Starting phenix.real_space_refine on Mon May 4 20:17:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.map" model { file = "/net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qt4_53346/05_2026/9qt4_53346.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 14772 2.51 5 N 3936 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23228 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Q" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "R" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "S" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5224 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 1 Chain: "B" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5224 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 1 Chain: "C" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5224 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 1 Chain: "D" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5224 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 1 Time building chain proxies: 4.94, per 1000 atoms: 0.21 Number of scatterers: 23228 At special positions: 0 Unit cell: (192.096, 191.268, 81.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 4368 8.00 N 3936 7.00 C 14772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 81 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 40 " - pdb=" SG CYS Q 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 81 " distance=2.04 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 87 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 81 " distance=2.04 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 87 " distance=2.04 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 81 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 26 sheets defined 25.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'P' and resid 33 through 47 removed outlier: 3.658A pdb=" N LEU P 37 " --> pdb=" O SER P 33 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER P 38 " --> pdb=" O ARG P 34 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLN P 41 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA P 42 " --> pdb=" O SER P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 4.179A pdb=" N PHE P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 85 Processing helix chain 'Q' and resid 34 through 46 removed outlier: 4.355A pdb=" N SER Q 38 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 75 Processing helix chain 'R' and resid 35 through 47 Processing helix chain 'R' and resid 70 through 76 removed outlier: 4.424A pdb=" N PHE R 74 " --> pdb=" O SER R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 47 removed outlier: 3.573A pdb=" N CYS S 40 " --> pdb=" O SER S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.005A pdb=" N PHE S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.917A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.653A pdb=" N ASP A 372 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 396 through 408 removed outlier: 4.278A pdb=" N ASP A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 404 " --> pdb=" O TRP A 400 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 414 through 424 removed outlier: 4.124A pdb=" N VAL A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 removed outlier: 4.039A pdb=" N LEU A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 452 Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.772A pdb=" N LYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 499 Processing helix chain 'A' and resid 499 through 504 removed outlier: 4.232A pdb=" N SER A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.270A pdb=" N VAL A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 664 through 670 removed outlier: 4.156A pdb=" N ILE A 667 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 669 " --> pdb=" O SER A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 850 Processing helix chain 'A' and resid 896 through 900 removed outlier: 4.166A pdb=" N GLN A 900 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.812A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.525A pdb=" N LYS B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 396 through 408 removed outlier: 4.035A pdb=" N ASP B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 414 through 424 removed outlier: 4.692A pdb=" N VAL B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 439 removed outlier: 4.197A pdb=" N LEU B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.741A pdb=" N LYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 499 removed outlier: 3.506A pdb=" N THR B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 3.541A pdb=" N GLU B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 removed outlier: 4.186A pdb=" N GLU B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.793A pdb=" N ILE B 667 " --> pdb=" O PRO B 664 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 669 " --> pdb=" O SER B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.566A pdb=" N GLY B 782 " --> pdb=" O ASP B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 849 removed outlier: 3.584A pdb=" N ILE B 849 " --> pdb=" O ARG B 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 4.222A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.682A pdb=" N ASP C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 396 through 408 removed outlier: 4.103A pdb=" N ASP C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 404 " --> pdb=" O TRP C 400 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 414 through 424 removed outlier: 4.101A pdb=" N GLY C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 439 removed outlier: 4.107A pdb=" N LEU C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.532A pdb=" N MET C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.573A pdb=" N LYS C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 479 removed outlier: 3.810A pdb=" N LYS C 479 " --> pdb=" O HIS C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 509 through 518 removed outlier: 4.203A pdb=" N ALA C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 664 through 670 removed outlier: 4.040A pdb=" N ILE C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN C 669 " --> pdb=" O SER C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 851 removed outlier: 4.503A pdb=" N GLN C 850 " --> pdb=" O ARG C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.528A pdb=" N SER C 922 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.901A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.586A pdb=" N LYS D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 removed outlier: 3.842A pdb=" N MET D 368 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 410 removed outlier: 4.161A pdb=" N ASN D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.680A pdb=" N SER D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 439 removed outlier: 4.272A pdb=" N LEU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.518A pdb=" N LYS D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 479 removed outlier: 3.897A pdb=" N LYS D 479 " --> pdb=" O HIS D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 476 through 479' Processing helix chain 'D' and resid 485 through 499 removed outlier: 3.598A pdb=" N THR D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 498 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 503 removed outlier: 3.710A pdb=" N LYS D 503 " --> pdb=" O LYS D 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 500 through 503' Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 542 through 546 removed outlier: 4.504A pdb=" N PHE D 546 " --> pdb=" O PRO D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 removed outlier: 3.808A pdb=" N ASN D 669 " --> pdb=" O SER D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 848 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'P' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'Q' and resid 23 through 29 removed outlier: 6.594A pdb=" N