Starting phenix.real_space_refine on Sat Oct 11 16:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_37916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_37916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_37916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_37916.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_37916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy5_37916/10_2025/8wy5_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-2.0-5842/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.23 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: 1.34 Conformation dependent library (CDL) restraints added in 758.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.06 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: 3.21 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3709 1.33 - 1.45: 3501 1.45 - 1.57: 9018 1.57 - 1.69: 160 1.69 - 1.81: 76 Bond restraints: 16464 Sorted by residual: bond pdb=" N ILE B 510 " pdb=" CA ILE B 510 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N SER B 508 " pdb=" CA SER B 508 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.65e+00 bond pdb=" N ASP B 511 " pdb=" CA ASP B 511 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.99e+00 bond pdb=" CA ASN B 551 " pdb=" CB ASN B 551 " ideal model delta sigma weight residual 1.522 1.554 -0.033 1.27e-02 6.20e+03 6.56e+00 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 21665 2.71 - 5.42: 616 5.42 - 8.14: 99 8.14 - 10.85: 62 10.85 - 13.56: 8 Bond angle restraints: 22450 Sorted by residual: angle pdb=" C LEU B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.54 134.94 -13.40 1.91e+00 2.74e-01 4.92e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 133.96 -12.42 1.91e+00 2.74e-01 4.23e+01 angle pdb=" C LYS B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 121.97 132.81 -10.84 1.80e+00 3.09e-01 3.63e+01 ... (remaining 22445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 9368 34.89 - 69.79: 455 69.79 - 104.68: 15 104.68 - 139.58: 0 139.58 - 174.47: 6 Dihedral angle restraints: 9844 sinusoidal: 4650 harmonic: 5194 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASP C 515 " pdb=" C ASP C 515 " pdb=" N LEU C 516 " pdb=" CA LEU C 516 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 9841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2414 0.140 - 0.280: 83 0.280 - 0.419: 5 0.419 - 0.559: 2 0.559 - 0.699: 6 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DA H 20 " pdb=" OP1 DA H 20 " pdb=" OP2 DA H 20 " pdb=" O5' DA H 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.59e+00 ... (remaining 2507 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 93 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 93 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL B 93 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 395 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO D 396 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 396 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 396 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 520 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ILE B 520 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 521 " -0.015 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5256 2.88 - 3.39: 12922 3.39 - 3.89: 26558 3.89 - 4.40: 29956 4.40 - 4.90: 49730 Nonbonded interactions: 124422 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG1 THR C 36 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.385 3.040 nonbonded pdb=" OG SER D 78 " pdb=" O ALA D 102 " model vdw 2.389 3.040 nonbonded pdb=" O ASP A 32 " pdb=" OG1 THR A 36 " model vdw 2.389 3.040 nonbonded pdb=" O ASP B 32 " pdb=" OG1 THR B 36 " model vdw 2.396 3.040 ... (remaining 124417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 16464 Z= 0.308 Angle : 1.175 13.561 22450 Z= 0.616 Chirality : 0.070 0.699 2510 Planarity : 0.006 0.081 2586 Dihedral : 18.379 174.473 6488 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.04 % Favored : 94.50 % Rotamer: Outliers : 0.18 % Allowed : 0.67 % Favored : 99.