Starting phenix.real_space_refine on Fri Mar 6 16:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqi_26695/03_2026/7uqi_26695.cif" } resolution = 3.8 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 122 5.16 5 C 20742 2.51 5 N 5529 2.21 5 O 6021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32424 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4591 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "B" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4612 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4607 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 32, 'TRANS': 545} Chain breaks: 2 Chain: "D" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4586 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "E" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4448 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 32, 'TRANS': 525} Chain breaks: 4 Chain: "F" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4519 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 32, 'TRANS': 534} Chain breaks: 3 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.69, per 1000 atoms: 0.24 Number of scatterers: 32424 At special positions: 0 Unit cell: (160.425, 148.781, 183.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 P 10 15.00 O 6021 8.00 N 5529 7.00 C 20742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7698 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 17 sheets defined 56.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.625A pdb=" N ILE A 416 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.515A pdb=" N LYS A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.208A pdb=" N LEU A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.875A pdb=" N TYR A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.869A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 490' Processing helix chain 'A' and resid 495 through 511 removed outlier: 3.559A pdb=" N ARG A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.361A pdb=" N LEU A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 547 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.641A pdb=" N ILE A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 643 Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.285A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 649' Processing helix chain 'A' and resid 663 through 674 removed outlier: 3.537A pdb=" N PHE A 667 " --> pdb=" O LYS A 663 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.629A pdb=" N ARG A 680 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 711 removed outlier: 5.486A pdb=" N ASP A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.959A pdb=" N GLU A 758 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.742A pdb=" N ALA A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 847 through 860 Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.563A pdb=" N VAL A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.257A pdb=" N ASP A 888 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 889 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 890' Processing helix chain 'A' and resid 902 through 910 Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.660A pdb=" N ILE A 924 " --> pdb=" O PRO A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 3.681A pdb=" N CYS A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1361 removed outlier: 3.626A pdb=" N ILE A1357 " --> pdb=" O SER A1353 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1361 " --> pdb=" O ILE A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1378 Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.611A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 4.076A pdb=" N LEU B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 442 removed outlier: 4.068A pdb=" N TYR B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.543A pdb=" N CYS B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.845A pdb=" N LEU B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 4.106A pdb=" N LEU B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 547 removed outlier: 4.355A pdb=" N ILE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.932A pdb=" N ALA B 566 " --> pdb=" O ARG B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 599 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 622 through 642 Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.572A pdb=" N PHE B 666 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 removed outlier: 3.511A pdb=" N SER B 680 " --> pdb=" O SER B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 4.822A pdb=" N ASP B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 703 " --> pdb=" O GLN B 699 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 752 through 765 removed outlier: 5.426A pdb=" N PHE B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.710A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 809 removed outlier: 4.510A pdb=" N GLU B 809 " --> pdb=" O SER B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 827 Processing helix chain 'B' and resid 837 through 845 removed outlier: 3.755A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 859 removed outlier: 3.830A pdb=" N ILE B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 883 removed outlier: 3.791A pdb=" N VAL B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.274A pdb=" N ASP B 887 " --> pdb=" O ILE B 884 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 889 " --> pdb=" O SER B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 917 removed outlier: 3.507A pdb=" N ILE B 905 " --> pdb=" O SER B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1338 Processing helix chain 'B' and resid 1342 through 1360 removed outlier: 3.622A pdb=" N SER B1360 " --> pdb=" O ILE B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1377 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 418 through 435 Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 459 through 471 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.606A pdb=" N LEU C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 547 removed outlier: 3.710A pdb=" N SER C 537 " --> pdb=" O GLN C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 587 through 599 Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 622 through 642 Processing helix chain 'C' and resid 643 through 647 Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.550A pdb=" N PHE C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS C 671 " --> pdb=" O MET C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 708 removed outlier: 5.100A pdb=" N ASP C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 703 " --> pdb=" O GLN C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.776A pdb=" N GLU C 757 " --> pdb=" O PHE