Starting phenix.real_space_refine on Sat Jun 14 09:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy5_37916/06_2025/8wy5_37916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy5_37916/06_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_37916/06_2025/8wy5_37916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy5_37916/06_2025/8wy5_37916.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy5_37916/06_2025/8wy5_37916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy5_37916/06_2025/8wy5_37916.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 76 5.49 5 S 48 5.16 5 C 10048 2.51 5 N 2664 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "D" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.77, per 1000 atoms: 0.67 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: 4.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3356 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 16 sheets defined 38.5% alpha, 15.3% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.889A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.687A pdb=" N PHE A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.713A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.632A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.633A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.723A pdb=" N TYR A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 399 " --> pdb=" O PRO A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.639A pdb=" N CYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.628A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 512 through 529 removed outlier: 3.626A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.537A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.572A pdb=" N VAL A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.542A pdb=" N GLU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.749A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.857A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 380 through 395 removed outlier: 4.130A pdb=" N LYS B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 4.062A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.429A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.568A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.622A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.646A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.718A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.954A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.798A pdb=" N PHE C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 94 removed outlier: 4.187A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.763A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.761A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.723A pdb=" N PHE C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 372 " --> pdb=" O ALA C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.521A pdb=" N ILE C 385 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.665A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 402 " --> pdb=" O TYR C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.779A pdb=" N CYS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.993A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.675A pdb=" N ARG C 481 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 501 removed outlier: 4.152A pdb=" N GLU C 499 " --> pdb=" O ASN C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.697A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.160A pdb=" N ILE C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.622A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.625A pdb=" N LEU C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.793A pdb=" N VAL C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.925A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.059A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.847A pdb=" N ALA D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.697A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.545A pdb=" N ALA D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.826A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.516A pdb=" N CYS D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 4.056A pdb=" N LEU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 4.009A pdb=" N LYS D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 501 removed outlier: 4.088A pdb=" N GLU D 499 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.872A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 523 through 529 removed outlier: 4.029A pdb=" N ILE D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.014A pdb=" N LYS D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.799A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 546' Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.823A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.975A pdb=" N VAL A 17 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 71 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.149A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 7.011A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.650A pdb=" N VAL B 17 