Starting phenix.real_space_refine on Fri Jul 3 20:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy5_37916/07_2026/8wy5_37916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy5_37916/07_2026/8wy5_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_37916/07_2026/8wy5_37916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy5_37916/07_2026/8wy5_37916.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy5_37916/07_2026/8wy5_37916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy5_37916/07_2026/8wy5_37916.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 3.15, per 1000 atoms: 0.20 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: 0.81 Conformation dependent library (CDL) restraints added in 456.3 milliseconds 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: 1.60 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: 2.15 Time building geometry restraints manager: 1.16 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=" C3' DT F 6 " pdb=" O3' DT F 6 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.32e+01 bond pdb=" C3' DT H 6 " pdb=" O3' DT H 6 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.19e+01 bond pdb=" C1' DC E 10 " pdb=" N1 DC E 10 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C3' DT G 14 " pdb=" O3' DT G 14 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.38e+01 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 21639 2.71 - 5.42: 642 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: 2411 0.140 - 0.280: 86 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 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.23e+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 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.89e+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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 1001)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 351 or resid 363 through 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.007 0.072 16464 Z= 0.418 Angle : 1.201 13.561 22450 Z= 0.717 Chirality : 0.071 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (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 ARG 0.007 0.001 ARG D 12 TYR 0.031 0.002 TYR D 113 PHE 0.035 0.003 PHE C 387 TRP 0.018 0.003 TRP B 126 HIS 0.005 0.001 HIS C 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.42 (16464) covalent geometry : angle 1.20109 / 0.72 (22450) hydrogen bonds : bond 0.22568 / 15.01 ( 516) hydrogen bonds : angle 8.94462 / 6.23 ( 1391) *********************** 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 : 0.570 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 388 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6356 (mt-10) 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 493 TYR cc_start: 0.7744 (m-80) cc_final: 0.7489 (m-80) 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: 0.6415 (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: 0.1197 time to fit residues: 49.1334 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 : 0.587 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN B 563 HIS C 13 ASN D 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.250996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.210717 restraints weight = 18904.906| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.20 r_work: 0.4096 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16464 Z= 0.168 Angle : 0.683 9.071 22450 Z= 0.381 Chirality : 0.049 0.286 2510 Planarity : 0.004 0.048 2586 Dihedral : 20.135 173.454 2759 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.04 % Favored : 94.56 % Rotamer: Outliers : 0.61 % Allowed : 8.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.17), residues: 1746 helix: -2.83 (0.16), residues: 514 sheet: -0.35 (0.28), residues: 356 loop : -1.99 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 504 TYR 0.023 0.002 TYR B 113 PHE 0.017 0.002 PHE B 11 TRP 0.005 0.002 TRP A 126 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (16464) covalent geometry : angle 0.68324 / 0.38 (22450) hydrogen bonds : bond 0.05957 / 3.84 ( 516) hydrogen bonds : angle 6.42004 / 4.47 ( 1391) *********************** 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 205 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5486 (t80) cc_final: 0.5122 (t80) REVERT: A 117 GLU cc_start: 0.6328 (tp30) cc_final: 0.6099 (tp30) REVERT: A 492 GLN cc_start: 0.8017 (pp30) cc_final: 0.7768 (pp30) REVERT: B 1 MET cc_start: 0.3926 (mtp) cc_final: 0.3040 (tpt) REVERT: B 507 LEU cc_start: 0.7619 (tp) cc_final: 0.7410 (tp) REVERT: C 296 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6120 (mtm180) REVERT: C 422 ASP cc_start: 0.6722 (m-30) cc_final: 0.6488 (p0) REVERT: C 545 MET cc_start: 0.6863 (mmt) cc_final: 0.6176 (mmt) REVERT: C 571 GLU cc_start: 0.6504 (mp0) cc_final: 0.6051 (mp0) REVERT: D 132 ASN cc_start: 0.6771 (t0) cc_final: 0.6570 (t0) REVERT: D 509 GLU cc_start: 0.6295 (pm20) cc_final: 0.6047 (pm20) outliers start: 10 outliers final: 3 residues processed: 202 average time/residue: 0.1169 time to fit residues: 34.8563 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 : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 HIS B 421 ASN C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.249999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.210477 restraints weight = 19006.038| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.19 r_work: 0.4060 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16464 Z= 0.138 Angle : 0.602 8.079 22450 Z= 0.339 Chirality : 0.048 0.329 2510 Planarity : 0.003 0.036 2586 Dihedral : 20.053 174.871 2759 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 0.74 % Allowed : 11.60 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 1746 helix: -1.69 (0.20), residues: 528 sheet: -0.44 (0.28), residues: 376 loop : -1.75 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 374 TYR 0.017 0.001 TYR D 113 PHE 0.014 0.001 PHE A 315 TRP 0.004 0.002 TRP B 126 HIS 0.011 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (16464) covalent geometry : angle 0.60240 / 0.34 (22450) hydrogen bonds : bond 0.04765 / 3.06 ( 516) hydrogen bonds : angle 5.87049 / 4.10 ( 1391) *********************** 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 187 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4761 (tpt) cc_final: 0.4415 (tpt) REVERT: A 105 PHE cc_start: 0.5520 (t80) cc_final: 0.5252 (t80) REVERT: A 388 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6785 (mt-10) REVERT: A 432 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: A 481 ARG cc_start: 0.8772 (mtp85) cc_final: 0.8225 (mtp180) REVERT: B 1 MET cc_start: 0.3720 (mtp) cc_final: 0.3141 (mmm) REVERT: B 481 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7933 (ptt180) REVERT: C 87 LYS cc_start: 0.6588 (mmtt) cc_final: 0.5302 (mttp) REVERT: D 392 ASP cc_start: 0.7071 (t0) cc_final: 0.6844 (t0) REVERT: D 566 PHE cc_start: 0.7803 (m-80) cc_final: 0.7449 (m-10) outliers start: 12 outliers final: 8 residues processed: 186 average time/residue: 0.1251 time to fit residues: 34.6020 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 544 ASN C 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.250804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.205129 restraints weight = 18891.405| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.65 r_work: 0.4005 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16464 Z= 0.141 Angle : 0.594 8.093 22450 Z= 0.332 Chirality : 0.048 0.325 2510 Planarity : 0.003 0.043 2586 Dihedral : 19.907 174.586 2759 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 0.80 % Allowed : 13.37 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.19), residues: 1746 helix: -1.12 (0.22), residues: 530 sheet: -0.46 (0.28), residues: 370 loop : -1.47 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.021 0.001 TYR A 493 PHE 0.014 0.001 PHE D 105 TRP 0.004 0.002 TRP B 126 HIS 0.006 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16464) covalent geometry : angle 0.59381 / 0.33 (22450) hydrogen bonds : bond 0.04419 / 2.81 ( 516) hydrogen bonds : angle 5.64707 / 3.94 ( 1391) *********************** 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 179 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4515 (tpt) cc_final: 0.4256 (tpt) REVERT: A 388 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6752 (mt-10) REVERT: A 563 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.3855 (m90) REVERT: B 1 MET cc_start: 0.3726 (mtp) cc_final: 0.3035 (tpt) REVERT: B 481 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8014 (ptt180) REVERT: C 87 LYS cc_start: 0.6653 (mmtt) cc_final: 0.5320 (mttp) REVERT: D 392 ASP cc_start: 0.7182 (t0) cc_final: 0.6922 (t0) REVERT: D 566 PHE cc_start: 0.7920 (m-80) cc_final: 0.7627 (m-10) outliers start: 13 outliers final: 9 residues processed: 176 average time/residue: 0.1264 time to fit residues: 32.9879 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 344 CYS 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 508 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.243159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199112 