Starting phenix.real_space_refine on Fri Oct 23 19:17:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.cif Found real_map, /net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25mj_80203/10_2026/25mj_80203.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6944 2.51 5 N 1700 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10597 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5265 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5265 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10597 At special positions: 0 Unit cell: (121.744, 95.656, 109.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 60 16.00 P 4 15.00 O 1887 8.00 N 1700 7.00 C 6944 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: 0.68 Conformation dependent library (CDL) restraints added in 364.8 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 3 sheets defined 53.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.612A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.010A pdb=" N LEU A 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.584A pdb=" N THR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.747A pdb=" N TYR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.632A pdb=" N TYR A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 182 through 192 Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.549A pdb=" N SER A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.962A pdb=" N GLY A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.178A pdb=" N VAL A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.757A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.589A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.512A pdb=" N PHE A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.606A pdb=" N ILE A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.584A pdb=" N PHE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 removed outlier: 3.644A pdb=" N THR A 309 " --> pdb=" O LEU A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 310 through 311 No H-bonds generated for 'chain 'A' and resid 310 through 311' Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.574A pdb=" N ASP A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.784A pdb=" N ILE A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.580A pdb=" N LEU A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 369 " --> pdb=" O ASP A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 370 through 399 removed outlier: 4.210A pdb=" N VAL A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.598A pdb=" N ASN A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 4.045A pdb=" N ALA A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 437 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.253A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 472 removed outlier: 3.771A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.517A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.519A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 520 through 534 removed outlier: 3.721A pdb=" N GLN A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.623A pdb=" N SER A 575 " --> pdb=" O PRO A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.680A pdb=" N ASN A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 581' Processing helix chain 'A' and resid 634 through 654 removed outlier: 4.291A pdb=" N GLU A 639 " --> pdb=" O PRO A 635 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.918A pdb=" N ARG A 724 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.610A pdb=" N PHE A 757 " --> pdb=" O HIS A 753 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.989A pdb=" N ALA A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 764 through 769' Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.712A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.654A pdb=" N TYR B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.615A pdb=" N PHE B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.643A pdb=" N TYR B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.568A pdb=" N ALA B 121 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.845A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.599A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.550A pdb=" N PHE B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.815A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 228 through 237 removed outlier: 4.180A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.564A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.602A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.656A pdb=" N TYR B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 309 removed outlier: 3.709A pdb=" N THR B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.540A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 4.222A pdb=" N ILE B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.100A pdb=" N VAL B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.159A pdb=" N SER B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 4.331A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 431 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 444 through 467 removed