Starting phenix.real_space_refine on Mon Jan 20 23:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy5_37916/01_2025/8wy5_37916.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 Ca 4 9.91 5 P 76 5.49 5 S 48 5.16 5 C 10048 2.51 5 N 2664 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "D" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.20, per 1000 atoms: 0.64 Number of scatterers: 16038 At special positions: 0 Unit cell: (118.44, 78.96, 185.64, 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) Ca 4 19.99 S 48 16.00 P 76 15.00 O 3198 8.00 N 2664 7.00 C 10048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.9 seconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3356 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 16 sheets defined 38.5% alpha, 15.3% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.889A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.687A pdb=" N PHE A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.713A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.632A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.633A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.723A pdb=" N TYR A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 399 " --> pdb=" O PRO A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.639A pdb=" N CYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.628A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 512 through 529 removed outlier: 3.626A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.537A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.572A pdb=" N VAL A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.542A pdb=" N GLU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.749A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.857A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 380 through 395 removed outlier: 4.130A pdb=" N LYS B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 4.062A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.429A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.568A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.622A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.646A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.718A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.954A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.798A pdb=" N PHE C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 94 removed outlier: 4.187A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.763A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.761A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.723A pdb=" N PHE C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 372 " --> pdb=" O ALA C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.521A pdb=" N ILE C 385 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.665A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 402 " --> pdb=" O TYR C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.779A pdb=" N CYS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.993A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.675A pdb=" N ARG C 481 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 501 removed outlier: 4.152A pdb=" N GLU C 499 " --> pdb=" O ASN C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.697A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.160A pdb=" N ILE C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.622A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.625A pdb=" N LEU C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.793A pdb=" N VAL C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.925A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.059A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.847A pdb=" N ALA D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.697A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.545A pdb=" N ALA D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.826A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.516A pdb=" N CYS D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 4.056A pdb=" N LEU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 4.009A pdb=" N LYS D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 501 removed outlier: 4.088A pdb=" N GLU D 499 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.872A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 523 through 529 removed outlier: 4.029A pdb=" N ILE D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.014A pdb=" N LYS D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.799A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 546' Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.823A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.975A pdb=" N VAL A 17 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 71 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.149A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 7.011A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.650A pdb=" N VAL B 17 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 71 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.526A pdb=" N TYR B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.613A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 375 