VAL Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP Q 58 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR Q 64 " --> pdb=" O ILE Q 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE Q 56 " --> pdb=" O THR Q 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 52 through 58 removed outlier: 3.612A pdb=" N ILE R 56 " --> pdb=" O THR R 64 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR R 64 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS R 91 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 24 through 28 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.005A pdb=" N LEU A 555 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 629 " --> pdb=" O TYR A 653 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 699 " --> pdb=" O ASP A 719 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 721 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 723 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 745 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A 765 " --> pdb=" O CYS A 790 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 831 through 833 removed outlier: 3.537A pdb=" N HIS A 871 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 915 removed outlier: 4.412A pdb=" N VAL A 915 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 921 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 475 Processing sheet with id=AB3, first strand: chain 'B' and resid 506 through 507 removed outlier: 5.999A pdb=" N LEU B 507 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP B 532 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 629 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 652 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 676 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN B 700 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 721 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 743 " --> pdb=" O ASN B 766 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 765 " --> pdb=" O CYS B 790 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 799 through 800 removed outlier: 3.558A pdb=" N LEU B 800 " --> pdb=" O SER B 820 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 857 through 860 removed outlier: 4.440A pdb=" N GLU B 986 " --> pdb=" O VAL B 893 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS B 871 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 877 through 880 Processing sheet with id=AB7, first strand: chain 'B' and resid 909 through 912 removed outlier: 3.718A pdb=" N PHE B 927 " --> pdb=" O LEU B 909 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 911 " --> pdb=" O LYS B 925 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AB9, first strand: chain 'C' and resid 506 through 507 removed outlier: 5.845A pdb=" N LEU C 507 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP C 532 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 529 " --> pdb=" O LYS C 556 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N TYR C 558 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE C 531 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 583 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 629 " --> pdb=" O TYR C 653 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE C 676 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASN C 702 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 723 " --> pdb=" O MET C 701 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE C 743 " --> pdb=" O ASN C 766 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 809 through 811 removed outlier: 6.143A pdb=" N LEU C 810 " --> pdb=" O TYR C 833 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 871 through 873 Processing sheet with id=AC3, first strand: chain 'C' and resid 877 through 880 Processing sheet with id=AC4, first strand: chain 'C' and resid 946 through 949 Processing sheet with id=AC5, first strand: chain 'D' and resid 473 through 475 removed outlier: 3.514A pdb=" N ARG D 481 " --> pdb=" O ASP D 475 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 506 through 507 removed outlier: 6.005A pdb=" N LEU D 507 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP D 532 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 529 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR D 558 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE D 531 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 629 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 676 " --> pdb=" O ASN D 700 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 699 " --> pdb=" O ASP D 719 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D 721 " --> pdb=" O LEU D 699 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 857 through 860 Processing sheet with id=AC8, first strand: chain 'D' and resid 913 through 915 556 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7613 1.35 - 1.47: 5141 1.47 - 1.59: 10714 1.59 - 1.71: 0 1.71 - 1.83: 204 Bond restraints: 23672 Sorted by residual: bond pdb=" N LEU P 39 " pdb=" CA LEU P 39 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 9.00e+00 bond pdb=" CA ASN C 692 " pdb=" CB ASN C 692 " ideal model delta sigma weight residual 1.528 1.566 -0.038 1.39e-02 5.18e+03 7.44e+00 bond pdb=" N LEU Q 48 " pdb=" CA LEU Q 48 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.39e+00 bond pdb=" N CYS P 40 " pdb=" CA CYS P 40 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.22e+00 bond pdb=" N ILE D 809 " pdb=" CA ILE D 809 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.99e+00 ... (remaining 23667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 31008 2.27 - 4.54: 888 4.54 - 6.80: 113 6.80 - 9.07: 27 9.07 - 11.34: 4 Bond angle restraints: 32040 Sorted by residual: angle pdb=" N VAL D 938 " pdb=" CA VAL D 938 " pdb=" C VAL D 938 " ideal model delta sigma weight residual 111.90 106.05 5.85 8.10e-01 1.52e+00 5.22e+01 angle pdb=" N ASP P 32 " pdb=" CA ASP P 32 " pdb=" C ASP P 32 " ideal model delta sigma weight residual 112.93 105.16 7.77 1.12e+00 7.97e-01 4.81e+01 angle pdb=" N LEU D 807 " pdb=" CA LEU D 807 " pdb=" C LEU D 807 " ideal model delta sigma weight residual 110.23 100.83 9.40 1.45e+00 4.76e-01 4.20e+01 angle pdb=" N HIS A 931 " pdb=" CA HIS A 931 " pdb=" C HIS A 931 " ideal model delta sigma weight residual 113.20 105.64 7.56 1.21e+00 6.83e-01 3.90e+01 angle pdb=" N ALA A 835 " pdb=" CA ALA A 835 " pdb=" C ALA A 835 " ideal model delta sigma weight residual 112.97 107.27 5.70 1.06e+00 8.90e-01 2.89e+01 ... (remaining 32035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.27: 12604 18.27 - 36.55: 1444 36.55 - 54.82: 321 54.82 - 73.09: 57 73.09 - 91.36: 30 Dihedral angle restraints: 14456 sinusoidal: 5844 harmonic: 8612 Sorted by residual: dihedral pdb=" CB CYS S 40 " pdb=" SG CYS S 40 " pdb=" SG CYS S 87 " pdb=" CB CYS S 87 " ideal model delta sinusoidal sigma weight residual -86.00 -0.08 -85.92 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 87 " pdb=" CB CYS R 87 " ideal model delta sinusoidal sigma weight residual 93.00 21.32 71.68 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CB CYS S 43 " pdb=" SG CYS S 43 " pdb=" SG CYS S 81 " pdb=" CB CYS S 81 " ideal model delta sinusoidal sigma weight residual 93.00 146.91 -53.91 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 14453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3044 0.061 - 0.122: 585 0.122 - 0.183: 69 0.183 - 0.244: 10 0.244 - 0.305: 4 Chirality restraints: 3712 Sorted by residual: chirality pdb=" CA LEU D 807 " pdb=" N LEU D 807 " pdb=" C LEU D 807 " pdb=" CB LEU D 807 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE B 809 " pdb=" CA ILE B 809 " pdb=" CG1 ILE B 809 " pdb=" CG2 ILE B 809 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR C 926 " pdb=" CA THR C 926 " pdb=" OG1 THR C 926 " pdb=" CG2 THR C 926 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3709 not shown) Planarity restraints: 4084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 805 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ARG