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 71 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.526A pdb=" N TYR B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.613A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 375 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 508 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 431 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.943A pdb=" N VAL C 17 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 71 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.326A pdb=" N LYS C 150 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 286 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 152 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLU C 288 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 154 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 25 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 335 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 403 through 407 removed outlier: 7.006A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.906A pdb=" N VAL D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 71 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.501A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 403 through 407 Processing sheet with id=AB7, first strand: chain 'D' and resid 435 through 437 434 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3709 1.33 - 1.45: 3501 1.45 - 1.57: 9018 1.57 - 1.69: 160 1.69 - 1.81: 76 Bond restraints: 16464 Sorted by residual: bond pdb=" N ILE B 510 " pdb=" CA ILE B 510 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N SER B 508 " pdb=" CA SER B 508 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.65e+00 bond pdb=" N ASP B 511 " pdb=" CA ASP B 511 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.99e+00 bond pdb=" CA ASN B 551 " pdb=" CB ASN B 551 " ideal model delta sigma weight residual 1.522 1.554 -0.033 1.27e-02 6.20e+03 6.56e+00 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 21665 2.71 - 5.42: 616 5.42 - 8.14: 99 8.14 - 10.85: 62 10.85 - 13.56: 8 Bond angle restraints: 22450 Sorted by residual: angle pdb=" C LEU B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.54 134.94 -13.40 1.91e+00 2.74e-01 4.92e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 133.96 -12.42 1.91e+00 2.74e-01 4.23e+01 angle pdb=" C LYS B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 121.97 132.81 -10.84 1.80e+00 3.09e-01 3.63e+01 ... (remaining 22445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 9368 34.89 - 69.79: 455 69.79 - 104.68: 15 104.68 - 139.58: 0 139.58 - 174.47: 6 Dihedral angle restraints: 9844 sinusoidal: 4650 harmonic: 5194 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASP C 515 " pdb=" C ASP C 515 " pdb=" N LEU C 516 " pdb=" CA LEU C 516 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 9841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2414 0.140 - 0.280: 83 0.280 - 0.419: 5 0.419 - 0.559: 2 0.559 - 0.699: 6 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DA H 20 " pdb=" OP1 DA H 20 " pdb=" OP2 DA H 20 " pdb=" O5' DA H 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.59e+00 ... (remaining 2507 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 93 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 93 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL B 93 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 395 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO D 396 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 396 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 396 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 520 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ILE B 520 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 521 " -0.015 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5256 2.88 - 3.39: 12922 3.39 - 3.89: 26558 3.89 - 4.40: 29956 4.40 - 4.90: 49730 Nonbonded interactions: 124422 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG1 THR C 36 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.385 3.040 nonbonded pdb=" OG SER D 78 " pdb=" O ALA D 102 " model vdw 2.389 3.040 nonbonded pdb=" O ASP A 32 " pdb=" OG1 THR A 36 " model vdw 2.389 3.040 nonbonded pdb=" O ASP B 32 " pdb=" OG1 THR B 36 " model vdw 2.396 3.040 ... (remaining 124417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 575 or resid 1001)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 351 or resid 363 through 575 or resid 1001)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 32.