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 508 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 431 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.943A pdb=" N VAL C 17 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 71 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.326A pdb=" N LYS C 150 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 286 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 152 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLU C 288 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 154 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 25 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 335 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 403 through 407 removed outlier: 7.006A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.906A pdb=" N VAL D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 71 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.501A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 403 through 407 Processing sheet with id=AB7, first strand: chain 'D' and resid 435 through 437 434 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 4.37 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: 3709 1.33 - 1.45: 3501 1.45 - 1.57: 9018 1.57 - 1.69: 160 1.69 - 1.81: 76 Bond restraints: 16464 Sorted by residual: bond pdb=" N ILE B 510 " pdb=" CA ILE B 510 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N SER B 508 " pdb=" CA SER B 508 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.65e+00 bond pdb=" N ASP B 511 " pdb=" CA ASP B 511 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.99e+00 bond pdb=" CA ASN B 551 " pdb=" CB ASN B 551 " ideal model delta sigma weight residual 1.522 1.554 -0.033 1.27e-02 6.20e+03 6.56e+00 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 21665 2.71 - 5.42: 616 5.42 - 8.14: 99 8.14 - 10.85: 62 10.85 - 13.56: 8 Bond angle restraints: 22450 Sorted by residual: angle pdb=" C LEU B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.54 134.94 -13.40 1.91e+00 2.74e-01 4.92e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 133.96 -12.42 1.91e+00 2.74e-01 4.23e+01 angle pdb=" C LYS B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 121.97 132.81 -10.84 1.80e+00 3.09e-01 3.63e+01 ... (remaining 22445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 9368 34.89 - 69.79: 455 69.79 - 104.68: 15 104.68 - 139.58: 0 139.58 - 174.47: 6 Dihedral angle restraints: 9844 sinusoidal: 4650 harmonic: 5194 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASP C 515 " pdb=" C ASP C 515 " pdb=" N LEU C 516 " pdb=" CA LEU C 516 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 9841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2414 0.140 - 0.280: 83 0.280 - 0.419: 5 0.419 - 0.559: 2 0.559 - 0.699: 6 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DA H 20 " pdb=" OP1 DA H 20 " pdb=" OP2 DA H 20 " pdb=" O5' DA H 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.59e+00 ... (remaining 2507 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 93 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 93 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL B 93 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 395 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO D 396 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 396 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 396 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 520 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ILE B 520 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 521 " -0.015 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5256 2.88 - 3.39: 12922 3.39 - 3.89: 26558 3.89 - 4.40: 29956 4.40 - 4.90: 49730 Nonbonded interactions: 124422 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG1 THR C 36 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.385 3.040 nonbonded pdb=" OG SER D 78 " pdb=" O ALA D 102 " model vdw 2.389 3.040 nonbonded pdb=" O ASP A 32 " pdb=" OG1 THR A 36 " model vdw 2.389 3.040 nonbonded pdb=" O ASP B 32 " pdb=" OG1 THR B 36 " model vdw 2.396 3.040 ... (remaining 124417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 575 or resid 1001)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 351 or resid 363 through 575 or resid 1001)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.510 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.006 0.076 16464 Z= 0.409 Angle : 1.175 13.561 22450 Z= 0.616 Chirality : 0.070 0.699 2510 Planarity : 0.006 0.081 2586 Dihedral : 18.379 174.473 6488 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.04 % Favored : 94.50 % Rotamer: Outliers : 0.18 % Allowed : 0.67 % Favored : 99.