restraints weight = 18790.784| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.41 r_work: 0.3981 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2739 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= 0.202 Angle : 0.667 8.652 22450 Z= 0.367 Chirality : 0.050 0.328 2510 Planarity : 0.004 0.045 2586 Dihedral : 19.917 173.377 2759 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 1.29 % Allowed : 15.34 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.19), residues: 1746 helix: -0.89 (0.22), residues: 544 sheet: -0.65 (0.28), residues: 366 loop : -1.44 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 12 TYR 0.026 0.002 TYR D 106 PHE 0.017 0.002 PHE C 28 TRP 0.008 0.003 TRP D 126 HIS 0.006 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (16464) covalent geometry : angle 0.66744 / 0.37 (22450) hydrogen bonds : bond 0.04977 / 3.15 ( 516) hydrogen bonds : angle 5.80127 / 4.04 ( 1391) *********************** 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 185 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 432 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: A 563 HIS cc_start: 0.4431 (OUTLIER) cc_final: 0.3749 (m90) REVERT: B 1 MET cc_start: 0.3702 (mtp) cc_final: 0.3249 (tpt) REVERT: B 504 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.6559 (mmt180) REVERT: B 514 ASN cc_start: 0.6204 (m-40) cc_final: 0.5711 (m-40) REVERT: C 87 LYS cc_start: 0.6825 (mmtt) cc_final: 0.5455 (mttp) REVERT: C 284 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 524 MET cc_start: 0.6532 (mtt) cc_final: 0.6126 (mmm) REVERT: D 392 ASP cc_start: 0.7190 (t0) cc_final: 0.6924 (t0) REVERT: D 514 ASN cc_start: 0.6257 (m-40) cc_final: 0.5958 (m110) REVERT: D 566 PHE cc_start: 0.7966 (m-80) cc_final: 0.7667 (m-10) outliers start: 21 outliers final: 13 residues processed: 181 average time/residue: 0.1149 time to fit residues: 31.5787 Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 125 LYS 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 367 SER Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 ASN C 483 ASN C 550 ASN D 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.244816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201799 restraints weight = 18665.480| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.35 r_work: 0.3999 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16464 Z= 0.142 Angle : 0.592 8.218 22450 Z= 0.331 Chirality : 0.048 0.326 2510 Planarity : 0.003 0.038 2586 Dihedral : 19.831 173.504 2758 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 1.35 % Allowed : 16.87 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1746 helix: -0.63 (0.23), residues: 528 sheet: -0.54 (0.29), residues: 366 loop : -1.30 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 504 TYR 0.014 0.001 TYR C 314 PHE 0.015 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (16464) covalent geometry : angle 0.59219 / 0.33 (22450) hydrogen bonds : bond 0.04251 / 2.70 ( 516) hydrogen bonds : angle 5.56422 / 3.88 ( 1391) *********************** 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 176 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6650 (mt-10) REVERT: A 563 HIS cc_start: 0.4438 (OUTLIER) cc_final: 0.3720 (m90) REVERT: B 1 MET cc_start: 0.3483 (mtp) cc_final: 0.3153 (tpt) REVERT: B 504 ARG cc_start: 0.7229 (mmm-85) cc_final: 0.6597 (mmt180) REVERT: C 87 LYS cc_start: 0.6798 (mmtt) cc_final: 0.5442 (mttp) REVERT: C 513 GLU cc_start: 0.4647 (mp0) cc_final: 0.4444 (mp0) REVERT: C 524 MET cc_start: 0.6409 (mtt) cc_final: 0.6077 (mmm) REVERT: D 284 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7393 (mt) REVERT: D 392 ASP cc_start: 0.7349 (t0) cc_final: 0.7100 (t0) REVERT: D 566 PHE cc_start: 0.7973 (m-80) cc_final: 0.7762 (m-10) outliers start: 22 outliers final: 14 residues processed: 173 average time/residue: 0.1147 time to fit residues: 29.9162 Evaluate side-chains 164 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 140 optimal weight: 0.2980 chunk 115 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 330 ASN D 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.245661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202235 restraints weight = 18565.415| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.37 r_work: 0.4006 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16464 Z= 0.122 Angle : 0.582 9.457 22450 Z= 0.322 Chirality : 0.047 0.316 2510 Planarity : 0.003 0.051 2586 Dihedral : 19.731 173.866 2758 