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 42.690 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.15), residues: 1746 helix: -4.48 (0.08), residues: 532 sheet: -0.56 (0.27), residues: 356 loop : -2.38 (0.16), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 126 HIS 0.005 0.001 HIS C 563 PHE 0.035 0.003 PHE C 387 TYR 0.031 0.002 TYR D 113 ARG 0.007 0.001 ARG D 12 Details of bonding type rmsd hydrogen bonds : bond 0.22568 ( 516) hydrogen bonds : angle 8.94462 ( 1391) covalent geometry : bond 0.00648 (16464) covalent geometry : angle 1.17538 (22450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5466 (t80) cc_final: 0.4895 (t80) REVERT: A 367 SER cc_start: 0.8211 (m) cc_final: 0.7982 (p) REVERT: A 507 LEU cc_start: 0.7896 (tp) cc_final: 0.7594 (tp) REVERT: B 1 MET cc_start: 0.4486 (mtp) cc_final: 0.3440 (tmm) REVERT: B 105 PHE cc_start: 0.4023 (t80) cc_final: 0.1745 (t80) REVERT: B 507 LEU cc_start: 0.7356 (tp) cc_final: 0.7116 (tp) REVERT: C 2 LYS cc_start: 0.6309 (ptpt) cc_final: 0.6103 (pptt) REVERT: C 106 TYR cc_start: 0.6638 (m-80) cc_final: 0.6419 (m-80) REVERT: C 388 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 550 ASN cc_start: 0.6972 (m-40) cc_final: 0.6358 (p0) REVERT: C 571 GLU cc_start: 0.6416 (mp0) cc_final: 0.5812 (mp0) REVERT: D 141 ASN cc_start: 0.7895 (m-40) cc_final: 0.7675 (m110) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.3051 time to fit residues: 124.1512 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 544 ASN B 563 HIS C 535 HIS D 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.250099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209797 restraints weight = 18944.087| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.36 r_work: 0.4069 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16464 Z= 0.145 Angle : 0.615 8.138 22450 Z= 0.339 Chirality : 0.045 0.179 2510 Planarity : 0.004 0.050 2586 Dihedral : 19.864 177.578 2759 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.10 % Favored : 94.56 % Rotamer: Outliers : 0.49 % Allowed : 8.16 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.17), residues: 1746 helix: -2.65 (0.17), residues: 528 sheet: -0.52 (0.28), residues: 366 loop : -1.93 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 126 HIS 0.003 0.001 HIS B 535 PHE 0.017 0.002 PHE B 11 TYR 0.015 0.001 TYR D 113 ARG 0.004 0.001 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 516) hydrogen bonds : angle 6.04969 ( 1391) covalent geometry : bond 0.00317 (16464) covalent geometry : angle 0.61490 (22450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4766 (tpt) cc_final: 0.4360 (tpt) REVERT: A 105 PHE cc_start: 0.5452 (t80) cc_final: 0.5119 (t80) REVERT: A 388 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 1 MET cc_start: 0.3664 (mtp) cc_final: 0.3188 (tmm) REVERT: C 87 LYS cc_start: 0.6611 (mmtt) cc_final: 0.5296 (mttp) REVERT: C 296 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.5894 (mtm180) REVERT: C 388 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 545 MET cc_start: 0.7300 (mmt) cc_final: 0.6370 (mmt) REVERT: D 509 GLU cc_start: 0.6250 (pm20) cc_final: 0.6008 (pm20) outliers start: 8 outliers final: 3 residues processed: 201 average time/residue: 0.3132 time to fit residues: 90.8874 Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS C 483 ASN D 61 HIS D 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.237274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.196403 restraints weight = 18622.628| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.20 r_work: 0.3925 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16464 Z= 0.252 Angle : 0.718 9.071 22450 Z= 0.392 Chirality : 0.049 0.172 2510 Planarity : 0.004 0.062 2586 Dihedral : 19.892 173.586 2759 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.24 % Favored : 93.36 % Rotamer: Outliers : 1.23 % Allowed : 12.88 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.18), residues: 1746 helix: -1.80 (0.19), residues: 556 sheet: -0.75 (0.28), residues: 366 loop : -1.74 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP B 126 HIS 0.008 0.001 HIS A 415 PHE 0.021 0.002 PHE A 315 TYR 0.019 0.002 TYR B 40 ARG 0.009 0.001 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 516) hydrogen bonds : angle 6.11086 ( 1391) covalent geometry : bond 0.00596 (16464) covalent geometry : angle 0.71839 (22450) *********************** 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 189 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5849 (t80) cc_final: 0.5513 (t80) REVERT: A 388 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 563 HIS cc_start: 0.4887 (OUTLIER) cc_final: 0.3834 (m90) REVERT: C 524 MET cc_start: 0.6609 (mtt) cc_final: 0.6270 (mmm) REVERT: D 87 LYS cc_start: 0.6688 (mptt) cc_final: 0.6413 (mttp) outliers start: 20 outliers final: 15 residues processed: 186 average time/residue: 0.3311 time to fit residues: 93.6480 Evaluate side-chains 165 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 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 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.242640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.197655 restraints weight = 18334.115| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.44 r_work: 0.3968 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16464 Z= 0.141 Angle : 0.590 8.612 22450 Z= 0.325 Chirality : 0.045 0.166 2510 Planarity : 0.003 0.044 2586 Dihedral : 19.579 175.508 2758 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 1.35 % Allowed : 15.64 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1746 helix: -1.21 (0.21), residues: 556 sheet: -0.61 (0.28), residues: 366 loop : -1.46 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 126 HIS 0.003 0.001 HIS C 415 PHE 0.018 0.001 PHE A 315 TYR 0.014 0.001 TYR D 113 ARG 0.004 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 