outlier: 3.720A pdb=" N HIS B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 4.005A pdb=" N VAL B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.647A pdb=" N PHE B 483 " --> pdb=" O TRP B 479 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 removed outlier: 4.304A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.514A pdb=" N LYS B 501 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.985A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.604A pdb=" N ILE B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 579 " --> pdb=" O SER B 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 580 " --> pdb=" O HIS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 removed outlier: 3.689A pdb=" N GLU B 639 " --> pdb=" O PRO B 635 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 723 removed outlier: 3.531A pdb=" N LYS B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 718 through 723' Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 753 through 761 Processing helix chain 'B' and resid 764 through 769 removed outlier: 3.581A pdb=" N LEU B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 607 through 611 removed outlier: 7.813A pdb=" N PHE A 620 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A 583 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 556 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS A 585 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 558 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL A 729 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 559 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 731 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 561 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY A 733 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N TYR A 563 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N THR A 735 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 779 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY B 733 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 554 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS B 585 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL B 556 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL B 587 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 558 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL B 589 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B 560 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 591 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 562 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE B 593 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE B 620 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 308 hydrogen bonds defined for protein. 867 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: 1.62 Time building geometry restraints manager: 0.93 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: 1943 1.33 - 1.45: 2781 1.45 - 1.57: 5998 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 10834 Sorted by residual: bond pdb=" CA GLU B 742 " pdb=" CB GLU B 742 " ideal model delta sigma weight residual 1.526 1.601 -0.075 1.53e-02 4.27e+03 2.39e+01 bond pdb=" N ASN A 565 " pdb=" CA ASN A 565 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.33e-02 5.65e+03 8.33e+00 bond pdb=" N ARG A 527 " pdb=" CA ARG A 527 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.28e-02 6.10e+03 8.21e+00 bond pdb=" N HIS A 759 " pdb=" CA HIS A 759 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 bond pdb=" CG HIS B 759 " pdb=" CD2 HIS B 759 " ideal model delta sigma weight residual 1.354 1.325 0.029 1.10e-02 8.26e+03 6.98e+00 ... (remaining 10829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 13903 1.83 - 3.67: 653 3.67 - 5.50: 113 5.50 - 7.33: 39 7.33 - 9.16: 8 Bond angle restraints: 14716 Sorted by residual: angle pdb=" N SER B 209 " pdb=" CA SER B 209 " pdb=" C SER B 209 " ideal model delta sigma weight residual 114.75 105.88 8.87 1.26e+00 6.30e-01 4.96e+01 angle pdb=" N MET B 519 " pdb=" CA MET B 519 " pdb=" C MET B 519 " ideal model delta sigma weight residual 114.75 106.97 7.78 1.26e+00 6.30e-01 3.82e+01 angle pdb=" N ARG B 400 " pdb=" CA ARG B 400 " pdb=" C ARG B 400 " ideal model delta sigma weight residual 114.75 106.97 7.78 1.26e+00 6.30e-01 3.81e+01 angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" C LEU A 270 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.76e+01 angle pdb=" N VAL B 98 " pdb=" CA VAL B 98 " pdb=" C VAL B 98 " ideal model delta sigma weight residual 111.91 106.53 5.38 8.90e-01 1.26e+00 3.65e+01 ... (remaining 14711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 5711 25.62 - 51.23: 552 51.23 - 76.85: 65 76.85 - 102.46: 7 102.46 - 128.08: 1 Dihedral angle restraints: 6336 sinusoidal: 2460 harmonic: 3876 Sorted by residual: dihedral pdb=" CD ARG A 527 " pdb=" NE ARG A 527 " pdb=" CZ ARG A 527 " pdb=" NH1 ARG A 527 " ideal model delta sinusoidal sigma weight residual 0.00 -56.33 56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 68.07 -128.08 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" CA ILE B 208 " pdb=" C ILE B 208 " pdb=" N SER B 209 " pdb=" CA SER B 209 