D 805 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 805 " 0.024 2.00e-02 2.50e+03 pdb=" N SER D 806 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 707 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C LEU D 707 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU D 707 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG D 708 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 730 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 731 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 731 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 731 " -0.032 5.00e-02 4.00e+02 ... (remaining 4081 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1905 2.74 - 3.28: 24760 3.28 - 3.82: 37904 3.82 - 4.36: 45738 4.36 - 4.90: 76172 Nonbonded interactions: 186479 Sorted by model distance: nonbonded pdb=" OD1 ASN S 57 " pdb=" OG1 THR S 64 " model vdw 2.196 3.040 nonbonded pdb=" ND2 ASN S 85 " pdb=" O TRP D 562 " model vdw 2.200 3.120 nonbonded pdb=" OG SER B 746 " pdb=" OD1 ASN B 766 " model vdw 2.207 3.040 nonbonded pdb=" OG SER D 768 " pdb=" O CYS D 790 " model vdw 2.228 3.040 nonbonded pdb=" O ARG P 34 " pdb=" NH1 ARG P 34 " model vdw 2.231 3.120 ... (remaining 186474 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.040 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.003 0.040 23680 Z= 0.202 Angle : 0.893 11.338 32056 Z= 0.518 Chirality : 0.049 0.305 3712 Planarity : 0.005 0.058 4084 Dihedral : 16.535 91.363 8816 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.61 % Favored : 87.98 % Rotamer: Outliers : 3.35 % Allowed : 22.67 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.15), residues: 2920 helix: -0.35 (0.22), residues: 618 sheet: -2.07 (0.25), residues: 387 loop : -2.38 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 846 TYR 0.024 0.002 TYR A 515 PHE 0.035 0.002 PHE B 948 TRP 0.039 0.002 TRP C 617 HIS 0.022 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00344 (23672) covalent geometry : angle 0.89187 (32040) SS BOND : bond 0.00515 ( 8) SS BOND : angle 2.17800 ( 16) hydrogen bonds : bond 0.22042 ( 556) hydrogen bonds : angle 8.52976 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 332 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 26 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6465 (tt) REVERT: P 32 ASP cc_start: 0.7976 (t0) cc_final: 0.7212 (m-30) REVERT: P 34 ARG cc_start: 0.7008 (tpt90) cc_final: 0.6625 (tpt90) REVERT: R 47 LYS cc_start: 0.8319 (tttt) cc_final: 0.8022 (mppt) REVERT: S 57 ASN cc_start: 0.7281 (t0) cc_final: 0.6961 (m110) REVERT: A 563 HIS cc_start: 0.7666 (p-80) cc_final: 0.7000 (m90) REVERT: A 636 CYS cc_start: 0.7056 (p) cc_final: 0.6768 (t) REVERT: A 721 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: A 730 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7865 (tp) REVERT: A 833 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: A 834 PHE cc_start: 0.6992 (m-80) cc_final: 0.6599 (m-80) REVERT: A 898 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7460 (t-90) REVERT: B 324 THR cc_start: 0.8843 (t) cc_final: 0.8610 (p) REVERT: B 542 SER cc_start: 0.8173 (m) cc_final: 0.7830 (p) REVERT: B 598 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 623 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6744 (pt) REVERT: B 718 GLU cc_start: 0.6352 (tm-30) cc_final: 0.5636 (tm-30) REVERT: B 719 ASP cc_start: 0.7487 (t70) cc_final: 0.6627 (p0) REVERT: B 764 HIS cc_start: 0.6290 (t70) cc_final: 0.5927 (t70) REVERT: B 788 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6710 (t0) REVERT: B 882 TYR cc_start: 0.2643 (OUTLIER) cc_final: 0.1310 (m-80) REVERT: C 354 CYS cc_start: 0.8300 (m) cc_final: 0.7899 (t) REVERT: C 678 MET cc_start: 0.6592 (ptp) cc_final: 0.6166 (ptm) REVERT: C 863 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6333 (tp) REVERT: C 902 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4772 (p90) REVERT: C 951 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.5290 (m-70) REVERT: D 513 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.5901 (mt) REVERT: D 549 MET cc_start: 0.6885 (tpt) cc_final: 0.6535 (tpt) REVERT: D 599 PHE cc_start: 0.5406 (OUTLIER) cc_final: 0.4724 (t80) REVERT: D 636 CYS cc_start: 0.7138 (m) cc_final: 0.6556 (t) REVERT: D 643 LEU cc_start: 0.8529 (mm) cc_final: 0.7884 (pp) REVERT: D 717 ILE cc_start: 0.8159 (mm) cc_final: 0.7542 (pt) REVERT: D 806 SER cc_start: -0.4227 (OUTLIER) cc_final: -0.5726 (m) REVERT: D 832 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6391 (mt) REVERT: D 846 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7343 (tmm-80) REVERT: D 857 TRP cc_start: 0.6820 (p-90) cc_final: 0.6338 (p-90) outliers start: 89 outliers final: 58 residues processed: 394 average time/residue: 0.1435 time to fit residues: 90.2577 Evaluate side-chains 377 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 303 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 871 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 806 SER Chi-restraints excluded: chain D residue 832 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN S 76 ASN A 645 ASN A 824 HIS B 614 GLN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS B 836 ASN C 505 GLN C 625 ASN C 829 ASN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 ASN ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 ASN ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095843 restraints weight = 69443.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095391 restraints weight = 41047.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096584 restraints weight = 27552.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097194 restraints weight = 22849.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097258 restraints weight = 19701.484| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 23680 Z= 0.225 Angle : 0.813 12.325 32056 Z= 0.419 Chirality : 0.050 0.322 3712 Planarity : 0.005 0.059 4084 Dihedral : 8.952 82.778 3262 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.57 % Favored : 87.09 % Rotamer: Outliers : 6.20 % Allowed : 19.77 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.15), residues: 2920 helix: -0.51 (0.21), residues: 629 sheet: -2.09 (0.25), residues: 414 loop : -2.45 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 706 TYR 0.033 0.003 TYR A 515 PHE 0.031 0.002 PHE D 754 TRP 0.020 0.002 TRP C 617 HIS 0.007 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00511 (23672) covalent geometry : angle 0.80804 (32040) SS BOND : bond 0.00732 ( 8) SS BOND : angle 4.16669 ( 16) hydrogen bonds : bond 0.05066 ( 556) hydrogen bonds : angle 6.94665 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 305 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 26 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6633 (tt) REVERT: P 34 ARG cc_start: 0.7469 (tpt90) cc_final: 0.7185 (tpt90) REVERT: Q 52 ARG cc_start: 0.6371 (tpm170) cc_final: 0.6153 (tpm170) REVERT: S 52 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.4281 (ttm110) REVERT: S 57 ASN cc_start: 0.7373 (t0) cc_final: 0.7151 (m110) REVERT: A 537 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5167 (t0) REVERT: A 563 HIS cc_start: 0.7832 (p-80) cc_final: 0.7166 (m90) REVERT: A 636 CYS cc_start: 0.7388 (p) cc_final: 0.7167 (t) REVERT: A 730 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (tp) REVERT: A 833 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5516 (m-80) REVERT: A 974 GLU cc_start: 0.5349 (mp0) cc_final: 0.4873 (tm-30) REVERT: B 324 THR cc_start: 0.8918 (t) cc_final: 0.8656 (p) REVERT: B 542 SER cc_start: 0.8306 (m) cc_final: 0.7867 (p) REVERT: B 571 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8281 (tp) REVERT: B 584 PHE cc_start: 0.7793 (t80) cc_final: 0.7588 (t80) REVERT: B 598 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: B 599 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5996 (t80) REVERT: B 608 MET cc_start: 0.7888 (mmm) cc_final: 0.7633 (mmm) REVERT: B 623 