516) hydrogen bonds : angle 5.62949 ( 1391) covalent geometry : bond 0.00316 (16464) covalent geometry : angle 0.58955 (22450) *********************** 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 178 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 563 HIS cc_start: 0.4745 (OUTLIER) cc_final: 0.3912 (m90) REVERT: B 513 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6629 (mm-30) REVERT: C 284 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7489 (mt) REVERT: C 524 MET cc_start: 0.6590 (mtt) cc_final: 0.6298 (mmm) outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 0.3456 time to fit residues: 91.4379 Evaluate side-chains 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 351 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 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 292 ILE Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.242741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.196940 restraints weight = 19073.024| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.26 r_work: 0.4001 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3442 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= 0.175 Angle : 0.615 8.130 22450 Z= 0.336 Chirality : 0.046 0.164 2510 Planarity : 0.003 0.043 2586 Dihedral : 19.492 174.571 2758 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.47 % Favored : 93.18 % Rotamer: Outliers : 1.78 % Allowed : 16.63 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1746 helix: -0.89 (0.22), residues: 570 sheet: -0.62 (0.29), residues: 366 loop : -1.38 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 126 HIS 0.003 0.001 HIS A 415 PHE 0.017 0.002 PHE A 315 TYR 0.014 0.002 TYR D 106 ARG 0.006 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 516) hydrogen bonds : angle 5.59470 ( 1391) covalent geometry : bond 0.00406 (16464) covalent geometry : angle 0.61504 (22450) *********************** 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 179 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 HIS cc_start: 0.4629 (OUTLIER) cc_final: 0.3769 (m90) REVERT: B 481 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8156 (ptm160) REVERT: C 284 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 510 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.7002 (pt) REVERT: C 524 MET cc_start: 0.6660 (mtt) cc_final: 0.6391 (mmm) REVERT: C 545 MET cc_start: 0.7044 (mmt) cc_final: 0.6268 (mmt) REVERT: D 87 LYS cc_start: 0.6684 (mptt) cc_final: 0.6354 (mttp) REVERT: D 284 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7488 (mt) REVERT: D 514 ASN cc_start: 0.6338 (m-40) cc_final: 0.5970 (m110) outliers start: 29 outliers final: 17 residues processed: 175 average time/residue: 0.2943 time to fit residues: 77.9455 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 : 1.897 ------------------------------------------------------------------------------- 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 351 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 545 MET 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 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 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 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.0270 chunk 147 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS D 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.245422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.199401 restraints weight = 18872.235| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.21 r_work: 0.4082 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3490 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= 0.126 Angle : 0.561 7.433 22450 Z= 0.308 Chirality : 0.044 0.158 2510 Planarity : 0.003 0.062 2586 Dihedral : 19.371 175.720 2758 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Rotamer: Outliers : 1.53 % Allowed : 17.91 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1746 helix: -0.50 (0.23), residues: 556 sheet: -0.58 (0.28), residues: 376 loop : -1.15 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 126 HIS 0.003 0.001 HIS A 415 PHE 0.016 0.001 PHE A 315 TYR 0.012 0.001 TYR D 113 ARG 0.004 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 516) hydrogen bonds : angle 5.32131 ( 1391) covalent geometry : bond 0.00280 (16464) covalent geometry : angle 0.56147 (22450) *********************** 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 190 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 563 HIS cc_start: 0.4509 (OUTLIER) cc_final: 0.3794 (m90) REVERT: B 13 ASN cc_start: 0.8095 (m110) cc_final: 0.7877 (m-40) REVERT: B 481 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8071 (ptm160) REVERT: C 63 HIS cc_start: 0.5926 (OUTLIER) cc_final: 0.4973 (t70) REVERT: C 510 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6930 (pt) outliers start: 25 outliers final: 13 residues processed: 185 average time/residue: 0.3105 time to fit residues: 87.1804 Evaluate side-chains 170 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 63 HIS 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 C residue 510 ILE Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS C 79 ASN D 143 ASN D 