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 875 0.032 - 0.064: 588 0.064 - 0.096: 176 0.096 - 0.127: 73 0.127 - 0.159: 14 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ASP A 123 " pdb=" N ASP A 123 " pdb=" C ASP A 123 " pdb=" CB ASP A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C2' ADP A 901 " pdb=" C1' ADP A 901 " pdb=" C3' ADP A 901 " pdb=" O2' ADP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA ASP A 201 " pdb=" N ASP A 201 " pdb=" C ASP A 201 " pdb=" CB ASP A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1723 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 527 " -0.875 9.50e-02 1.11e+02 3.92e-01 9.39e+01 pdb=" NE ARG A 527 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 527 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 527 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 527 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 527 " 0.618 9.50e-02 1.11e+02 2.77e-01 4.68e+01 pdb=" NE ARG B 527 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 527 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 527 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 527 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 526 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL B 526 " -0.061 2.00e-02 2.50e+03 pdb=" O VAL B 526 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 527 " 0.021 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 4263 2.91 - 3.46: 10142 3.46 - 4.02: 17740 4.02 - 4.58: 27109 4.58 - 5.14: 39891 Nonbonded interactions: 99145 Sorted by model distance: nonbonded pdb=" O ASN A 599 " pdb=" ND2 ASN A 599 " model vdw 2.347 3.120 nonbonded pdb=" N ASN B 565 " pdb=" OD1 ASN B 565 " model vdw 2.359 3.120 nonbonded pdb=" O GLN A 296 " pdb=" NE2 GLN A 296 " model vdw 2.380 3.120 nonbonded pdb=" O ASP A 123 " pdb=" OD1 ASP A 123 " model vdw 2.394 3.040 nonbonded pdb=" NH2 ARG A 527 " pdb=" O HOH A1001 " model vdw 2.406 3.120 ... (remaining 99140 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 0.005 0.075 10834 Z= 0.246 Angle : 0.950 9.163 14716 Z= 0.612 Chirality : 0.047 0.159 1726 Planarity : 0.012 0.392 1786 Dihedral : 18.751 128.076 3856 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.98 % Favored : 91.64 % Rotamer: Outliers : 3.81 % Allowed : 35.64 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.19), residues: 1316 helix: -4.08 (0.12), residues: 784 sheet: -0.37 (0.50), residues: 104 loop : -2.38 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 527 TYR 0.016 0.002 TYR A 628 PHE 0.016 0.001 PHE B 182 TRP 0.010 0.001 TRP B 298 HIS 0.006 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.25 (10834) covalent geometry : angle 0.94989 / 0.61 (14716) hydrogen bonds : bond 0.30697 / 19.77 ( 308) hydrogen bonds : angle 10.19015 / 7.14 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.482 Fit side-chains REVERT: A 59 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6741 (mpp) REVERT: A 78 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7293 (pp) REVERT: A 92 LYS cc_start: 0.7181 (mtpm) cc_final: 0.5846 (mmtt) REVERT: A 181 LYS cc_start: 0.7438 (ttpt) cc_final: 0.7135 (tttt) REVERT: A 354 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6865 (p90) REVERT: A 579 SER cc_start: 0.8260 (t) cc_final: 0.7931 (m) REVERT: A 625 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7120 (mpp-170) REVERT: B 181 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6396 (tppt) REVERT: B 197 MET cc_start: 0.7660 (mmt) cc_final: 0.7404 (mmt) REVERT: B 291 ARG cc_start: 0.6772 (mtm180) cc_final: 0.4781 (mmt180) REVERT: B 309 THR cc_start: 0.7719 (p) cc_final: 0.7146 (p) REVERT: B 430 MET cc_start: 0.7377 (ttp) cc_final: 0.6961 (ttp) REVERT: B 570 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (mm) outliers start: 44 outliers final: 33 residues processed: 175 average time/residue: 0.1046 time to fit residues: 25.8519 Evaluate side-chains 169 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 762 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 296 GLN A 759 HIS B 147 ASN B 565 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110632 restraints weight = 12607.715| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.10 r_work: 0.3084 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10834 Z= 0.187 Angle : 0.704 8.512 14716 Z= 0.364 Chirality : 0.045 0.169 1726 Planarity : 0.005 0.044 1786 Dihedral : 9.657 124.164 1543 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.75 % Favored : 91.87 % Rotamer: Outliers : 7.44 % Allowed : 30.45 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.65 (0.19), residues: 1316 helix: -3.62 (0.14), residues: 776 sheet: -0.31 (0.47), residues: 104 loop : -2.28 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 541 TYR 0.012 0.002 TYR B 626 PHE 0.016 0.001 PHE B 182 TRP 0.010 0.001 TRP B 298 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (10834) covalent geometry : angle 0.70362 / 0.36 (14716) hydrogen bonds : bond 0.05946 / 3.81 ( 308) hydrogen bonds : angle 6.05467 / 4.19 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 146 time to evaluate : 0.300 Fit side-chains REVERT: A 78 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 