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00648 (16464) covalent geometry : angle 1.17538 (22450) hydrogen bonds : bond 0.22568 ( 516) hydrogen bonds : angle 8.94462 ( 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 : 0.599 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: 0.7593 (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: 0.6416 (mp0) cc_final: 0.5812 (mp0) REVERT: D 141 ASN cc_start: 0.7895 (m-40) cc_final: 0.7675 (m110) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.1378 time to fit residues: 55.9876 Evaluate side-chains 166 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN B 415 HIS B 544 ASN B 563 HIS C 535 HIS D 13 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.251106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.205552 restraints weight = 18852.392| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.52 r_work: 0.4031 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16464 Z= 0.154 Angle : 0.625 8.228 22450 Z= 0.345 Chirality : 0.046 0.177 2510 Planarity : 0.004 0.052 2586 Dihedral : 19.867 177.479 2759 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 0.43 % Allowed : 8.53 % Favored : 91.04 % 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 aren not related in a simple way. whole: -2.83 (0.17), residues: 1746 helix: -2.62 (0.17), residues: 528 sheet: -0.54 (0.28), residues: 366 loop : -1.93 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 481 TYR 0.015 0.002 TYR B 113 PHE 0.019 0.002 PHE B 11 TRP 0.006 0.002 TRP B 126 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00344 (16464) covalent geometry : angle 0.62516 (22450) hydrogen bonds : bond 0.04498 ( 516) hydrogen bonds : angle 6.07078 ( 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 206 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4782 (tpt) cc_final: 0.4356 (tpt) REVERT: A 105 PHE cc_start: 0.5459 (t80) cc_final: 0.5109 (t80) REVERT: A 117 GLU cc_start: 0.6499 (tp30) cc_final: 0.6160 (tp30) REVERT: A 388 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6644 (mt-10) REVERT: B 1 MET cc_start: 0.3731 (mtp) cc_final: 0.3161 (tpt) REVERT: C 87 LYS cc_start: 0.6590 (mmtt) cc_final: 0.5248 (mttp) REVERT: C 125 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7370 (mtpp) REVERT: C 296 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6171 (mtm180) REVERT: C 388 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 545 MET cc_start: 0.7188 (mmt) cc_final: 0.6309 (mmt) REVERT: D 509 GLU cc_start: 0.6266 (pm20) cc_final: 0.6015 (pm20) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.1414 time to fit residues: 42.3938 Evaluate side-chains 173 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 ASN D 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.243528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.200125 restraints weight = 18826.366| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.35 r_work: 0.3981 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16464 Z= 0.191 Angle : 0.646 8.804 22450 Z= 0.354 Chirality : 0.047 0.171 2510 Planarity : 0.004 0.055 2586 Dihedral : 19.774 174.751 2759 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.90 % Favored : 93.76 % Rotamer: Outliers : 1.29 % Allowed : 12.39 % Favored : 86.32 % 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 aren not related in a simple way. whole: -2.25 (0.18), residues: 1746 helix: -1.72 (0.20), residues: 542 sheet: -0.62 (0.28), residues: 366 loop : -1.67 (0.18), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 12 TYR 0.018 0.002 TYR D 106 PHE 0.019 0.002 PHE D 316 TRP 0.007 0.002 TRP B 126 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00442 (16464) covalent geometry : angle 0.64599 (22450) hydrogen bonds : bond 0.04715 ( 516) hydrogen bonds : angle 5.86686 ( 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: 21 poor density : 166 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5572 (t80) cc_final: 0.5274 (t80) REVERT: A 388 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6620 (mt-10) REVERT: A 563 HIS cc_start: 0.4461 (OUTLIER) cc_final: 0.3723 (m90) REVERT: B 1 MET cc_start: 0.3495 (mtp) cc_final: 0.3247 (tpt) REVERT: C 296 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6107 (mtm180) REVERT: C 492 GLN cc_start: 0.7932 (pp30) cc_final: 0.7564 (pp30) REVERT: C 524 MET cc_start: 0.6536 (mtt) cc_final: 0.6193 (mmm) outliers start: 21 outliers final: 15 residues processed: 183 average time/residue: 0.1309 time to fit residues: 35.6401 Evaluate side-chains 173 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 390 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 86 THR 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 D residue 86 THR Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.245606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.203041 restraints weight = 18702.962| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.30 r_work: 0.4017 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16464 Z= 0.130 Angle : 0.563 8.651 22450 Z= 0.311 Chirality : 0.044 0.164 2510 Planarity : 0.003 0.039 2586 Dihedral : 19.494 175.998 2758 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.38 % Favored : 94.27 % Rotamer: Outliers : 1.23 % Allowed : 15.09 % Favored : 83.68 % 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 aren not related in a simple way. whole: -1.77 (0.19), residues: 1746 helix: -1.15 (0.21), residues: 556 sheet: -0.44 (0.28), residues: 362 loop : -1.45 