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6843 (pt) REVERT: B 700 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7084 (p0) REVERT: B 718 GLU cc_start: 0.6609 (tm-30) cc_final: 0.5848 (tm-30) REVERT: B 719 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6162 (p0) REVERT: B 764 HIS cc_start: 0.6296 (t70) cc_final: 0.5948 (t70) REVERT: B 788 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7170 (t0) REVERT: B 882 TYR cc_start: 0.2747 (OUTLIER) cc_final: 0.1389 (m-80) REVERT: B 911 TYR cc_start: 0.4830 (OUTLIER) cc_final: 0.2889 (m-80) REVERT: B 975 PHE cc_start: 0.4096 (OUTLIER) cc_final: 0.3047 (m-10) REVERT: C 678 MET cc_start: 0.6632 (ptp) cc_final: 0.6043 (ptm) REVERT: C 863 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6102 (tp) REVERT: C 892 VAL cc_start: 0.2731 (OUTLIER) cc_final: 0.2199 (t) REVERT: C 902 PHE cc_start: 0.5237 (OUTLIER) cc_final: 0.4676 (p90) REVERT: C 946 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5269 (p90) REVERT: C 951 HIS cc_start: 0.5445 (OUTLIER) cc_final: 0.5148 (m-70) REVERT: D 531 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: D 589 TYR cc_start: 0.8212 (t80) cc_final: 0.7979 (t80) REVERT: D 599 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5133 (t80) REVERT: D 717 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (pt) REVERT: D 789 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.0990 (tp) outliers start: 165 outliers final: 95 residues processed: 429 average time/residue: 0.1424 time to fit residues: 98.4792 Evaluate side-chains 394 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 275 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 700 ASN Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 750 ASN Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 927 PHE Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 199 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 76 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 736 HIS C 473 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.125599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096074 restraints weight = 68843.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096874 restraints weight = 42961.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097498 restraints weight = 28871.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.097887 restraints weight = 26140.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098404 restraints weight = 21989.051| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23680 Z= 0.146 Angle : 0.731 9.878 32056 Z= 0.376 Chirality : 0.047 0.263 3712 Planarity : 0.005 0.055 4084 Dihedral : 8.306 80.515 3210 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.27 % Favored : 88.36 % Rotamer: Outliers : 5.94 % Allowed : 21.05 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.15), residues: 2920 helix: -0.40 (0.21), residues: 633 sheet: -2.11 (0.25), residues: 426 loop : -2.48 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 709 TYR 0.025 0.002 TYR A 515 PHE 0.027 0.002 PHE B 440 TRP 0.023 0.002 TRP C 617 HIS 0.006 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00326 (23672) covalent geometry : angle 0.72784 (32040) SS BOND : bond 0.01359 ( 8) SS BOND : angle 3.30086 ( 16) hydrogen bonds : bond 0.04079 ( 556) hydrogen bonds : angle 6.56704 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 315 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 48 LEU cc_start: 0.8772 (mt) cc_final: 0.8569 (mp) REVERT: R 47 LYS cc_start: 0.8359 (tttt) cc_final: 0.7975 (mppt) REVERT: S 57 ASN cc_start: 0.7352 (t0) cc_final: 0.7137 (m110) REVERT: A 563 HIS cc_start: 0.7813 (p-80) cc_final: 0.7149 (m90) REVERT: A 589 TYR cc_start: 0.8186 (t80) cc_final: 0.7764 (t80) REVERT: A 636 CYS cc_start: 0.7257 (p) cc_final: 0.6985 (t) REVERT: A 730 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 833 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.5627 (m-80) REVERT: A 974 GLU cc_start: 0.5702 (mp0) cc_final: 0.5163 (tm-30) REVERT: B 324 THR cc_start: 0.8897 (t) cc_final: 0.8641 (p) REVERT: B 423 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 542 SER cc_start: 0.8232 (m) cc_final: 0.7860 (p) REVERT: B 571 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 584 PHE cc_start: 0.7835 (t80) cc_final: 0.7596 (t80) REVERT: B 598 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 599 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5975 (t80) REVERT: B 623 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6934 (pt) REVERT: B 636 CYS cc_start: 0.6759 (t) cc_final: 0.6500 (t) REVERT: B 677 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: B 718 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6177 (tm-30) REVERT: B 764 HIS cc_start: 0.6084 (t70) cc_final: 0.5757 (t70) REVERT: B 788 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7067 (t0) REVERT: B 882 TYR cc_start: 0.2703 (OUTLIER) cc_final: 0.1355 (m-80) REVERT: B 911 TYR cc_start: 0.4478 (OUTLIER) cc_final: 0.2177 (m-80) REVERT: B 942 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.5024 (mt) REVERT: B 950 PHE cc_start: 0.6834 (t80) cc_final: 0.6564 (t80) REVERT: B 975 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3266 (m-10) REVERT: C 608 MET cc_start: 0.8037 (mmm) cc_final: 0.7761 (mmm) REVERT: C 678 MET cc_start: 0.6583 (ptp) cc_final: 0.6121 (ptm) REVERT: C 701 MET cc_start: 0.8024 (mpp) cc_final: 0.7682 (mpp) REVERT: C 863 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6194 (tp) REVERT: C 892 VAL cc_start: 0.2712 (OUTLIER) cc_final: 0.2381 (t) REVERT: C 946 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5407 (p90) REVERT: C 951 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.5256 (m-70) REVERT: D 552 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8093 (pt) REVERT: D 589 TYR cc_start: 0.8135 (t80) cc_final: 0.7893 (t80) REVERT: D 599 PHE cc_start: 0.5639 (OUTLIER) cc_final: 0.4855 (t80) REVERT: D 636 CYS cc_start: 0.7239 (m) cc_final: 0.6672 (t) REVERT: D 715 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7682 (m) REVERT: D 717 ILE cc_start: 0.8236 (mm) cc_final: 0.7672 (pt) REVERT: D 789 LEU cc_start: 0.2119 (OUTLIER) cc_final: 0.1641 (tt) REVERT: D 846 ARG cc_start: 0.7761 (tmm160) cc_final: 0.7496 (tmm-80) REVERT: D 857 TRP cc_start: 0.6582 (p-90) cc_final: 0.5945 (p-90) REVERT: D 880 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5789 (pt) REVERT: D 887 ARG cc_start: 0.5170 (OUTLIER) cc_final: 0.4159 (mtm-85) outliers start: 158 outliers final: 90 residues processed: 433 average time/residue: 0.1431 time to fit residues: 100.2916 Evaluate side-chains 390 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 278 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 715 THR Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 273 optimal weight: 0.0270 chunk 277 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS B 736 HIS ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096545 restraints weight = 68606.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096808 restraints weight = 36957.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.097813 restraints weight = 25372.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098167 restraints weight = 22270.