92 LYS cc_start: 0.7696 (mtpm) cc_final: 0.6428 (mmtt) REVERT: A 108 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (mt) REVERT: A 119 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 181 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7437 (tttt) REVERT: A 287 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7210 (mt) REVERT: A 354 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7628 (p90) REVERT: A 573 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 579 SER cc_start: 0.9049 (t) cc_final: 0.8753 (m) REVERT: A 734 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 181 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.6909 (tppt) REVERT: B 197 MET cc_start: 0.8294 (mmt) cc_final: 0.8035 (mmt) REVERT: B 291 ARG cc_start: 0.7577 (mtm180) cc_final: 0.5558 (mmt180) REVERT: B 491 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: B 570 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8652 (mm) REVERT: B 583 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8505 (m) outliers start: 86 outliers final: 44 residues processed: 219 average time/residue: 0.0878 time to fit residues: 28.2723 Evaluate side-chains 194 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 750 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [65, 57, 106, 52, 62, 10, 130, 34, 70, 92, 56] chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN A 524 GLN B 524 GLN B 565 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112864 restraints weight = 12530.061| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.09 r_work: 0.3135 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10834 Z= 0.124 Angle : 0.621 8.629 14716 Z= 0.321 Chirality : 0.043 0.155 1726 Planarity : 0.004 0.040 1786 Dihedral : 8.569 121.969 1512 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.84 % Favored : 92.86 % Rotamer: Outliers : 5.88 % Allowed : 30.97 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.31 (0.20), residues: 1316 helix: -3.28 (0.15), residues: 776 sheet: -0.06 (0.47), residues: 104 loop : -2.31 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 541 TYR 0.010 0.001 TYR B 289 PHE 0.018 0.001 PHE A 502 TRP 0.010 0.001 TRP B 258 HIS 0.002 0.000 HIS B 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10834) covalent geometry : angle 0.62088 / 0.32 (14716) hydrogen bonds : bond 0.04601 / 2.92 ( 308) hydrogen bonds : angle 5.43364 / 3.77 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 145 time to evaluate : 0.334 Fit side-chains REVERT: A 78 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 92 LYS cc_start: 0.7675 (mtpm) cc_final: 0.6538 (mmtt) REVERT: A 119 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 181 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7531 (tttt) REVERT: A 287 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 288 TYR cc_start: 0.7804 (m-10) cc_final: 0.7211 (m-10) REVERT: A 354 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7653 (p90) REVERT: A 473 TRP cc_start: 0.8713 (m-10) cc_final: 0.8407 (m-10) REVERT: A 541 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7355 (ttm110) REVERT: A 573 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 579 SER cc_start: 0.8996 (t) cc_final: 0.8708 (m) REVERT: A 625 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8112 (mtp180) REVERT: A 734 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 760 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8228 (ttpt) REVERT: B 92 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7395 (ttmm) REVERT: B 291 ARG cc_start: 0.7671 (mtm180) cc_final: 0.5539 (mmt-90) REVERT: B 324 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7807 (ttm110) REVERT: B 479 TRP cc_start: 0.8061 (m-10) cc_final: 0.7195 (m100) REVERT: B 491 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: B 570 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 68 outliers final: 37 residues processed: 207 average time/residue: 0.0963 time to fit residues: 28.7115 Evaluate side-chains 189 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 782 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [76, 120, 16, 122, 82, 62, 94, 56, 6, 61, 23] chunk 76 optimal weight: 20.0000 chunk 120 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115643 restraints weight = 12458.871| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.79 r_work: 0.3167 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10834 Z= 0.111 Angle : 0.589 9.085 14716 Z= 0.303 Chirality : 0.042 0.144 1726 Planarity : 0.004 0.038 1786 Dihedral : 8.008 121.156 1502 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 5.71 % Allowed : 30.10 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.01 (0.20), residues: 1316 helix: -3.06 (0.16), residues: 784 sheet: 0.00 (0.47), residues: 106 loop : -2.11 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 541 TYR 0.011 0.001 TYR B 533 PHE 0.013 0.001 PHE B 182 TRP 0.009 0.001 TRP B 258 HIS 0.002 0.000 HIS B 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10834) covalent geometry : angle 0.58923 / 0.30 (14716) hydrogen bonds : bond 0.04071 / 2.57 ( 308) hydrogen bonds : angle 5.15800 / 3.58 