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 12 TYR 0.013 0.001 TYR D 113 PHE 0.016 0.001 PHE A 315 TRP 0.003 0.001 TRP B 126 HIS 0.002 0.001 HIS C 415 Details of bonding type rmsd covalent geometry : bond 0.00287 (16464) covalent geometry : angle 0.56342 (22450) hydrogen bonds : bond 0.03861 ( 516) hydrogen bonds : angle 5.46644 ( 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 186 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 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: 0.7043 (mt-10) cc_final: 0.6662 (mt-10) REVERT: A 476 LYS cc_start: 0.5665 (mptt) cc_final: 0.5191 (mmtm) REVERT: A 563 HIS cc_start: 0.4435 (OUTLIER) cc_final: 0.3785 (m90) REVERT: C 87 LYS cc_start: 0.6851 (mmtt) cc_final: 0.5524 (mttp) REVERT: C 524 MET cc_start: 0.6612 (mtt) cc_final: 0.6296 (mmm) REVERT: D 392 ASP cc_start: 0.7300 (t0) cc_final: 0.7025 (t0) outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 0.1253 time to fit residues: 34.8690 Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain B residue 292 ILE 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 D residue 94 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 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 = 0.4660 r_free = 0.4660 target = 0.243402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.196116 restraints weight = 18510.284| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.38 r_work: 0.4025 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16464 Z= 0.157 Angle : 0.595 9.298 22450 Z= 0.325 Chirality : 0.045 0.161 2510 Planarity : 0.003 0.040 2586 Dihedral : 19.424 174.923 2758 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.84 % Favored : 93.76 % Rotamer: Outliers : 1.90 % Allowed : 15.71 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.19), residues: 1746 helix: -0.80 (0.22), residues: 556 sheet: -0.52 (0.28), residues: 366 loop : -1.32 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 12 TYR 0.014 0.001 TYR B 106 PHE 0.020 0.002 PHE D 543 TRP 0.004 0.002 TRP D 126 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00360 (16464) covalent geometry : angle 0.59454 (22450) hydrogen bonds : bond 0.04117 ( 516) hydrogen bonds : angle 5.44894 ( 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 193 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6857 (mt-10) REVERT: A 476 LYS cc_start: 0.5799 (mptt) cc_final: 0.5268 (mmtm) REVERT: A 563 HIS cc_start: 0.4529 (OUTLIER) cc_final: 0.3774 (m90) REVERT: C 284 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 510 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6985 (pt) REVERT: C 524 MET cc_start: 0.6554 (mtt) cc_final: 0.6282 (mmm) REVERT: C 571 GLU cc_start: 0.6457 (mp0) cc_final: 0.6092 (mp0) REVERT: D 514 ASN cc_start: 0.6367 (m-40) cc_final: 0.6005 (m110) outliers start: 31 outliers final: 19 residues processed: 187 average time/residue: 0.1292 time to fit residues: 35.9018 Evaluate side-chains 173 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 117 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.247512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.203810 restraints weight = 18926.839| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.22 r_work: 0.4062 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16464 Z= 0.120 Angle : 0.554 7.656 22450 Z= 0.304 Chirality : 0.044 0.157 2510 Planarity : 0.003 0.031 2586 Dihedral : 19.303 175.839 2758 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.44 % Favored : 94.16 % Rotamer: Outliers : 1.23 % Allowed : 16.81 % Favored : 81.96 % 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 aren not related in a simple way. whole: -1.23 (0.20), residues: 1746 helix: -0.48 (0.23), residues: 554 sheet: -0.47 (0.28), residues: 376 loop : -1.13 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 12 TYR 0.011 0.001 TYR D 113 PHE 0.017 0.001 PHE D 543 TRP 0.004 0.001 TRP D 126 HIS 0.002 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00261 (16464) covalent geometry : angle 0.55371 (22450) hydrogen bonds : bond 0.03557 ( 516) hydrogen bonds : angle 5.18167 ( 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 182 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.5839 (mptt) cc_final: 0.5636 (mptt) REVERT: A 563 HIS cc_start: 0.4420 (OUTLIER) cc_final: 0.3789 (m90) REVERT: B 481 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7671 (ptt180) REVERT: C 524 MET cc_start: 0.6596 (mtt) cc_final: 0.6364 (mmm) REVERT: C 571 GLU cc_start: 0.6436 (mp0) cc_final: 0.6072 (mp0) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.1228 time to fit residues: 33.4595 Evaluate side-chains 157 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 94 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 140 optimal weight: 0.0060 