421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.244387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.198630 restraints weight = 19004.089| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 2.27 r_work: 0.4061 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3596 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= 0.140 Angle : 0.585 8.178 22450 Z= 0.319 Chirality : 0.045 0.154 2510 Planarity : 0.003 0.049 2586 Dihedral : 19.341 175.358 2758 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.01 % Favored : 93.64 % Rotamer: Outliers : 1.47 % Allowed : 18.34 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1746 helix: -0.34 (0.23), residues: 556 sheet: -0.53 (0.28), residues: 366 loop : -1.07 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.003 0.001 HIS A 427 PHE 0.021 0.001 PHE D 543 TYR 0.012 0.001 TYR C 314 ARG 0.004 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 516) hydrogen bonds : angle 5.30378 ( 1391) covalent geometry : bond 0.00318 (16464) covalent geometry : angle 0.58542 (22450) *********************** 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 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 476 LYS cc_start: 0.4840 (mptt) cc_final: 0.4523 (mmtm) REVERT: A 563 HIS cc_start: 0.4446 (OUTLIER) cc_final: 0.3785 (m90) REVERT: B 13 ASN cc_start: 0.8123 (m110) cc_final: 0.7911 (m-40) REVERT: B 130 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7169 (tt) REVERT: C 117 GLU cc_start: 0.6649 (tp30) cc_final: 0.6392 (tp30) REVERT: C 284 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7541 (mt) REVERT: C 510 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6967 (pt) REVERT: D 284 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7491 (mt) outliers start: 24 outliers final: 16 residues processed: 180 average time/residue: 0.3349 time to fit residues: 92.3889 Evaluate side-chains 175 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 429 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4678 r_free = 0.4678 target = 0.244961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.199047 restraints weight = 18863.342| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.13 r_work: 0.4060 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16464 Z= 0.132 Angle : 0.574 8.029 22450 Z= 0.312 Chirality : 0.044 0.152 2510 Planarity : 0.003 0.043 2586 Dihedral : 19.260 175.590 2758 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.90 % Favored : 93.76 % Rotamer: Outliers : 1.60 % Allowed : 18.28 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1746 helix: -0.12 (0.23), residues: 540 sheet: -0.59 (0.28), residues: 376 loop : -0.96 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.003 0.001 HIS B 427 PHE 0.019 0.001 PHE D 543 TYR 0.011 0.001 TYR C 314 ARG 0.003 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 516) hydrogen bonds : angle 5.18677 ( 1391) covalent geometry : bond 0.00296 (16464) covalent geometry : angle 0.57381 (22450) *********************** 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 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6709 (mt-10) REVERT: A 476 LYS cc_start: 0.4901 (mptt) cc_final: 0.4606 (mmtm) REVERT: A 563 HIS cc_start: 0.4370 (OUTLIER) cc_final: 0.3756 (m90) REVERT: B 30 MET cc_start: 0.7582 (mmm) cc_final: 0.7377 (mmm) REVERT: B 130 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7047 (tt) REVERT: C 117 GLU cc_start: 0.6713 (tp30) cc_final: 0.6467 (tp30) REVERT: C 284 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7513 (mt) REVERT: C 510 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6929 (pt) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.2674 time to fit residues: 73.7750 Evaluate side-chains 171 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 429 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR 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 B residue 344 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 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 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 104 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** 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 = 0.4646 r_free = 0.4646 target = 0.240925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.193168 restraints weight = 18776.591| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.14 r_work: 0.4034 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16464 Z= 0.194 Angle : 0.650 8.097 22450 Z= 0.351 Chirality : 0.047 0.151 2510 Planarity : 0.004 0.042 2586 Dihedral : 19.319 174.272 2758 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.99 % Favored : 92.67 % Rotamer: Outliers : 2.02 % Allowed : 18.53 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1746 helix: -0.34 (0.22), residues: 570 sheet: -0.69 (0.28), residues: 364 loop : -1.11 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 126 HIS 0.003 0.001 HIS A 427 PHE 0.018 0.002 PHE D 543 TYR 0.014 0.002 TYR D 106 ARG 0.006 0.001 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 516) hydrogen bonds : angle 5.47918 ( 1391) covalent geometry : bond 0.00454 (16464) covalent geometry : angle 0.64979 (22450) *********************** 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 