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.15), residues: 1746 helix: -4.48 (0.08), residues: 532 sheet: -0.56 (0.27), residues: 356 loop : -2.38 (0.16), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 126 HIS 0.005 0.001 HIS C 563 PHE 0.035 0.003 PHE C 387 TYR 0.031 0.002 TYR D 113 ARG 0.007 0.001 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5466 (t80) cc_final: 0.4895 (t80) REVERT: A 367 SER cc_start: 0.8211 (m) cc_final: 0.7982 (p) REVERT: A 507 LEU cc_start: 0.7896 (tp) cc_final: 0.7594 (tp) REVERT: B 1 MET cc_start: 0.4486 (mtp) cc_final: 0.3440 (tmm) REVERT: B 105 PHE cc_start: 0.4023 (t80) cc_final: 0.1745 (t80) REVERT: B 507 LEU cc_start: 0.7356 (tp) cc_final: 0.7116 (tp) REVERT: C 2 LYS cc_start: 0.6309 (ptpt) cc_final: 0.6103 (pptt) REVERT: C 106 TYR cc_start: 0.6638 (m-80) cc_final: 0.6419 (m-80) REVERT: C 388 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 550 ASN cc_start: 0.6972 (m-40) cc_final: 0.6358 (p0) REVERT: C 571 GLU cc_start: 0.6416 (mp0) cc_final: 0.5812 (mp0) REVERT: D 141 ASN cc_start: 0.7895 (m-40) cc_final: 0.7675 (m110) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.3184 time to fit residues: 129.1631 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 544 ASN B 563 HIS C 535 HIS D 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.250099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209795 restraints weight = 18944.100| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.36 r_work: 0.4069 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16464 Z= 0.195 Angle : 0.615 8.138 22450 Z= 0.339 Chirality : 0.045 0.179 2510 Planarity : 0.004 0.050 2586 Dihedral : 19.864 177.578 2759 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.10 % Favored : 94.56 % Rotamer: Outliers : 0.49 % Allowed : 8.16 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.17), residues: 1746 helix: -2.65 (0.17), residues: 528 sheet: -0.52 (0.28), residues: 366 loop : -1.93 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 126 HIS 0.003 0.001 HIS B 535 PHE 0.017 0.002 PHE B 11 TYR 0.015 0.001 TYR D 113 ARG 0.004 0.001 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4772 (tpt) cc_final: 0.4363 (tpt) REVERT: A 105 PHE cc_start: 0.5452 (t80) cc_final: 0.5117 (t80) REVERT: A 388 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 1 MET cc_start: 0.3666 (mtp) cc_final: 0.3188 (tmm) REVERT: C 87 LYS cc_start: 0.6612 (mmtt) cc_final: 0.5293 (mttp) REVERT: C 296 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.5887 (mtm180) REVERT: C 388 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7355 (mt-10) REVERT: C 545 MET cc_start: 0.7291 (mmt) cc_final: 0.6356 (mmt) REVERT: D 509 GLU cc_start: 0.6249 (pm20) cc_final: 0.6007 (pm20) outliers start: 8 outliers final: 3 residues processed: 201 average time/residue: 0.3163 time to fit residues: 92.0192 Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS C 483 ASN D 61 HIS D 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.238070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.191723 restraints weight = 18294.794| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.42 r_work: 0.3904 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16464 Z= 0.412 Angle : 0.761 9.156 22450 Z= 0.413 Chirality : 0.051 0.192 2510 Planarity : 0.005 0.061 2586 Dihedral : 19.931 172.832 2759 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.59 % Favored : 93.01 % Rotamer: Outliers : 1.35 % Allowed : 13.13 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.18), residues: 1746 helix: -1.86 (0.19), residues: 572 sheet: -0.87 (0.28), residues: 366 loop : -1.79 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP C 126 HIS 0.007 0.002 HIS A 415 PHE 0.022 0.003 PHE D 316 TYR 0.021 0.002 TYR B 40 ARG 0.010 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5957 (t80) cc_final: 0.5566 (t80) REVERT: A 563 HIS cc_start: 0.4892 (OUTLIER) cc_final: 0.3731 (m90) REVERT: A 566 PHE cc_start: 0.7566 (m-10) cc_final: 0.7339 (m-10) REVERT: C 524 MET cc_start: 0.6629 (mtt) cc_final: 0.6322 (mmm) REVERT: D 87 LYS cc_start: 0.6697 (mptt) cc_final: 0.6407 (mttp) REVERT: D 514 ASN cc_start: 0.6374 (m-40) cc_final: 0.6062 (m110) outliers start: 22 outliers final: 17 residues processed: 188 average time/residue: 0.3104 time to fit residues: 86.4143 Evaluate side-chains 171 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.241341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.196127 restraints weight = 18290.563| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.35 r_work: 0.3960 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16464 Z= 0.211 Angle : 0.603 8.605 22450 Z= 0.332 Chirality : 0.046 0.163 2510 Planarity : 0.003 0.046 2586 Dihedral : 19.590 175.181 2758 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 1.47 % Allowed : 16.13 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1746 helix: -1.23 (0.21), residues: 570 sheet: -0.72 (0.28), residues: 366 loop : -1.50 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 126 HIS 0.003 0.001 HIS C 415 PHE 0.017 0.001 PHE A 315 TYR 0.013 0.001 TYR D 113 ARG 0.005 0.000 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 HIS cc_start: 0.4835 (OUTLIER) cc_final: 0.3983 (m90) REVERT: B 493 TYR cc_start: 0.8047 (m-80) cc_final: 0.7847 (m-80) REVERT: C 284 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7438 (mt) REVERT: C 524 MET cc_start: 0.6554 (mtt) cc_final: 0.6281 (mmm) REVERT: D 87 LYS cc_start: 0.6598 (mptt) cc_final: 0.6275 (mttp) REVERT: D 514 ASN cc_start: 0.6231 (m-40) cc_final: 0.5906 (m110) outliers start: 24 outliers final: 12 residues processed: 187 average time/residue: 0.2956 time to fit residues: 81.8102 Evaluate side-chains 166 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN C 63 HIS D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.235681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189660 restraints weight = 18623.248| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.37 r_work: 0.3946 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16464 Z= 0.358 Angle : 0.693 8.220 22450 Z= 0.376 Chirality : 0.049 0.177 2510 Planarity : 0.004 0.049 2586 Dihedral : 19.592 173.660 2758 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.33 % Favored : 92.33 % Rotamer: Outliers : 2.52 % Allowed : 16.