cc_final: 0.7274 (tttt) REVERT: J 121 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4996 (mp) REVERT: J 136 ARG cc_start: 0.3949 (mmp80) cc_final: 0.3630 (tpp80) REVERT: J 145 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.4355 (pp20) REVERT: J 149 ARG cc_start: 0.6550 (mtm-85) cc_final: 0.6286 (mtm-85) REVERT: J 150 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5215 (tp) REVERT: J 160 LYS cc_start: 0.7491 (mttm) cc_final: 0.6946 (mmtt) REVERT: J 165 ASN cc_start: 0.6665 (t0) cc_final: 0.6206 (t0) REVERT: L 81 GLU cc_start: 0.7849 (tt0) cc_final: 0.7340 (mt-10) REVERT: L 85 ARG cc_start: 0.5925 (tmm160) cc_final: 0.5286 (ttm-80) REVERT: L 89 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: L 105 ARG cc_start: 0.6602 (mtm-85) cc_final: 0.6268 (ttp-110) outliers start: 74 outliers final: 55 residues processed: 357 average time/residue: 0.2107 time to fit residues: 116.4331 Evaluate side-chains 351 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 147 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 363 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101103 restraints weight = 45827.966| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.55 r_work: 0.3116 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30015 Z= 0.114 Angle : 0.520 9.413 40658 Z= 0.265 Chirality : 0.043 0.194 4560 Planarity : 0.004 0.049 5330 Dihedral : 4.062 44.847 4180 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.01 % Allowed : 16.32 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.43 (0.14), residues: 3764 helix: 1.59 (0.14), residues: 1513 sheet: -0.40 (0.22), residues: 571 loop : -0.64 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 130 TYR 0.008 0.001 TYR F 463 PHE 0.024 0.001 PHE A 230 TRP 0.008 0.001 TRP B 119 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00262 (30015) covalent geometry : angle 0.52040 (40658) hydrogen bonds : bond 0.04007 ( 1235) hydrogen bonds : angle 4.26150 ( 3558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6358 (mmm) cc_final: 0.5699 (pmm) REVERT: A 179 THR cc_start: 0.7016 (m) cc_final: 0.6617 (p) REVERT: A 268 GLU cc_start: 0.8150 (tp30) cc_final: 0.7894 (tt0) REVERT: B 38 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6780 (tt0) REVERT: B 54 ASP cc_start: 0.7647 (p0) cc_final: 0.7276 (p0) REVERT: B 130 ARG cc_start: 0.7383 (ptt-90) cc_final: 0.6583 (mtm110) REVERT: B 436 ASP cc_start: 0.7919 (m-30) cc_final: 0.7627 (m-30) REVERT: B 467 ILE cc_start: 0.8511 (tt) cc_final: 0.8192 (mp) REVERT: B 480 GLU cc_start: 0.7721 (mp0) cc_final: 0.7240 (mt-10) REVERT: B 493 ASP cc_start: 0.7984 (t0) cc_final: 0.7782 (t0) REVERT: C 241 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8214 (tt) REVERT: C 268 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 547 ARG cc_start: 0.8113 (tpp-160) cc_final: 0.7913 (ttm110) REVERT: D 61 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: D 258 THR cc_start: 0.6295 (OUTLIER) cc_final: 0.5970 (m) REVERT: D 388 ASN cc_start: 0.8455 (m-40) cc_final: 0.8227 (m-40) REVERT: D 456 LYS cc_start: 0.6452 (mmmt) cc_final: 0.6154 (mtmt) REVERT: E 275 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7462 (mt-10) REVERT: E 302 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: E 450 GLU cc_start: 0.6320 (mp0) cc_final: 0.5894 (mm-30) REVERT: E 466 LYS cc_start: 0.5724 (mmtm) cc_final: 0.4743 (mmtm) REVERT: F 25 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7634 (pptt) REVERT: F 394 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7551 (tptp) REVERT: G 47 MET cc_start: 0.7457 (ptm) cc_final: 0.6972 (ptt) REVERT: G 152 GLU cc_start: 0.7835 (tp30) cc_final: 0.7566 (tp30) REVERT: G 180 GLN cc_start: 0.8736 (tt0) cc_final: 0.8484 (mt0) REVERT: G 195 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8183 (tptt) REVERT: H 18 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2573 (mp) REVERT: H 63 MET cc_start: 0.3906 (mmm) cc_final: 0.3071 (mtm) REVERT: H 91 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6277 (tmm-80) REVERT: H 104 LEU cc_start: 0.3827 (mp) cc_final: 0.3617 (tp) REVERT: J 82 GLU cc_start: 0.5546 (mm-30) cc_final: 0.5276 (mm-30) REVERT: J 119 LYS cc_start: 0.7608 (ttpt) cc_final: 0.7311 (tttt) REVERT: J 121 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.5013 (mp) REVERT: J 136 ARG cc_start: 0.3943 (mmp80) cc_final: 0.3572 (tpp80) REVERT: J 145 GLU cc_start: 0.4614 (OUTLIER) cc_final: 0.2772 (mm-30) REVERT: J 149 ARG cc_start: 0.6557 (mtm-85) cc_final: 0.6293 (mtm-85) REVERT: J 150 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5224 (tp) REVERT: J 160 LYS cc_start: 0.7549 (mttm) cc_final: 0.7002 (mmtt) REVERT: J 165 ASN cc_start: 0.6674 (t0) cc_final: 0.6202 (t0) REVERT: L 74 GLN cc_start: 0.7230 (tt0) cc_final: 0.6653 (mt0) REVERT: L 81 GLU cc_start: 0.7851 (tt0) cc_final: 0.7351 (mt-10) REVERT: L 85 ARG cc_start: 0.5924 (tmm160) cc_final: 0.5260 (ttm-80) REVERT: L 89 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: L 105 ARG cc_start: 0.6643 (mtm-85) cc_final: 0.6298 (ttp-110) outliers start: 62 outliers final: 50 residues processed: 346 average time/residue: 0.2038 time to fit residues: 110.5420 Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 348 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100431 restraints weight = 46139.617| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.56 r_work: 0.3087 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30015 Z= 0.146 Angle : 0.553 9.639 40658 Z= 0.281 Chirality : 0.045 0.210 4560 Planarity : 0.005 0.046 5330 Dihedral : 4.218 46.673 4180 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.24 % Allowed : 16.19 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.32 (0.14), residues: 3764 helix: 1.48 (0.14), residues: 1521 sheet: -0.46 (0.22), residues: 568 loop : -0.68 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 130 TYR 0.012 0.001 TYR F 383 PHE 0.032 0.001 PHE A 230 TRP 0.008 0.001 TRP B 119 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00349 (30015) covalent geometry : angle 0.55316 (40658) hydrogen bonds : bond 0.04496 ( 1235) hydrogen bonds : angle 4.33523 ( 3558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8016.68 seconds wall clock time: 137 minutes 25.11 seconds (8245.11 seconds total)