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098274 restraints weight = 19914.410| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23680 Z= 0.136 Angle : 0.711 9.679 32056 Z= 0.364 Chirality : 0.047 0.252 3712 Planarity : 0.004 0.053 4084 Dihedral : 7.991 78.750 3201 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.10 % Favored : 88.53 % Rotamer: Outliers : 5.60 % Allowed : 22.56 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2920 helix: -0.35 (0.21), residues: 634 sheet: -2.03 (0.25), residues: 431 loop : -2.49 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 709 TYR 0.024 0.002 TYR C 653 PHE 0.023 0.001 PHE C 927 TRP 0.023 0.001 TRP C 617 HIS 0.006 0.001 HIS B 736 Details of bonding type rmsd covalent geometry : bond 0.00306 (23672) covalent geometry : angle 0.70844 (32040) SS BOND : bond 0.00619 ( 8) SS BOND : angle 2.95904 ( 16) hydrogen bonds : bond 0.03691 ( 556) hydrogen bonds : angle 6.32178 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 312 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 LYS cc_start: 0.8286 (tttt) cc_final: 0.7929 (mppt) REVERT: S 53 MET cc_start: 0.7675 (mmm) cc_final: 0.7260 (mmm) REVERT: A 563 HIS cc_start: 0.7780 (p-80) cc_final: 0.7151 (m90) REVERT: A 589 TYR cc_start: 0.8206 (t80) cc_final: 0.7869 (t80) REVERT: A 730 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8095 (tp) REVERT: A 833 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: A 974 GLU cc_start: 0.5785 (mp0) cc_final: 0.5373 (tm-30) REVERT: B 324 THR cc_start: 0.8874 (t) cc_final: 0.8632 (p) REVERT: B 423 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 542 SER cc_start: 0.8254 (m) cc_final: 0.7895 (p) REVERT: B 571 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 598 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: B 599 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.5971 (t80) REVERT: B 608 MET cc_start: 0.7858 (mmm) cc_final: 0.7556 (mmm) REVERT: B 623 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6896 (pt) REVERT: B 636 CYS cc_start: 0.6977 (t) cc_final: 0.6579 (t) REVERT: B 700 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7025 (p0) REVERT: B 718 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6184 (tm-30) REVERT: B 764 HIS cc_start: 0.5879 (t70) cc_final: 0.5518 (t70) REVERT: B 788 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7286 (t0) REVERT: B 882 TYR cc_start: 0.2506 (OUTLIER) cc_final: 0.1123 (m-80) REVERT: B 911 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.2182 (m-80) REVERT: B 932 MET cc_start: 0.3650 (mmp) cc_final: 0.3449 (mmp) REVERT: B 950 PHE cc_start: 0.6854 (t80) cc_final: 0.6590 (t80) REVERT: B 975 PHE cc_start: 0.4072 (OUTLIER) cc_final: 0.3113 (m-10) REVERT: C 678 MET cc_start: 0.6502 (ptp) cc_final: 0.6174 (ptm) REVERT: C 863 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6201 (tp) REVERT: C 892 VAL cc_start: 0.2692 (OUTLIER) cc_final: 0.2436 (t) REVERT: C 902 PHE cc_start: 0.5109 (OUTLIER) cc_final: 0.4591 (p90) REVERT: C 946 HIS cc_start: 0.5990 (OUTLIER) cc_final: 0.5379 (p90) REVERT: D 526 ILE cc_start: 0.8737 (mp) cc_final: 0.8531 (mm) REVERT: D 552 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (pt) REVERT: D 589 TYR cc_start: 0.8155 (t80) cc_final: 0.7827 (t80) REVERT: D 599 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4797 (t80) REVERT: D 636 CYS cc_start: 0.7282 (m) cc_final: 0.6710 (t) REVERT: D 715 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (m) REVERT: D 717 ILE cc_start: 0.8267 (mm) cc_final: 0.7636 (pt) REVERT: D 796 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7562 (mtt90) REVERT: D 832 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6837 (mt) REVERT: D 846 ARG cc_start: 0.7716 (tmm160) cc_final: 0.7488 (tmm-80) REVERT: D 857 TRP cc_start: 0.6725 (p-90) cc_final: 0.6051 (p-90) REVERT: D 948 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6842 (t80) outliers start: 149 outliers final: 95 residues processed: 431 average time/residue: 0.1427 time to fit residues: 99.1658 Evaluate side-chains 390 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 275 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 40 CYS Chi-restraints excluded: chain P residue 46 ASN Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 715 THR Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 228 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.123910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094927 restraints weight = 68378.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094934 restraints weight = 38338.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095946 restraints weight = 26459.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096275 restraints weight = 23202.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096409 restraints weight = 20758.306| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23680 Z= 0.178 Angle : 0.740 9.121 32056 Z= 0.378 Chirality : 0.048 0.249 3712 Planarity : 0.005 0.051 4084 Dihedral : 7.939 77.835 3196 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.99 % Favored : 87.64 % Rotamer: Outliers : 6.13 % Allowed : 22.56 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.15), residues: 2920 helix: -0.34 (0.21), residues: 629 sheet: -2.02 (0.26), residues: 410 loop : -2.54 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 709 TYR 0.029 0.002 TYR A 515 PHE 0.030 0.002 PHE C 927 TRP 0.022 0.002 TRP C 617 HIS 0.006 0.001 HIS C 951 Details of bonding type rmsd covalent geometry : bond 0.00409 (23672) covalent geometry : angle 0.73762 (32040) SS BOND : bond 0.00559 ( 8) SS BOND : angle 2.76689 ( 16) hydrogen bonds : bond 0.03903 ( 556) hydrogen bonds : angle 6.32477 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 294 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 LYS cc_start: 0.8346 (tttt) cc_final: 0.7976 (mppt) REVERT: S 53 MET cc_start: 0.7825 (mmm) cc_final: 0.7340 (mmm) REVERT: A 563 HIS cc_start: 0.7843 (p-80) cc_final: 0.7261 (m90) REVERT: A 589 TYR cc_start: 0.8314 (t80) cc_final: 0.7866 (t80) REVERT: A 833 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5603 (m-80) REVERT: A 974 GLU cc_start: 0.5684 (mp0) cc_final: 0.5312 (tm-30) REVERT: B 324 THR cc_start: 0.8929 (t) cc_final: 0.8679 (p) REVERT: B 542 SER cc_start: 0.8270 (m) cc_final: 0.7893 (p) REVERT: B 571 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8252 (tp) REVERT: B 598 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: B 599 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 623 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6941 (pt) REVERT: B 700 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7039 (p0) REVERT: B 718 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6178 (tm-30) REVERT: B 764 HIS cc_start: 0.5696 (t70) cc_final: 0.5456 (t70) REVERT: B 882 TYR cc_start: 0.2511 (OUTLIER) cc_final: 0.1061 (m-80) REVERT: B 911 TYR cc_start: 0.4572 (OUTLIER) cc_final: 0.2785 (m-80) REVERT: B 950 PHE cc_start: 0.6890 (t80) cc_final: 0.6639 (t80) REVERT: B 975 PHE cc_start: 0.4195 (OUTLIER) cc_final: 0.3023 (m-10) REVERT: B 987 CYS cc_start: -0.0794 (OUTLIER) cc_final: -0.1396 (p) REVERT: C 863 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6430 (mt) REVERT: C 902 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4610 (p90) REVERT: C 932 MET cc_start: 0.5686 (mmm) cc_final: 0.5439 (mmm) REVERT: C 946 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.5031 (p90) REVERT: D 526 ILE cc_start: 0.8816 (mp) cc_final: 0.8571 (mm) REVERT: D 549 MET cc_start: 0.7117 (tpt) cc_final: 0.6892 (tpt) REVERT: D 552 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (pt) REVERT: D 589 TYR cc_start: 0.8195 (t80) cc_final: 0.7872 (t80) REVERT: D 599 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.4898 (t80) REVERT: D 636 CYS cc_start: 0.7208 (m) cc_final: 0.6656 (t) REVERT: D 857 TRP cc_start: 0.6847 (p-90) cc_final: 0.6197 (p-90) REVERT: D 948 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7003 (t80) outliers start: 163 outliers final: 109 residues processed: 422 average time/residue: 0.1345 time to fit residues: 91.6230 Evaluate side-chains 402 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 277 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 32 ASP Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 675 HIS Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Chi-restraints excluded: chain D residue 948 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 204 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 ASN ** D 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.121736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093801 restraints weight = 70221.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093460 restraints weight = 50110.