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1746 helix: -1.02 (0.21), residues: 570 sheet: -0.89 (0.29), residues: 364 loop : -1.49 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP D 126 HIS 0.004 0.001 HIS B 535 PHE 0.020 0.002 PHE A 315 TYR 0.019 0.002 TYR C 40 ARG 0.008 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 HIS cc_start: 0.4711 (OUTLIER) cc_final: 0.3742 (m90) REVERT: C 63 HIS cc_start: 0.5972 (OUTLIER) cc_final: 0.5069 (t70) REVERT: C 284 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7556 (mt) REVERT: C 510 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.7011 (pt) REVERT: C 524 MET cc_start: 0.6775 (mtt) cc_final: 0.6561 (mmm) REVERT: C 545 MET cc_start: 0.7233 (mmt) cc_final: 0.6535 (mmt) REVERT: D 87 LYS cc_start: 0.6734 (mptt) cc_final: 0.6424 (mttp) REVERT: D 284 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7473 (mt) REVERT: D 514 ASN cc_start: 0.6481 (m-40) cc_final: 0.6125 (m110) outliers start: 41 outliers final: 25 residues processed: 192 average time/residue: 0.2814 time to fit residues: 80.9095 Evaluate side-chains 177 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 312 TYR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS C 350 ASN D 350 ASN D 421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.243922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.198557 restraints weight = 18796.111| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.27 r_work: 0.4056 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16464 Z= 0.177 Angle : 0.581 7.544 22450 Z= 0.319 Chirality : 0.045 0.158 2510 Planarity : 0.003 0.062 2586 Dihedral : 19.428 175.793 2758 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.29 % Allowed : 18.96 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1746 helix: -0.62 (0.22), residues: 570 sheet: -0.72 (0.28), residues: 376 loop : -1.21 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.007 0.001 HIS D 61 PHE 0.017 0.001 PHE A 315 TYR 0.013 0.001 TYR D 113 ARG 0.003 0.000 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.6029 (mptt) cc_final: 0.5824 (mptt) REVERT: A 563 HIS cc_start: 0.4515 (OUTLIER) cc_final: 0.3824 (m90) REVERT: C 510 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6908 (pt) REVERT: D 87 LYS cc_start: 0.6723 (mptt) cc_final: 0.6403 (mttp) outliers start: 21 outliers final: 12 residues processed: 176 average time/residue: 0.2849 time to fit residues: 76.1279 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN D 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.243367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.197642 restraints weight = 18907.661| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.30 r_work: 0.4041 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16464 Z= 0.202 Angle : 0.596 7.420 22450 Z= 0.324 Chirality : 0.045 0.154 2510 Planarity : 0.003 0.049 2586 Dihedral : 19.366 175.460 2758 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.24 % Favored : 93.41 % Rotamer: Outliers : 1.23 % Allowed : 19.51 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1746 helix: -0.45 (0.22), residues: 570 sheet: -0.64 (0.28), residues: 374 loop : -1.15 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.003 0.001 HIS A 427 PHE 0.021 0.001 PHE D 543 TYR 0.013 0.001 TYR D 113 ARG 0.004 0.000 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.6333 (mptt) cc_final: 0.6021 (mptt) REVERT: A 563 HIS cc_start: 0.4453 (OUTLIER) cc_final: 0.3735 (m90) REVERT: C 284 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7516 (mt) REVERT: C 510 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6904 (pt) REVERT: D 87 LYS cc_start: 0.6692 (mptt) cc_final: 0.6404 (mttp) REVERT: D 130 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7069 (tt) REVERT: D 284 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7505 (mt) REVERT: D 514 ASN cc_start: 0.6472 (m-40) cc_final: 0.6062 (m110) outliers start: 20 outliers final: 12 residues processed: 174 average time/residue: 0.2779 time to fit residues: 73.2682 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.240674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193780 restraints weight = 18734.833| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.25 r_work: 0.4008 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16464 Z= 0.282 Angle : 0.649 7.304 22450 Z= 0.352 Chirality : 0.047 0.152 2510 Planarity : 0.004 0.045 2586 Dihedral : 19.399 174.582 2758 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.45 % Favored : 92.21 % Rotamer: Outliers : 1.60 % Allowed : 19.82 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1746 helix: -0.45 (0.22), residues: 570 sheet: -0.77 (0.28), residues: 364 loop : -1.17 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 126 HIS 0.004 0.001 HIS A 427 PHE 0.019 0.002 PHE D 543 