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.248488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.202372 restraints weight = 18897.143| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.22 r_work: 0.4113 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16464 Z= 0.113 Angle : 0.542 7.359 22450 Z= 0.296 Chirality : 0.043 0.154 2510 Planarity : 0.003 0.066 2586 Dihedral : 19.213 175.784 2758 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.15 % Favored : 94.44 % Rotamer: Outliers : 1.29 % Allowed : 17.73 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.20), residues: 1746 helix: -0.10 (0.23), residues: 542 sheet: -0.37 (0.28), residues: 378 loop : -0.97 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 504 TYR 0.011 0.001 TYR B 412 PHE 0.022 0.001 PHE D 543 TRP 0.005 0.001 TRP A 126 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00243 (16464) covalent geometry : angle 0.54213 (22450) hydrogen bonds : bond 0.03418 ( 516) hydrogen bonds : angle 5.03643 ( 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: 21 poor density : 151 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 HIS cc_start: 0.4107 (OUTLIER) cc_final: 0.3889 (m-70) REVERT: B 481 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7382 (ptt180) REVERT: C 63 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.4820 (t70) REVERT: C 284 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7472 (mt) REVERT: C 492 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: C 510 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6870 (pt) REVERT: C 524 MET cc_start: 0.6542 (mtt) cc_final: 0.6324 (mmm) REVERT: C 571 GLU cc_start: 0.6382 (mp0) cc_final: 0.6043 (mp0) REVERT: D 284 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7343 (mt) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 0.1165 time to fit residues: 30.3565 Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 367 SER 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 314 TYR Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 296 ARG 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 492 GLN Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 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 = 0.4674 r_free = 0.4674 target = 0.244406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.198795 restraints weight = 18910.341| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.26 r_work: 0.4059 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16464 Z= 0.164 Angle : 0.598 7.378 22450 Z= 0.326 Chirality : 0.045 0.150 2510 Planarity : 0.003 0.053 2586 Dihedral : 19.234 174.811 2758 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.96 % Favored : 93.64 % Rotamer: Outliers : 1.41 % Allowed : 17.91 % 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 aren not related in a simple way. whole: -0.98 (0.20), residues: 1746 helix: -0.13 (0.23), residues: 540 sheet: -0.48 (0.28), residues: 366 loop : -0.99 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 12 TYR 0.015 0.001 TYR B 106 PHE 0.022 0.002 PHE D 543 TRP 0.005 0.002 TRP D 126 HIS 0.006 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00380 (16464) covalent geometry : angle 0.59771 (22450) hydrogen bonds : bond 0.04027 ( 516) hydrogen bonds : angle 5.25729 ( 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 175 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.4888 (mptt) cc_final: 0.4615 (mmtm) REVERT: A 563 HIS cc_start: 0.4524 (OUTLIER) cc_final: 0.3764 (m90) REVERT: B 13 ASN cc_start: 0.8173 (m110) cc_final: 0.7807 (m-40) REVERT: C 284 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7564 (mt) REVERT: C 492 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7780 (pp30) REVERT: C 510 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6912 (pt) REVERT: D 284 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7497 (mt) outliers start: 23 outliers final: 13 residues processed: 173 average time/residue: 0.1234 time to fit residues: 32.2087 Evaluate side-chains 164 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE 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 B residue 314 TYR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 492 GLN Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 350 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.243996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199767 restraints weight = 18945.489| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.21 r_work: 0.4022 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16464 Z= 0.158 Angle : 0.604 8.298 22450 Z= 0.328 Chirality : 0.046 0.150 2510 Planarity : 0.003 0.046 2586 Dihedral : 19.215 174.954 2758 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.73 % Favored : 93.87 % Rotamer: Outliers : 1.35 % Allowed : 17.85 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.20), residues: 1746 helix: -0.13 (0.23), residues: 540 sheet: -0.54 (0.28), residues: 366 loop : -0.94 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 12 TYR 0.013 0.001 TYR B 106 PHE 0.020 0.002 PHE D 543 TRP 0.007 0.002 TRP D 126 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00363 (16464) covalent geometry : angle 0.60365 (22450) hydrogen bonds : bond 0.03947 ( 516) hydrogen bonds : angle 5.27165 ( 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 176 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3063 (tpt) cc_final: 0.1478 (ptt) REVERT: A 476 LYS cc_start: 0.4939 (mptt) cc_final: 0.4630 (mmtm) REVERT: A 563 HIS cc_start: 0.4523 (OUTLIER) cc_final: 0.3770 (m90) REVERT: C 1 MET cc_start: 0.2842 (tpt) cc_final: 0.1753 (ptt) REVERT: C 284 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 510 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6773 (pt) REVERT: C 513 GLU cc_start: 0.4841 (mp0) cc_final: 0.4613 (mp0) REVERT: D 284 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7463 (mt) outliers start: 22 outliers final: 15 residues processed: 172 average time/residue: 0.1164 time to fit residues: 30.8645 Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE 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 B residue 314 TYR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 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 = 0.4671 r_free = 0.4671 target = 0.244079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.198593 restraints weight = 18802.882| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.27 r_work: 0.4009 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16464 Z= 0.178 Angle : 0.781 59.177 22450 Z= 0.451 Chirality : 0.046 0.375 2510 Planarity : 0.003 0.067 2586 Dihedral : 19.214 174.965 2758 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.90 % Favored : 93.70 % Rotamer: Outliers : 1.35 % Allowed : 18.04 % Favored : 80.61 % 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 aren not related in a simple way. whole: -0.98 (0.20), residues: 1746 helix: -0.13 (0.23), residues: 540 sheet: -0.56 (0.28), residues: 366 loop : -0.95 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.014 0.001 TYR C 493 PHE 0.020 0.001 PHE D 543 TRP 0.006 0.001 TRP D 126 HIS 0.003 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00390 (16464) covalent geometry : angle 0.78055 (22450) hydrogen bonds : bond 0.03998 ( 516) hydrogen bonds : angle 5.27971 ( 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: 22 poor density : 146 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3028 (tpt) cc_final: 0.1444 (ptt) REVERT: A 476 LYS cc_start: 0.4918 (mptt) cc_final: 0.4603 (mmtm) REVERT: A 563 HIS cc_start: 0.4477 (OUTLIER) cc_final: 0.3716 (m90) REVERT: B 76 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5997 (p0) REVERT: B 130 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7075 (tt) REVERT: C 1 MET cc_start: 0.2876 (tpt) cc_final: 0.1763 (ptt) REVERT: C 284 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7524 (mt) REVERT: C 510 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6754 (pt) REVERT: C 513 GLU cc_start: 0.4860 (mp0) cc_final: 0.4623 (mp0) REVERT: D 284 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7470 (mt) outliers start: 22 outliers final: 15 residues processed: 166 average time/residue: 0.1181 time to fit residues: 30.0770 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 505 ILE 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 76 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.244128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200045 restraints weight = 18766.669| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.19 r_work: 0.4024 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16464 Z= 0.178 Angle : 0.781 59.177 22450 Z= 0.451 Chirality : 0.046 0.375 2510 Planarity : 0.003 0.067 2586 Dihedral : 19.214 174.965 2758 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.90 % Favored : 93.70 % Rotamer: Outliers : 1.29 % Allowed : 18.16 % Favored : 80.55 % 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 aren not related in a simple way. whole: -0.98 (0.20), residues: 1746 helix: -0.13 (0.23), residues: 540 sheet: -0.56 (0.28), residues: 366 loop : -0.95 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.014 0.001 TYR C 493 PHE 0.020 0.001 PHE D 543 TRP 0.006 0.001 TRP D 126 HIS 0.003 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00390 (16464) covalent geometry : angle 0.78055 (22450) hydrogen bonds : bond 0.03998 ( 516) hydrogen bonds : angle 5.27971 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3669.76 seconds wall clock time: 63 minutes 52.91 seconds (3832.91 seconds total)