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.093983 restraints weight = 37231.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094419 restraints weight = 33166.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095004 restraints weight = 27291.339| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 23680 Z= 0.295 Angle : 0.884 10.959 32056 Z= 0.451 Chirality : 0.053 0.357 3712 Planarity : 0.006 0.058 4084 Dihedral : 8.368 59.908 3185 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.84 % Favored : 85.79 % Rotamer: Outliers : 6.99 % Allowed : 23.31 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.14), residues: 2920 helix: -0.77 (0.20), residues: 627 sheet: -1.98 (0.27), residues: 371 loop : -2.68 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 709 TYR 0.039 0.003 TYR A 515 PHE 0.025 0.002 PHE B 933 TRP 0.024 0.002 TRP A 617 HIS 0.006 0.002 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00669 (23672) covalent geometry : angle 0.88019 (32040) SS BOND : bond 0.01048 ( 8) SS BOND : angle 3.89025 ( 16) hydrogen bonds : bond 0.04835 ( 556) hydrogen bonds : angle 6.88750 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 273 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.6553 (tpm170) cc_final: 0.6323 (tpm170) REVERT: S 30 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.4200 (pptt) REVERT: S 53 MET cc_start: 0.7813 (mmm) cc_final: 0.7369 (mmm) REVERT: S 76 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (p0) REVERT: A 563 HIS cc_start: 0.7810 (p-80) cc_final: 0.7448 (m90) REVERT: A 589 TYR cc_start: 0.8303 (t80) cc_final: 0.7905 (t80) REVERT: A 678 MET cc_start: 0.7720 (mpt) cc_final: 0.7501 (mpt) REVERT: A 833 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5394 (m-80) REVERT: A 943 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: A 974 GLU cc_start: 0.5254 (mp0) cc_final: 0.4949 (tm-30) REVERT: A 979 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5857 (m-80) REVERT: B 542 SER cc_start: 0.8150 (m) cc_final: 0.7715 (p) REVERT: B 571 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 598 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: B 599 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.5956 (t80) REVERT: B 623 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7095 (pt) REVERT: B 700 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7536 (p0) REVERT: B 718 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6411 (tm-30) REVERT: B 882 TYR cc_start: 0.2494 (OUTLIER) cc_final: 0.0885 (m-80) REVERT: B 911 TYR cc_start: 0.5157 (OUTLIER) cc_final: 0.2836 (m-80) REVERT: B 975 PHE cc_start: 0.4634 (OUTLIER) cc_final: 0.3125 (m-10) REVERT: B 987 CYS cc_start: -0.0855 (OUTLIER) cc_final: -0.1622 (p) REVERT: C 538 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 813 ASP cc_start: 0.7691 (m-30) cc_final: 0.7106 (p0) REVERT: C 902 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4835 (p90) REVERT: C 946 HIS cc_start: 0.5671 (OUTLIER) cc_final: 0.5448 (p90) REVERT: C 974 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: D 526 ILE cc_start: 0.8913 (mp) cc_final: 0.8669 (mm) REVERT: D 589 TYR cc_start: 0.8250 (t80) cc_final: 0.7920 (t80) REVERT: D 599 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5062 (t80) REVERT: D 680 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8220 (t) REVERT: D 710 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: D 717 ILE cc_start: 0.8439 (mm) cc_final: 0.7985 (pt) outliers start: 186 outliers final: 123 residues processed: 437 average time/residue: 0.1379 time to fit residues: 97.9882 Evaluate side-chains 398 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 255 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 32 ASP Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 979 TYR Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 829 ASN Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 934 ASN Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 633 ARG Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 974 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 675 HIS Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 710 PHE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 165 optimal weight: 0.0060 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 ASN ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.125660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096788 restraints weight = 68801.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097148 restraints weight = 38342.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098137 restraints weight = 26433.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098456 restraints weight = 23750.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098620 restraints weight = 20604.592| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23680 Z= 0.128 Angle : 0.756 11.931 32056 Z= 0.382 Chirality : 0.048 0.278 3712 Planarity : 0.005 0.050 4084 Dihedral : 7.727 59.725 3182 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.89 % Favored : 88.73 % Rotamer: Outliers : 4.92 % Allowed : 25.49 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.15), residues: 2920 helix: -0.45 (0.21), residues: 643 sheet: -2.00 (0.26), residues: 399 loop : -2.59 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 34 TYR 0.022 0.001 TYR D 442 PHE 0.031 0.002 PHE B 440 TRP 0.030 0.002 TRP C 617 HIS 0.007 0.001 HIS C 951 Details of bonding type rmsd covalent geometry : bond 0.00284 (23672) covalent geometry : angle 0.75146 (32040) SS BOND : bond 0.00623 ( 8) SS BOND : angle 3.79449 ( 16) hydrogen bonds : bond 0.03561 ( 556) hydrogen bonds : angle 6.22587 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 311 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 34 ARG cc_start: 0.7751 (tpt90) cc_final: 0.7499 (tpt90) REVERT: R 47 LYS cc_start: 0.8217 (tttt) cc_final: 0.7873 (mppt) REVERT: S 30 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.4286 (pptt) REVERT: S 76 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7451 (p0) REVERT: A 491 MET cc_start: 0.8464 (tmm) cc_final: 0.8211 (ttt) REVERT: A 563 HIS cc_start: 0.7724 (p-80) cc_final: 0.7135 (m90) REVERT: A 589 TYR cc_start: 0.8251 (t80) cc_final: 0.7785 (t80) REVERT: A 608 MET cc_start: 0.7751 (mmm) cc_final: 0.7539 (mmm) REVERT: A 714 PRO cc_start: 0.6139 (Cg_endo) cc_final: 0.5925 (Cg_exo) REVERT: A 718 GLU cc_start: 0.7533 (tp30) cc_final: 0.7306 (tp30) REVERT: A 730 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 740 LEU cc_start: 0.8283 (mt) cc_final: 0.8056 (mp) REVERT: A 833 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.5298 (m-80) REVERT: A 974 GLU cc_start: 0.5662 (mp0) cc_final: 0.5327 (tm-30) REVERT: A 980 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8181 (pptt) REVERT: B 324 THR cc_start: 0.8913 (t) cc_final: 0.8664 (p) REVERT: B 423 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 542 SER cc_start: 0.8134 (m) cc_final: 0.7829 (p) REVERT: B 598 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 599 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5876 (t80) REVERT: B 623 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7052 (pt) REVERT: B 700 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7161 (p0) REVERT: B 794 CYS cc_start: 0.6313 (m) cc_final: 0.5960 (p) REVERT: B 882 TYR cc_start: 0.2430 (OUTLIER) cc_final: 0.0860 (m-80) REVERT: B 911 TYR cc_start: 0.4828 (OUTLIER) cc_final: 0.2657 (m-80) REVERT: B 975 PHE cc_start: 0.4584 (OUTLIER) cc_final: 0.3416 (m-10) REVERT: B 987 CYS cc_start: -0.0979 (OUTLIER) cc_final: -0.1600 (p) REVERT: C 608 MET cc_start: 0.8045 (mmm) cc_final: 0.7842 (mmm) REVERT: C 709 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.4810 (mmp80) REVERT: C 758 LEU cc_start: 0.8385 (mt) cc_final: 0.8133 (mt) REVERT: C 832 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6024 (pp) REVERT: C 902 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4555 (p90) REVERT: C 925 LYS cc_start: 0.7447 (tptp) cc_final: 0.7214 (pttt) REVERT: C 974 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: D 526 ILE cc_start: 0.8771 (mp) cc_final: 0.8550 (mm) REVERT: D 589 TYR cc_start: 0.8108 (t80) cc_final: 0.7810 (t80) REVERT: D 599 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5047 (t80) REVERT: D 636 CYS cc_start: 0.7075 (m) cc_final: 0.6614 (t) REVERT: D 680 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (t) outliers start: 131 outliers final: 83 residues processed: 416 average time/residue: 0.1430 time to fit residues: 95.3273 Evaluate side-chains 379 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 277 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 851 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 974 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 118 optimal weight: 0.0040 chunk 181 optimal weight: 3.