TYR 0.014 0.002 TYR B 113 ARG 0.007 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.6443 (mptt) cc_final: 0.5937 (mmtm) REVERT: A 563 HIS cc_start: 0.4384 (OUTLIER) cc_final: 0.3597 (m90) REVERT: C 284 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7556 (mt) REVERT: C 510 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6858 (pt) REVERT: D 87 LYS cc_start: 0.6781 (mptt) cc_final: 0.6463 (mttp) REVERT: D 130 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7098 (mp) REVERT: D 284 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7486 (mt) REVERT: D 514 ASN cc_start: 0.6549 (m-40) cc_final: 0.6125 (m110) outliers start: 26 outliers final: 18 residues processed: 183 average time/residue: 0.2777 time to fit residues: 77.6027 Evaluate side-chains 176 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 170 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.241382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.194825 restraints weight = 18751.523| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.23 r_work: 0.3995 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16464 Z= 0.245 Angle : 0.626 7.636 22450 Z= 0.339 Chirality : 0.046 0.152 2510 Planarity : 0.003 0.038 2586 Dihedral : 19.271 175.439 2758 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.70 % Favored : 92.96 % Rotamer: Outliers : 1.72 % Allowed : 20.00 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1746 helix: -0.36 (0.22), residues: 570 sheet: -0.90 (0.28), residues: 376 loop : -1.06 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 126 HIS 0.004 0.001 HIS A 427 PHE 0.018 0.002 PHE D 543 TYR 0.013 0.002 TYR B 113 ARG 0.005 0.000 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.6543 (mptt) cc_final: 0.6245 (mptt) REVERT: A 563 HIS cc_start: 0.4449 (OUTLIER) cc_final: 0.3722 (m90) REVERT: B 106 TYR cc_start: 0.7016 (m-80) cc_final: 0.6814 (m-80) REVERT: B 481 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7772 (ptt180) REVERT: C 1 MET cc_start: 0.3037 (tpt) cc_final: 0.1898 (ptt) REVERT: C 284 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7500 (mt) REVERT: C 510 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6845 (pt) REVERT: D 87 LYS cc_start: 0.6780 (mptt) cc_final: 0.6514 (mttp) REVERT: D 130 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7087 (mp) REVERT: D 284 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7453 (mt) REVERT: D 514 ASN cc_start: 0.6423 (m-40) cc_final: 0.6014 (m110) outliers start: 28 outliers final: 20 residues processed: 182 average time/residue: 0.2673 time to fit residues: 75.3854 Evaluate side-chains 174 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN C 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.241747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.195493 restraints weight = 18881.463| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.21 r_work: 0.4000 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16464 Z= 0.223 Angle : 0.621 13.683 22450 Z= 0.336 Chirality : 0.046 0.199 2510 Planarity : 0.003 0.037 2586 Dihedral : 19.048 175.479 2758 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.90 % Rotamer: Outliers : 1.66 % Allowed : 20.37 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1746 helix: -0.19 (0.23), residues: 556 sheet: -0.91 (0.28), residues: 378 loop : -0.95 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 126 HIS 0.004 0.001 HIS A 427 PHE 0.018 0.001 PHE D 543 TYR 0.013 0.001 TYR B 113 ARG 0.004 0.000 ARG C 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 476 LYS cc_start: 0.6728 (mptt) cc_final: 0.6373 (mptt) REVERT: A 536 TYR cc_start: 0.7032 (t80) cc_final: 0.5888 (t80) REVERT: A 563 HIS cc_start: 0.4485 (OUTLIER) cc_final: 0.3809 (m90) REVERT: B 13 ASN cc_start: 0.8191 (m110) cc_final: 0.7983 (m-40) REVERT: C 1 MET cc_start: 0.2900 (tpt) cc_final: 0.1883 (ptt) REVERT: C 284 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7497 (mt) REVERT: C 510 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6888 (pt) REVERT: D 87 LYS cc_start: 0.6761 (mptt) cc_final: 0.6516 (mttp) REVERT: D 284 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7478 (mt) outliers start: 27 outliers final: 20 residues processed: 182 average time/residue: 0.2830 time to fit residues: 80.0377 Evaluate side-chains 177 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.241544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195722 restraints weight = 18837.747| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.15 r_work: 0.4039 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16464 Z= 0.226 Angle : 0.623 12.421 22450 Z= 0.337 Chirality : 0.046 0.198 2510 Planarity : 0.003 0.038 2586 Dihedral : 18.963 175.541 2758 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.64 % Favored : 93.01 % Rotamer: Outliers : 1.90 % Allowed : 20.31 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1746 helix: -0.15 (0.23), residues: 556 sheet: -0.93 (0.27), residues: 378 loop : -0.95 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 126 HIS 0.004 0.001 HIS A 427 PHE 0.018 0.002 PHE D 543 TYR 0.014 0.001 TYR B 106 ARG 0.004 0.000 ARG C 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7591.41 seconds wall clock time: 138 minutes 18.71 seconds (8298.71 seconds total)