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 0.319 Fit side-chains REVERT: A 78 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7926 (pp) REVERT: A 92 LYS cc_start: 0.7591 (mtpm) cc_final: 0.6413 (mmtt) REVERT: A 119 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7348 (mp) REVERT: A 181 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7502 (tttt) REVERT: A 287 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7070 (mt) REVERT: A 288 TYR cc_start: 0.7673 (m-10) cc_final: 0.7061 (m-10) REVERT: A 354 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 473 TRP cc_start: 0.8579 (m-10) cc_final: 0.8251 (m-10) REVERT: A 573 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 579 SER cc_start: 0.8966 (t) cc_final: 0.8700 (m) REVERT: A 625 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: A 734 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: B 78 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 181 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.6793 (tppt) REVERT: B 182 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.6211 (t80) REVERT: B 291 ARG cc_start: 0.7532 (mtm180) cc_final: 0.5510 (mmt-90) REVERT: B 324 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7384 (ttm110) REVERT: B 479 TRP cc_start: 0.8023 (m-10) cc_final: 0.7147 (m100) REVERT: B 491 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: B 533 TYR cc_start: 0.8401 (t80) cc_final: 0.8159 (t80) REVERT: B 583 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 600 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.7244 (ttm-80) REVERT: B 745 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7446 (mm) outliers start: 66 outliers final: 34 residues processed: 208 average time/residue: 0.1013 time to fit residues: 29.8817 Evaluate side-chains 189 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 750 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [41, 13, 42, 70, 96, 120, 74, 87, 86, 71, 53] chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN B 565 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112703 restraints weight = 12415.819| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.97 r_work: 0.3156 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10834 Z= 0.103 Angle : 0.560 6.649 14716 Z= 0.288 Chirality : 0.042 0.153 1726 Planarity : 0.004 0.044 1786 Dihedral : 7.434 119.851 1495 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 4.93 % Allowed : 30.88 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.69 (0.21), residues: 1316 helix: -2.83 (0.16), residues: 786 sheet: 0.12 (0.48), residues: 106 loop : -1.91 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 541 TYR 0.011 0.001 TYR B 533 PHE 0.013 0.001 PHE B 182 TRP 0.008 0.001 TRP B 258 HIS 0.002 0.000 HIS B 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (10834) covalent geometry : angle 0.56049 / 0.29 (14716) hydrogen bonds : bond 0.03783 / 2.39 ( 308) hydrogen bonds : angle 4.93994 / 3.43 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 0.414 Fit side-chains REVERT: A 78 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7963 (pp) REVERT: A 92 LYS cc_start: 0.7605 (mtpm) cc_final: 0.6422 (mmtt) REVERT: A 108 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 112 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8345 (tm) REVERT: A 119 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 287 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7018 (mt) REVERT: A 288 TYR cc_start: 0.7662 (m-10) cc_final: 0.7152 (m-10) REVERT: A 354 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7390 (p90) REVERT: A 356 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 473 TRP cc_start: 0.8566 (m-10) cc_final: 0.8251 (m-10) REVERT: A 541 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7166 (ttm110) REVERT: A 573 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 579 SER cc_start: 0.8915 (t) cc_final: 0.8651 (m) REVERT: A 724 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7346 (ttp-170) REVERT: A 734 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: B 78 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7717 (pp) REVERT: B 181 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6814 (tppt) REVERT: B 197 MET cc_start: 0.8102 (mmt) cc_final: 0.7847 (mmt) REVERT: B 291 ARG cc_start: 0.7517 (mtm180) cc_final: 0.5351 (mmt-90) REVERT: B 324 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7340 (ttm110) REVERT: B 479 TRP cc_start: 0.7930 (m-10) cc_final: 0.7061 (m100) REVERT: B 491 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: B 533 TYR cc_start: 0.8370 (t80) cc_final: 0.8162 (t80) REVERT: B 583 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8448 (m) REVERT: B 600 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.7056 (ttm-80) outliers start: 57 outliers final: 29 residues processed: 202 average time/residue: 0.0957 time to fit residues: 27.8025 Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 745 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [70, 73, 130, 82, 78, 109, 24, 77, 63, 114, 129] chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 240 GLN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112998 