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 ASN C 871 HIS ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.123151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094914 restraints weight = 69025.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094434 restraints weight = 39908.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095485 restraints weight = 27750.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095885 restraints weight = 23552.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095993 restraints weight = 20959.402| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23680 Z= 0.194 Angle : 0.791 11.128 32056 Z= 0.400 Chirality : 0.049 0.274 3712 Planarity : 0.005 0.053 4084 Dihedral : 7.662 59.855 3174 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.71 % Favored : 86.92 % Rotamer: Outliers : 5.15 % Allowed : 25.83 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2920 helix: -0.53 (0.21), residues: 635 sheet: -1.87 (0.27), residues: 380 loop : -2.60 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 709 TYR 0.029 0.002 TYR A 515 PHE 0.037 0.002 PHE C 440 TRP 0.027 0.002 TRP A 913 HIS 0.006 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00446 (23672) covalent geometry : angle 0.78626 (32040) SS BOND : bond 0.00650 ( 8) SS BOND : angle 3.87015 ( 16) hydrogen bonds : bond 0.04016 ( 556) hydrogen bonds : angle 6.31636 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 279 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 47 LYS cc_start: 0.8254 (tttt) cc_final: 0.7926 (mppt) REVERT: S 30 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.4317 (pptt) REVERT: S 53 MET cc_start: 0.7671 (mmm) cc_final: 0.7451 (mmm) REVERT: S 76 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 563 HIS cc_start: 0.7797 (p-80) cc_final: 0.7301 (m90) REVERT: A 589 TYR cc_start: 0.8288 (t80) cc_final: 0.7803 (t80) REVERT: A 714 PRO cc_start: 0.6466 (Cg_endo) cc_final: 0.6234 (Cg_exo) REVERT: A 730 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 792 SER cc_start: 0.7038 (m) cc_final: 0.6474 (t) REVERT: A 833 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5416 (m-80) REVERT: A 932 MET cc_start: 0.4297 (mtm) cc_final: 0.4056 (mtp) REVERT: A 972 MET cc_start: 0.5244 (mmm) cc_final: 0.4985 (mmm) REVERT: A 974 GLU cc_start: 0.5723 (mp0) cc_final: 0.5253 (tm-30) REVERT: B 423 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 542 SER cc_start: 0.8203 (m) cc_final: 0.7853 (p) REVERT: B 571 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 598 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 599 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5928 (t80) REVERT: B 623 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7081 (pt) REVERT: B 639 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 700 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7206 (p0) REVERT: B 718 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6179 (tm-30) REVERT: B 882 TYR cc_start: 0.2484 (OUTLIER) cc_final: 0.0861 (m-80) REVERT: B 911 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.2801 (m-80) REVERT: B 975 PHE cc_start: 0.4680 (OUTLIER) cc_final: 0.3430 (m-10) REVERT: B 987 CYS cc_start: -0.0928 (OUTLIER) cc_final: -0.1569 (p) REVERT: C 709 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5017 (mmp80) REVERT: C 902 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4607 (p90) REVERT: D 526 ILE cc_start: 0.8831 (mp) cc_final: 0.8607 (mm) REVERT: D 589 TYR cc_start: 0.8148 (t80) cc_final: 0.7799 (t80) REVERT: D 599 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5120 (t80) REVERT: D 636 CYS cc_start: 0.7128 (m) cc_final: 0.6625 (t) REVERT: D 680 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8252 (t) REVERT: D 710 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4981 (m-80) outliers start: 137 outliers final: 95 residues processed: 394 average time/residue: 0.1450 time to fit residues: 92.0239 Evaluate side-chains 375 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 261 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 681 CYS Chi-restraints excluded: chain D residue 710 PHE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.123830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094995 restraints weight = 69646.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095304 restraints weight = 40067.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096129 restraints weight = 26892.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096517 restraints weight = 23917.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096679 restraints weight = 20979.591| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23680 Z= 0.169 Angle : 0.781 11.717 32056 Z= 0.394 Chirality : 0.049 0.268 3712 Planarity : 0.005 0.051 4084 Dihedral : 7.577 59.675 3174 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.29 % Favored : 87.33 % Rotamer: Outliers : 4.62 % Allowed : 26.47 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 2920 helix: -0.53 (0.21), residues: 639 sheet: -1.85 (0.27), residues: 368 loop : -2.62 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 709 TYR 0.026 0.002 TYR A 515 PHE 0.019 0.002 PHE C 948 TRP 0.032 0.002 TRP A 617 HIS 0.007 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00390 (23672) covalent geometry : angle 0.77728 (32040) SS BOND : bond 0.00665 ( 8) SS BOND : angle 3.65135 ( 16) hydrogen bonds : bond 0.03818 ( 556) hydrogen bonds : angle 6.21130 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 277 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 27 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7832 (ptp-170) REVERT: R 47 LYS cc_start: 0.8224 (tttt) cc_final: 0.7907 (mppt) REVERT: S 30 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.4315 (pptt) REVERT: S 76 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7396 (p0) REVERT: A 563 HIS cc_start: 0.7781 (p-80) cc_final: 0.7238 (m90) REVERT: A 589 TYR cc_start: 0.8248 (t80) cc_final: 0.7794 (t80) REVERT: A 714 PRO cc_start: 0.6320 (Cg_endo) cc_final: 0.6097 (Cg_exo) REVERT: A 730 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7977 (tp) REVERT: A 792 SER cc_start: 0.7066 (m) cc_final: 0.6429 (t) REVERT: A 833 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: A 972 MET cc_start: 0.5329 (mmm) cc_final: 0.5095 (mmm) REVERT: A 974 GLU cc_start: 0.5618 (mp0) cc_final: 0.5262 (tm-30) REVERT: B 542 SER cc_start: 0.8302 (m) cc_final: 0.7912 (p) REVERT: B 571 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 598 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: B 599 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6031 (t80) REVERT: B 623 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7026 (pt) REVERT: B 639 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: B 661 VAL cc_start: 0.8949 (t) cc_final: 0.8678 (p) REVERT: B 700 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7166 (p0) REVERT: B 718 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6199 (tm-30) REVERT: B 719 ASP cc_start: 0.7632 (t0) cc_final: 0.7390 (t0) REVERT: B 882 TYR cc_start: 0.2418 (OUTLIER) cc_final: 0.0794 (m-80) REVERT: B 