195 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7415 (tt) REVERT: A 388 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6632 (mt-10) REVERT: A 476 LYS cc_start: 0.4938 (mptt) cc_final: 0.4671 (mmtm) REVERT: A 563 HIS cc_start: 0.4381 (OUTLIER) cc_final: 0.3661 (m90) REVERT: B 130 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7225 (tt) REVERT: C 63 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.4941 (t70) REVERT: C 117 GLU cc_start: 0.6781 (tp30) cc_final: 0.6532 (tp30) REVERT: C 130 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7291 (tt) REVERT: C 284 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7523 (mt) REVERT: C 481 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8182 (mtp180) REVERT: C 492 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: C 510 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6792 (pt) REVERT: C 545 MET cc_start: 0.7042 (mmt) cc_final: 0.6138 (mmt) REVERT: D 87 LYS cc_start: 0.6731 (mptt) cc_final: 0.6473 (mttp) REVERT: D 284 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7451 (mt) REVERT: D 514 ASN cc_start: 0.6454 (m-40) cc_final: 0.6041 (m110) outliers start: 33 outliers final: 20 residues processed: 192 average time/residue: 0.3097 time to fit residues: 92.1732 Evaluate side-chains 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 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 B residue 344 CYS Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 492 GLN Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 138 optimal weight: 0.0070 chunk 119 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS D 330 ASN D 350 ASN D 421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.242555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197009 restraints weight = 18938.455| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.18 r_work: 0.4015 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16464 Z= 0.151 Angle : 0.606 7.654 22450 Z= 0.328 Chirality : 0.045 0.151 2510 Planarity : 0.003 0.038 2586 Dihedral : 19.192 175.830 2758 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.84 % Favored : 93.81 % Rotamer: Outliers : 1.78 % Allowed : 19.14 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1746 helix: -0.23 (0.22), residues: 570 sheet: -0.80 (0.27), residues: 380 loop : -0.98 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 126 HIS 0.003 0.001 HIS A 427 PHE 0.018 0.001 PHE D 543 TYR 0.012 0.001 TYR B 106 ARG 0.004 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 516) hydrogen bonds : angle 5.31960 ( 1391) covalent geometry : bond 0.00345 (16464) covalent geometry : angle 0.60621 (22450) ********************** 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 187 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7287 (tt) REVERT: A 388 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6805 (mt-10) REVERT: A 476 LYS cc_start: 0.4977 (mptt) cc_final: 0.4708 (mmtm) REVERT: A 536 TYR cc_start: 0.6910 (t80) cc_final: 0.6099 (t80) REVERT: A 563 HIS cc_start: 0.4505 (OUTLIER) cc_final: 0.3891 (m90) REVERT: B 76 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5839 (p0) REVERT: B 130 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (tt) REVERT: C 1 MET cc_start: 0.2880 (tpt) cc_final: 0.1596 (ptt) REVERT: C 63 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5101 (t70) REVERT: C 117 GLU cc_start: 0.6789 (tp30) cc_final: 0.6532 (tp30) REVERT: C 130 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7334 (tt) REVERT: C 284 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 510 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6794 (pt) REVERT: D 87 LYS cc_start: 0.6739 (mptt) cc_final: 0.6513 (mttp) REVERT: D 284 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7464 (mt) outliers start: 29 outliers final: 19 residues processed: 183 average time/residue: 0.2540 time to fit residues: 71.5286 Evaluate side-chains 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 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 B residue 344 CYS Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.242681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.196085 restraints weight = 18860.441| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.22 r_work: 0.4047 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 16464 Z= 0.203 Angle : 0.798 59.174 22450 Z= 0.463 Chirality : 0.050 1.115 2510 Planarity : 0.004 0.100 2586 Dihedral : 19.192 175.831 2758 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.84 % Favored : 93.81 % Rotamer: Outliers : 1.84 % Allowed : 18.83 % Favored : 79.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1746 helix: -0.23 (0.22), residues: 570 sheet: -0.81 (0.27), residues: 380 loop : -1.01 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 126 HIS 0.003 0.001 HIS A 427 PHE 0.018 0.001 PHE D 543 TYR 0.019 0.001 TYR C 493 ARG 0.003 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 516) hydrogen bonds : angle 5.31953 ( 1391) covalent geometry : bond 0.00434 (16464) covalent geometry : angle 0.79763 (22450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8180.94 seconds wall clock time: 146 minutes 11.05 seconds (8771.05 seconds total)