restraints weight = 12465.810| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10834 Z= 0.103 Angle : 0.556 6.669 14716 Z= 0.284 Chirality : 0.042 0.136 1726 Planarity : 0.004 0.037 1786 Dihedral : 7.021 118.791 1488 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 5.02 % Allowed : 30.71 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.41 (0.21), residues: 1316 helix: -2.62 (0.17), residues: 786 sheet: 0.18 (0.48), residues: 106 loop : -1.76 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 541 TYR 0.013 0.001 TYR B 500 PHE 0.011 0.001 PHE B 182 TRP 0.007 0.001 TRP B 258 HIS 0.002 0.000 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (10834) covalent geometry : angle 0.55579 / 0.28 (14716) hydrogen bonds : bond 0.03763 / 2.36 ( 308) hydrogen bonds : angle 4.89945 / 3.38 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.422 Fit side-chains REVERT: A 56 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.5767 (mpt180) REVERT: A 92 LYS cc_start: 0.7541 (mtpm) cc_final: 0.6352 (mmtt) REVERT: A 108 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 112 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8344 (tm) REVERT: A 119 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7399 (mp) REVERT: A 287 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6995 (mt) REVERT: A 354 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7534 (p90) REVERT: A 356 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 473 TRP cc_start: 0.8563 (m-10) cc_final: 0.8254 (m-10) REVERT: A 490 ILE cc_start: 0.7507 (pt) cc_final: 0.7238 (mt) REVERT: A 492 MET cc_start: 0.7566 (mmm) cc_final: 0.7351 (mmm) REVERT: A 541 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7194 (ttm110) REVERT: A 573 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 579 SER cc_start: 0.8860 (t) cc_final: 0.8590 (m) REVERT: A 625 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8080 (mtp180) REVERT: A 724 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7407 (ttp-110) REVERT: A 734 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: B 78 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7737 (pp) REVERT: B 181 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.6868 (tppt) REVERT: B 197 MET cc_start: 0.8077 (mmt) cc_final: 0.7845 (mmt) REVERT: B 291 ARG cc_start: 0.7476 (mtm180) cc_final: 0.5305 (mmt-90) REVERT: B 324 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7359 (ttm110) REVERT: B 479 TRP cc_start: 0.7843 (m-10) cc_final: 0.7026 (m100) REVERT: B 491 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: B 570 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 583 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8484 (m) REVERT: B 600 ARG cc_start: 0.7266 (mtt-85) cc_final: 0.7014 (ttm-80) outliers start: 58 outliers final: 31 residues processed: 203 average time/residue: 0.1021 time to fit residues: 29.2695 Evaluate side-chains 200 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [21, 126, 7, 64, 17, 55, 83, 58, 40, 14, 79] chunk 21 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114479 restraints weight = 12412.608| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.65 r_work: 0.3137 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10834 Z= 0.141 Angle : 0.599 7.523 14716 Z= 0.306 Chirality : 0.044 0.145 1726 Planarity : 0.004 0.050 1786 Dihedral : 7.137 120.802 1483 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.09 % Rotamer: Outliers : 5.28 % Allowed : 30.10 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.39 (0.21), residues: 1316 helix: -2.57 (0.16), residues: 786 sheet: 0.04 (0.48), residues: 108 loop : -1.78 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 541 TYR 0.012 0.001 TYR B 450 PHE 0.012 0.001 PHE B 182 TRP 0.008 0.001 TRP B 258 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (10834) covalent geometry : angle 0.59851 / 0.31 (14716) hydrogen bonds : bond 0.04477 / 2.83 ( 308) hydrogen bonds : angle 5.07084 / 3.49 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 0.405 Fit side-chains REVERT: A 56 ARG cc_start: 0.6890 (ttm-80) cc_final: 0.5803 (mpt180) REVERT: A 92 LYS cc_start: 0.7422 (mtpm) cc_final: 0.6425 (mmtt) REVERT: A 108 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 112 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (tm) REVERT: A 119 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7361 (mp) REVERT: A 287 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6989 (mt) REVERT: A 354 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7575 (p90) REVERT: A 356 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 473 TRP cc_start: 0.8608 (m-10) cc_final: 0.8275 (m-10) REVERT: A 541 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7166 (ttm110) REVERT: A 573 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 579 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 625 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8051 (mtp180) REVERT: A 724 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7403 (ttp-110) REVERT: A 734 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 764 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 