C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 793 Processing helix chain 'C' and resid 802 through 807 Processing helix chain 'C' and resid 813 through 828 Processing helix chain 'C' and resid 837 through 845 removed outlier: 3.936A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 859 Processing helix chain 'C' and resid 877 through 882 removed outlier: 3.571A pdb=" N ASN C 882 " --> pdb=" O SER C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 889 removed outlier: 4.240A pdb=" N ASP C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 889 " --> pdb=" O SER C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 918 removed outlier: 4.015A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1338 removed outlier: 3.571A pdb=" N ILE C1327 " --> pdb=" O THR C1323 " (cutoff:3.500A) Processing helix chain 'C' and resid 1342 through 1360 removed outlier: 3.632A pdb=" N ILE C1356 " --> pdb=" O SER C1352 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C1360 " --> pdb=" O ILE C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1377 Processing helix chain 'D' and resid 418 through 430 removed outlier: 3.703A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.929A pdb=" N TYR D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.638A pdb=" N ALA D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 506 removed outlier: 3.719A pdb=" N ARG D 498 " --> pdb=" O GLY D 494 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 520 through 523 Processing helix chain 'D' and resid 532 through 546 removed outlier: 4.332A pdb=" N SER D 537 " --> pdb=" O GLN D 533 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 587 through 599 Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 622 through 642 Processing helix chain 'D' and resid 643 through 646 removed outlier: 4.086A pdb=" N TYR D 646 " --> pdb=" O PRO D 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 643 through 646' Processing helix chain 'D' and resid 662 through 673 removed outlier: 4.373A pdb=" N LEU D 668 " --> pdb=" O SER D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 5.133A pdb=" N ASP D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLN D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 703 " --> pdb=" O GLN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 728 Processing helix chain 'D' and resid 753 through 758 Processing helix chain 'D' and resid 763 through 767 removed outlier: 3.955A pdb=" N GLN D 766 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 767 " --> pdb=" O GLU D 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 763 through 767' Processing helix chain 'D' and resid 781 through 793 Processing helix chain 'D' and resid 802 through 806 Processing helix chain 'D' and resid 813 through 828 Processing helix chain 'D' and resid 837 through 845 removed outlier: 3.709A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 858 Processing helix chain 'D' and resid 876 through 883 Processing helix chain 'D' and resid 884 through 889 removed outlier: 4.104A pdb=" N ASP D 887 " --> pdb=" O ILE D 884 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA D 889 " --> pdb=" O SER D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 917 removed outlier: 3.501A pdb=" N ILE D 905 " --> pdb=" O SER D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 1323 through 1338 Processing helix chain 'D' and resid 1342 through 1360 removed outlier: 3.721A pdb=" N SER D1360 " --> pdb=" O ILE D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1367 through 1377 Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.586A pdb=" N ASP E 414 " --> pdb=" O ASN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.653A pdb=" N LEU E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 470 Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 519 through 524 removed outlier: 3.951A pdb=" N LEU E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 547 removed outlier: 3.716A pdb=" N ASP E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 removed outlier: 3.891A pdb=" N ALA E 566 " --> pdb=" O ARG E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 589 through 597 removed outlier: 3.621A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 616 removed outlier: 3.602A pdb=" N ILE E 611 " --> pdb=" O SER E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 642 removed outlier: 4.066A pdb=" N ARG E 627 " --> pdb=" O GLY E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 646 removed outlier: 4.055A pdb=" N TYR E 646 " --> pdb=" O PRO E 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 643 through 646' Processing helix chain 'E' and resid 662 through 671 removed outlier: 3.887A pdb=" N PHE E 666 " --> pdb=" O LYS E 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 712 removed outlier: 5.699A pdb=" N ASP E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLN E 699 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN E 701 " --> pdb=" O ALA E 697 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN E 702 " --> pdb=" O ASP E 698 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 703 " --> pdb=" O GLN E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 765 Processing helix chain 'E' and resid 781 through 793 Processing helix chain 'E' and resid 802 through 807 Processing helix chain 'E' and resid 813 through 828 Processing helix chain 'E' and resid 837 through 845 removed outlier: 4.423A pdb=" N ASN E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 845 " --> pdb=" O TRP E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 859 Processing helix chain 'E' and resid 877 through 882 Processing helix chain 'E' and resid 883 through 889 removed outlier: 4.199A pdb=" N ASP E 887 " --> pdb=" O ILE E 884 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA E 889 " --> pdb=" O SER E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 917 removed outlier: 4.168A pdb=" N ASN E 911 " --> pdb=" O ARG E 907 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 912 " --> pdb=" O TYR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 1323 through 1338 removed outlier: 3.689A pdb=" N ILE E1327 " --> pdb=" O THR E1323 " (cutoff:3.500A) Processing helix chain 'E' and resid 1342 through 1360 removed outlier: 3.902A pdb=" N SER E1360 " --> pdb=" O ILE E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1368 through 1377 Processing helix chain 'F' and resid 411 through 415 removed outlier: 3.813A pdb=" N ILE F 415 " --> pdb=" O PHE F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 429 removed outlier: 3.749A pdb=" N LYS F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 428 " --> pdb=" O GLN F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.851A pdb=" N LEU F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 440 removed outlier: 3.873A pdb=" N