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.10 % Allowed : 17.36 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1746 helix: -0.43 (0.23), residues: 530 sheet: -0.37 (0.29), residues: 362 loop : -1.19 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.014 0.001 TYR C 314 PHE 0.014 0.001 PHE A 315 TRP 0.002 0.001 TRP D 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (16464) covalent geometry : angle 0.58188 / 0.32 (22450) hydrogen bonds : bond 0.03997 / 2.52 ( 516) hydrogen bonds : angle 5.36129 / 3.75 ( 1391) *********************** 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 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6706 (mt-10) REVERT: A 481 ARG cc_start: 0.8804 (mtp85) cc_final: 0.8262 (mtp180) REVERT: A 563 HIS cc_start: 0.4266 (OUTLIER) cc_final: 0.3651 (m90) REVERT: B 1 MET cc_start: 0.3488 (mtp) cc_final: 0.3144 (tpt) REVERT: B 504 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6678 (mmt180) REVERT: C 87 LYS cc_start: 0.6712 (mmtt) cc_final: 0.5438 (mttp) REVERT: C 125 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6764 (mtpp) REVERT: C 513 GLU cc_start: 0.4610 (mp0) cc_final: 0.4409 (mp0) REVERT: C 524 MET cc_start: 0.6273 (mtt) cc_final: 0.6004 (mmm) REVERT: D 392 ASP cc_start: 0.7364 (t0) cc_final: 0.7076 (t0) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.1145 time to fit residues: 29.4173 Evaluate side-chains 161 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain A residue 344 CYS 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 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN C 538 GLN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.243232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.200082 restraints weight = 18722.137| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.28 r_work: 0.4001 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16464 Z= 0.168 Angle : 0.616 8.216 22450 Z= 0.340 Chirality : 0.048 0.319 2510 Planarity : 0.003 0.044 2586 Dihedral : 19.739 173.671 2758 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % Rotamer: Outliers : 1.10 % Allowed : 18.04 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1746 helix: -0.40 (0.23), residues: 540 sheet: -0.51 (0.28), residues: 366 loop : -1.16 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 12 TYR 0.024 0.002 TYR D 106 PHE 0.016 0.002 PHE A 315 TRP 0.007 0.002 TRP B 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16464) covalent geometry : angle 0.61577 / 0.34 (22450) hydrogen bonds : bond 0.04347 / 2.75 ( 516) hydrogen bonds : angle 5.47361 / 3.82 ( 1391) *********************** 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 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 481 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8281 (mtp180) REVERT: A 563 HIS cc_start: 0.4402 (OUTLIER) cc_final: 0.3714 (m90) REVERT: B 1 MET cc_start: 0.3622 (mtp) cc_final: 0.3262 (tpt) REVERT: B 504 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.6710 (mmt180) REVERT: C 87 LYS cc_start: 0.6859 (mmtt) cc_final: 0.5505 (mttp) REVERT: C 524 MET cc_start: 0.6221 (mtt) cc_final: 0.5973 (mmm) REVERT: D 284 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7377 (mt) REVERT: D 392 ASP cc_start: 0.7323 (t0) cc_final: 0.7035 (t0) REVERT: D 514 ASN cc_start: 0.6176 (m-40) cc_final: 0.5849 (m110) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 0.1273 time to fit residues: 33.4170 Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 125 LYS 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 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 331 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN C 538 GLN D 330 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 = 0.4630 r_free = 0.4630 target = 0.245044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.191675 restraints weight = 18703.425| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.51 r_work: 0.3978 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16464 Z= 0.152 Angle : 0.603 9.145 22450 Z= 0.333 Chirality : 0.048 0.320 2510 Planarity : 0.003 0.083 2586 Dihedral : 19.735 173.477 2758 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % Rotamer: Outliers : 1.10 % Allowed : 18.22 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1746 helix: -0.35 (0.23), residues: 540 sheet: -0.51 (0.28), residues: 366 loop : -1.10 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 12 TYR 0.012 0.001 TYR C 314 PHE 0.015 0.001 PHE A 315 TRP 0.004 0.002 TRP D 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16464) covalent geometry : angle 0.60268 / 0.33 (22450) hydrogen bonds : bond 0.04182 / 2.64 ( 516) hydrogen bonds : angle 5.43916 / 3.80 ( 1391) *********************** 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 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 HIS cc_start: 0.4239 (OUTLIER) cc_final: 0.3545 (m90) REVERT: B 1 MET cc_start: 0.3641 (mtp) cc_final: 0.3264 (tpt) REVERT: B 504 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.6707 (mmt180) REVERT: C 125 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6679 (mtpp) REVERT: C 524 MET cc_start: 0.6196 (mtt) cc_final: 0.5960 (mmm) REVERT: D 143 ASN cc_start: 0.6522 (m110) cc_final: 0.6313 (m-40) REVERT: D 284 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (mt) REVERT: D 514 ASN cc_start: 0.6216 (m-40) cc_final: 0.5880 (m110) outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.1234 time to fit residues: 32.4154 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 74 THR 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 25 ASN Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 125 LYS 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 284 ILE Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 150 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 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 = 0.4650 r_free = 0.4650 target = 0.247209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.197676 restraints weight = 18626.027| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.38 r_work: 0.4025 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16464 Z= 0.119 Angle : 0.571 8.657 22450 Z= 0.318 Chirality : 0.047 0.316 2510 Planarity : 0.003 0.070 2586 Dihedral : 19.654 173.962 2758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.38 % Favored : 94.27 % Rotamer: Outliers : 0.74 % Allowed : 18.53 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1746 helix: -0.19 (0.23), residues: 542 sheet: -0.25 (0.28), residues: 368 loop : -1.02 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 526 TYR 0.016 0.001 TYR D 106 PHE 0.014 0.001 PHE A 315 TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (16464) covalent geometry : angle 0.57082 / 0.32 (22450) hydrogen bonds : bond 0.03821 / 2.40 ( 516) hydrogen bonds : angle 5.23484 / 3.66 ( 1391) ********************** 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 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASN cc_start: 0.5824 (m-40) cc_final: 0.5579 (m110) REVERT: A 563 HIS cc_start: 0.4174 (OUTLIER) cc_final: 0.3579 (m90) REVERT: B 1 MET cc_start: 0.3646 (mtp) cc_final: 0.3224 (tpt) REVERT: B 130 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6983 (tt) REVERT: B 481 ARG cc_start: 0.7940 (ptm160) cc_final: 0.7673 (ptt180) REVERT: B 504 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.6793 (mmt180) REVERT: C 87 LYS cc_start: 0.6830 (mmtt) cc_final: 0.5442 (mttp) REVERT: C 125 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6621 (mtpp) REVERT: C 510 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6992 (pt) REVERT: C 524 MET cc_start: 0.6253 (mtt) cc_final: 0.6045 (mmm) outliers start: 12 outliers final: 7 residues processed: 167 average time/residue: 0.1233 time to fit residues: 31.4477 Evaluate side-chains 158 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 0.0000 chunk 40 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 421 ASN D 143 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 = 0.4646 r_free = 0.4646 target = 0.246370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.204292 restraints weight = 18665.369| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.39 r_work: 0.4021 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16464 Z= 0.116 Angle : 0.575 9.128 22450 Z= 0.318 Chirality : 0.046 0.314 2510 Planarity : 0.003 0.067 2586 Dihedral : 19.570 174.397 2758 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.33 % Favored : 94.33 % Rotamer: Outliers : 0.74 % Allowed : 18.40 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1746 helix: -0.08 (0.23), residues: 542 sheet: -0.21 (0.28), residues: 368 loop : -0.95 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.013 0.001 TYR B 412 PHE 0.014 0.001 PHE A 315 TRP 0.005 0.001 TRP C 126 HIS 0.002 0.000 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (16464) covalent geometry : angle 0.57474 / 0.32 (22450) hydrogen bonds : bond 0.03716 / 2.34 ( 516) hydrogen bonds : angle 5.13370 / 3.60 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.09 seconds wall clock time: 58 minutes 28.47 seconds (3508.47 seconds total)