181 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.6761 (tppt) REVERT: B 291 ARG cc_start: 0.7482 (mtm180) cc_final: 0.5312 (mmt-90) REVERT: B 324 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7292 (ttm110) REVERT: B 479 TRP cc_start: 0.7902 (m-10) cc_final: 0.7081 (m100) REVERT: B 491 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: B 570 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 583 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8520 (m) REVERT: B 600 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.7043 (ttm-80) outliers start: 61 outliers final: 39 residues processed: 191 average time/residue: 0.1034 time to fit residues: 28.0134 Evaluate side-chains 193 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [6, 5, 120, 96, 69, 54, 11, 94, 19, 3, 56] chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 54 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 240 GLN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114837 restraints weight = 12302.197| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.97 r_work: 0.3182 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10834 Z= 0.092 Angle : 0.544 7.041 14716 Z= 0.277 Chirality : 0.041 0.144 1726 Planarity : 0.004 0.038 1786 Dihedral : 6.658 115.519 1483 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 4.33 % Allowed : 31.06 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.03 (0.22), residues: 1316 helix: -2.28 (0.17), residues: 786 sheet: 0.17 (0.48), residues: 106 loop : -1.61 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 541 TYR 0.018 0.001 TYR B 500 PHE 0.010 0.001 PHE B 182 TRP 0.006 0.001 TRP B 258 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (10834) covalent geometry : angle 0.54401 / 0.28 (14716) hydrogen bonds : bond 0.03331 / 2.08 ( 308) hydrogen bonds : angle 4.70401 / 3.23 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.290 Fit side-chains REVERT: A 56 ARG cc_start: 0.6687 (ttm-80) cc_final: 0.5821 (mpt180) REVERT: A 92 LYS cc_start: 0.7429 (mtpm) cc_final: 0.6372 (mmtt) REVERT: A 112 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8235 (tm) REVERT: A 119 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7328 (mp) REVERT: A 354 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7459 (p90) REVERT: A 356 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 473 TRP cc_start: 0.8490 (m-10) cc_final: 0.8178 (m-10) REVERT: A 541 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7107 (ttm110) REVERT: A 573 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 579 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8393 (m) REVERT: A 625 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8037 (mtp180) REVERT: A 734 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 172 MET cc_start: 0.7364 (tpt) cc_final: 0.6976 (tpp) REVERT: B 181 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.6718 (tppt) REVERT: B 193 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: B 291 ARG cc_start: 0.7491 (mtm180) cc_final: 0.5186 (mmt-90) REVERT: B 309 THR cc_start: 0.8342 (p) cc_final: 0.7848 (p) REVERT: B 324 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7118 (ttm110) REVERT: B 479 TRP cc_start: 0.7789 (m-10) cc_final: 0.6956 (m100) REVERT: B 568 ASN cc_start: 0.6394 (m110) cc_final: 0.5938 (t0) REVERT: B 570 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 600 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6927 (ttm-80) outliers start: 50 outliers final: 25 residues processed: 193 average time/residue: 0.1084 time to fit residues: 29.2919 Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [34, 129, 89, 57, 9, 67, 103, 1, 49, 95, 101] chunk 34 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 240 GLN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112035 restraints weight = 12405.908| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.97 r_work: 0.3090 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10834 Z= 0.111 Angle : 0.568 7.353 14716 Z= 0.289 Chirality : 0.042 0.180 1726 Planarity : 0.004 0.043 1786 Dihedral : 6.691 117.181 1482 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.81 % Allowed : 31.23 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.89 (0.22), residues: 1316 helix: -2.17 (0.17), residues: 786 sheet: 0.21 (0.48), residues: 106 loop : -1.56 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 541 TYR 0.017 0.001 TYR B 500 PHE 0.022 0.001 PHE A 502 TRP 0.006 0.001 TRP B 258 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10834) covalent geometry : angle 0.56843 / 0.29 (14716) hydrogen bonds : bond 0.03835 / 2.42 ( 308) hydrogen bonds : angle 4.79720 / 3.30 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.403 Fit side-chains REVERT: A 56 ARG cc_start: 0.6732 (ttm-80) cc_final: 0.5857 (mpt180) REVERT: A 92 LYS cc_start: 0.7370 (mtpm) cc_final: 0.6283 (mmtt) REVERT: A 112 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8186 (tm) REVERT: A 119 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 354 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7480 (p90) REVERT: A 356 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8334 (p) REVERT: A 473 TRP cc_start: 0.8484 (m-10) cc_final: 0.8183 (m-10) REVERT: A 492 MET cc_start: 0.7322 (mmm) cc_final: 0.7121 (mmm) REVERT: A 541 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7043 (ttm110) REVERT: A 573 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 579 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8279 (m) REVERT: A 625 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8042 (mpp-170) REVERT: A 734 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 93 ASP cc_start: 0.8231 (t70) cc_final: 0.7366 (t0) REVERT: B 172 MET cc_start: 0.7284 (tpt) cc_final: 0.6907 (tpp) REVERT: B 181 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6670 (tppt) REVERT: B 193 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7546 (ttm) REVERT: B 197 MET cc_start: 0.7940 (mmt) cc_final: 0.7704 (mmt) REVERT: B 291 ARG cc_start: 0.7419 (mtm180) cc_final: 0.5108 (mmt-90) REVERT: B 324 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7037 (ttm110) REVERT: B 600 ARG cc_start: 0.7245 (mtt-85) cc_final: 0.6916 (ttm-80) outliers start: 44 outliers final: 28 residues processed: 177 average time/residue: 0.1036 time to fit residues: 25.7331 Evaluate side-chains 180 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [57, 20, 127, 97, 54, 104, 4, 50, 124, 98, 115] chunk 57 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 124 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 240 GLN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.146658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117413 restraints weight = 12239.821| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.83 r_work: 0.3197 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10834 Z= 0.090 Angle : 0.542 7.019 14716 Z= 0.275 Chirality : 0.041 0.154 1726 Planarity : 0.004 0.046 1786 Dihedral : 6.352 112.679 1482 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 3.20 % Allowed : 31.75 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.54 (0.23), residues: 1316 helix: -1.89 (0.18), residues: 782 sheet: 0.24 (0.48), residues: 108 loop : -1.40 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 541 TYR 0.017 0.001 TYR B 533 PHE 0.022 0.001 PHE A 502 TRP 0.006 0.001 TRP A 370 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (10834) covalent geometry : angle 0.54159 / 0.27 (14716) hydrogen bonds : bond 0.03185 / 1.99 ( 308) hydrogen bonds : angle 4.58007 / 3.15 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.378 Fit side-chains REVERT: A 92 LYS cc_start: 0.7413 (mtpm) cc_final: 0.6370 (mmtt) REVERT: A 112 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (tm) REVERT: A 119 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 288 TYR cc_start: 0.7510 (m-10) cc_final: 0.6969 (m-10) REVERT: A 354 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7459 (p90) REVERT: A 356 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 473 TRP cc_start: 0.8471 (m-10) cc_final: 0.8171 (m-10) REVERT: A 541 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7016 (ttm110) REVERT: A 573 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 579 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 734 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 93 ASP cc_start: 0.8236 (t70) cc_final: 0.7388 (t0) REVERT: B 181 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.6723 (tppt) REVERT: B 193 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7623 (ttm) REVERT: B 197 MET cc_start: 0.7879 (mmt) cc_final: 0.7677 (mmt) REVERT: B 291 ARG cc_start: 0.7506 (mtm180) cc_final: 0.5156 (mmt180) REVERT: B 309 THR cc_start: 0.8322 (p) cc_final: 0.7824 (p) REVERT: B 324 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7026 (ttm110) REVERT: B 600 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6900 (ttm-80) outliers start: 37 outliers final: 22 residues processed: 176 average time/residue: 0.0993 time to fit residues: 24.4209 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [28, 111, 22, 122, 99, 94, 73, 27, 0, 92, 34] chunk 28 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 22 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 73 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113932 restraints weight = 12444.623| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.96 r_work: 0.3226 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10834 Z= 0.108 Angle : 0.562 7.130 14716 Z= 0.285 Chirality : 0.042 0.147 1726 Planarity : 0.004 0.036 1786 Dihedral : 6.353 113.473 1481 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 3.63 % Allowed : 31.57 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.46 (0.23), residues: 1316 helix: -1.81 (0.18), residues: 782 sheet: 0.23 (0.48), residues: 108 loop : -1.39 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 724 TYR 0.022 0.001 TYR A 644 PHE 0.021 0.001 PHE A 502 TRP 0.007 0.001 TRP B 298 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10834) covalent geometry : angle 0.56250 / 0.28 (14716) hydrogen bonds : bond 0.03711 / 2.33 ( 308) hydrogen bonds : angle 4.68992 / 3.23 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2781.45 seconds wall clock time: 48 minutes 9.41 seconds (2889.41 seconds total)