911 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.2798 (m-80) REVERT: B 975 PHE cc_start: 0.4658 (OUTLIER) cc_final: 0.3436 (m-10) REVERT: B 987 CYS cc_start: -0.0874 (OUTLIER) cc_final: -0.1538 (p) REVERT: C 440 PHE cc_start: 0.7893 (m-80) cc_final: 0.7525 (m-80) REVERT: C 709 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5046 (mmp80) REVERT: C 758 LEU cc_start: 0.8432 (mt) cc_final: 0.8143 (mt) REVERT: C 902 PHE cc_start: 0.5184 (OUTLIER) cc_final: 0.4609 (p90) REVERT: D 526 ILE cc_start: 0.8813 (mp) cc_final: 0.8595 (mm) REVERT: D 589 TYR cc_start: 0.8112 (t80) cc_final: 0.7783 (t80) REVERT: D 599 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5130 (t80) REVERT: D 636 CYS cc_start: 0.7078 (m) cc_final: 0.6636 (t) REVERT: D 680 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8255 (t) REVERT: D 710 PHE cc_start: 0.5227 (OUTLIER) cc_final: 0.4939 (m-80) outliers start: 123 outliers final: 98 residues processed: 378 average time/residue: 0.1505 time to fit residues: 91.0756 Evaluate side-chains 381 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 264 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 681 CYS Chi-restraints excluded: chain D residue 710 PHE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 149 optimal weight: 30.0000 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 185 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 ASN ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 HIS ** D 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.123935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096031 restraints weight = 69887.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095635 restraints weight = 45383.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096301 restraints weight = 34281.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096589 restraints weight = 29661.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096958 restraints weight = 25740.489| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23680 Z= 0.197 Angle : 0.805 11.520 32056 Z= 0.406 Chirality : 0.049 0.277 3712 Planarity : 0.005 0.050 4084 Dihedral : 7.672 59.514 3174 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.95 % Favored : 86.71 % Rotamer: Outliers : 4.77 % Allowed : 26.20 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2920 helix: -0.57 (0.21), residues: 636 sheet: -1.87 (0.27), residues: 375 loop : -2.65 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 846 TYR 0.028 0.002 TYR A 515 PHE 0.019 0.002 PHE B 754 TRP 0.035 0.002 TRP A 617 HIS 0.006 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00451 (23672) covalent geometry : angle 0.80158 (32040) SS BOND : bond 0.00594 ( 8) SS BOND : angle 3.31608 ( 16) hydrogen bonds : bond 0.04037 ( 556) hydrogen bonds : angle 6.27885 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 267 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 27 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7828 (ptp-170) REVERT: R 47 LYS cc_start: 0.8210 (tttt) cc_final: 0.7909 (mppt) REVERT: S 30 LYS cc_start: 0.5603 (OUTLIER) cc_final: 0.4408 (pptt) REVERT: S 76 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (p0) REVERT: A 563 HIS cc_start: 0.7695 (p-80) cc_final: 0.7303 (m90) REVERT: A 589 TYR cc_start: 0.8241 (t80) cc_final: 0.7807 (t80) REVERT: A 678 MET cc_start: 0.7570 (mpt) cc_final: 0.7293 (mpt) REVERT: A 730 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 745 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (mm) REVERT: A 833 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: A 972 MET cc_start: 0.5214 (mmm) cc_final: 0.4961 (mmm) REVERT: A 974 GLU cc_start: 0.5552 (mp0) cc_final: 0.5318 (tm-30) REVERT: B 571 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8203 (tp) REVERT: B 598 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: B 599 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5998 (t80) REVERT: B 623 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7012 (pt) REVERT: B 639 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: B 661 VAL cc_start: 0.8978 (t) cc_final: 0.8717 (p) REVERT: B 700 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7230 (p0) REVERT: B 718 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6306 (tm-30) REVERT: B 882 TYR cc_start: 0.2358 (OUTLIER) cc_final: 0.0611 (m-80) REVERT: B 911 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.3116 (m-80) REVERT: B 948 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5457 (t80) REVERT: B 975 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3378 (m-10) REVERT: B 987 CYS cc_start: -0.0853 (OUTLIER) cc_final: -0.1596 (p) REVERT: C 440 PHE cc_start: 0.7869 (m-80) cc_final: 0.7636 (m-80) REVERT: C 451 MET cc_start: 0.6933 (pmm) cc_final: 0.6720 (pmm) REVERT: C 709 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5068 (mmp80) REVERT: C 758 LEU cc_start: 0.8408 (mt) cc_final: 0.8111 (mt) REVERT: C 902 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4685 (p90) REVERT: D 526 ILE cc_start: 0.8844 (mp) cc_final: 0.8623 (mm) REVERT: D 589 TYR cc_start: 0.8141 (t80) cc_final: 0.7820 (t80) REVERT: D 599 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5088 (t80) REVERT: D 636 CYS cc_start: 0.6974 (m) cc_final: 0.6590 (t) REVERT: D 680 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 710 PHE cc_start: 0.5310 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: D 832 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7385 (mt) outliers start: 127 outliers final: 97 residues processed: 372 average time/residue: 0.1464 time to fit residues: 88.6337 Evaluate side-chains 376 residues out of total 2660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 257 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 882 TYR Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 911 TYR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 987 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 710 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 897 ASN Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 681 CYS Chi-restraints excluded: chain D residue 710 PHE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 CYS Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 871 HIS Chi-restraints excluded: chain D residue 927 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 273 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 ASN ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 ASN ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN D 785 ASN ** D 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.123886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094890 restraints weight = 68186.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095233 restraints weight = 39452.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095916 restraints weight = 27885.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096105 restraints weight = 25993.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096963 restraints weight = 21544.497| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23680 Z= 0.148 Angle : 0.776 10.848 32056 Z= 0.390 Chirality : 0.048 0.258 3712 Planarity : 0.005 0.050 4084 Dihedral : 7.453 59.847 3172 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.50 % Favored : 87.16 % Rotamer: Outliers : 4.62 % Allowed : 26.65 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 2920 helix: -0.48 (0.21), residues: 637 sheet: -1.93 (0.28), residues: 358 loop : -2.62 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 846 TYR 0.022 0.002 TYR A 515 PHE 0.028 0.002 PHE B 531 TRP 0.032 0.002 TRP A 617 HIS 0.011 0.001 HIS C 898 Details of bonding type rmsd covalent geometry : bond 0.00338 (23672) covalent geometry : angle 0.77339 (32040) SS BOND : bond 0.00615 ( 8) SS BOND : angle 3.07711 ( 16) hydrogen bonds : bond 0.03717 ( 556) hydrogen bonds : angle 6.13675 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.45 seconds wall clock time: 64 minutes 25.89 seconds (3865.89 seconds total)