TYR F 439 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 469 Processing helix chain 'F' and resid 492 through 510 removed outlier: 4.500A pdb=" N ALA F 496 " --> pdb=" O TRP F 492 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 524 Processing helix chain 'F' and resid 539 through 547 Processing helix chain 'F' and resid 563 through 567 removed outlier: 4.069A pdb=" N VAL F 567 " --> pdb=" O PRO F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 599 removed outlier: 3.577A pdb=" N THR F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 616 Processing helix chain 'F' and resid 624 through 642 removed outlier: 3.531A pdb=" N SER F 628 " --> pdb=" O ALA F 624 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 648 removed outlier: 3.703A pdb=" N ARG F 647 " --> pdb=" O PRO F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 668 removed outlier: 3.801A pdb=" N PHE F 666 " --> pdb=" O LYS F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 711 removed outlier: 5.289A pdb=" N ASP F 698 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN F 699 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU F 703 " --> pdb=" O GLN F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 753 through 765 removed outlier: 3.663A pdb=" N GLU F 757 " --> pdb=" O PHE F 753 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 761 " --> pdb=" O GLU F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 793 removed outlier: 3.740A pdb=" N ALA F 787 " --> pdb=" O GLN F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 807 Processing helix chain 'F' and resid 813 through 828 Processing helix chain 'F' and resid 837 through 845 removed outlier: 3.839A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 859 Processing helix chain 'F' and resid 877 through 882 removed outlier: 3.760A pdb=" N ASN F 882 " --> pdb=" O SER F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 885 through 889 removed outlier: 3.766A pdb=" N ALA F 889 " --> pdb=" O SER F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 917 removed outlier: 3.516A pdb=" N TYR F 908 " --> pdb=" O ASN F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 1323 through 1338 removed outlier: 3.507A pdb=" N ILE F1327 " --> pdb=" O THR F1323 " (cutoff:3.500A) Processing helix chain 'F' and resid 1342 through 1360 removed outlier: 3.620A pdb=" N SER F1360 " --> pdb=" O ILE F1356 " (cutoff:3.500A) Processing helix chain 'F' and resid 1366 through 1377 Processing helix chain 'G' and resid 955 through 993 removed outlier: 4.315A pdb=" N GLY G 985 " --> pdb=" O ILE G 981 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU G 989 " --> pdb=" O GLY G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 995 through 999 removed outlier: 3.867A pdb=" N LYS G 999 " --> pdb=" O ARG G 996 " (cutoff:3.500A) Processing helix chain 'G' and resid 1003 through 1009 removed outlier: 4.075A pdb=" N LEU G1007 " --> pdb=" O ASP G1003 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS G1009 " --> pdb=" O ALA G1005 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1056 removed outlier: 3.648A pdb=" N ASN G1055 " --> pdb=" O GLU G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1060 through 1078 removed outlier: 4.005A pdb=" N PHE G1064 " --> pdb=" O GLU G1060 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE G1078 " --> pdb=" O ASP G1074 " (cutoff:3.500A) Processing helix chain 'G' and resid 1080 through 1102 Processing helix chain 'G' and resid 1103 through 1131 Processing helix chain 'H' and resid 955 through 993 removed outlier: 3.991A pdb=" N GLY H 985 " --> pdb=" O ILE H 981 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU H 986 " --> pdb=" O LYS H 982 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU H 989 " --> pdb=" O GLY H 985 " (cutoff:3.500A) Processing helix chain 'H' and resid 995 through 999 removed outlier: 3.755A pdb=" N LYS H 999 " --> pdb=" O ARG H 996 " (cutoff:3.500A) Processing helix chain 'H' and resid 1003 through 1009 removed outlier: 4.160A pdb=" N LEU H1007 " --> pdb=" O ASP H1003 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS H1009 " --> pdb=" O ALA H1005 " (cutoff:3.500A) Processing helix chain 'H' and resid 1047 through 1056 removed outlier: 3.673A pdb=" N ASN H1055 " --> pdb=" O GLU H1051 " (cutoff:3.500A) Processing helix chain 'H' and resid 1060 through 1078 removed outlier: 4.281A pdb=" N PHE H1064 " --> pdb=" O GLU H1060 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H1078 " --> pdb=" O ASP H1074 " (cutoff:3.500A) Processing helix chain 'H' and resid 1080 through 1102 Processing helix chain 'H' and resid 1103 through 1131 Processing helix chain 'I' and resid 955 through 993 removed outlier: 4.183A pdb=" N GLY I 985 " --> pdb=" O ILE I 981 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU I 986 " --> pdb=" O LYS I 982 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU I 989 " --> pdb=" O GLY I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 995 through 999 removed outlier: 3.831A pdb=" N LYS I 999 " --> pdb=" O ARG I 996 " (cutoff:3.500A) Processing helix chain 'I' and resid 1003 through 1009 removed outlier: 4.174A pdb=" N LEU I1007 " --> pdb=" O ASP I1003 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS I1009 " --> pdb=" O ALA I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1047 through 1056 Processing helix chain 'I' and resid 1060 through 1078 removed outlier: 4.328A pdb=" N PHE I1064 " --> pdb=" O GLU I1060 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE I1078 " --> pdb=" O ASP I1074 " (cutoff:3.500A) Processing helix chain 'I' and resid 1080 through 1102 Processing helix chain 'I' and resid 1103 through 1131 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 485 removed outlier: 6.841A pdb=" N THR A 480 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 517 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 482 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 519 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG A 484 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER A 514 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 559 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 516 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA A 561 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 518 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 451 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR A 562 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 453 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 798 through 801 removed outlier: 3.523A pdb=" N LEU A 872 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 773 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA A 873 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 775 " --> pdb=" O ALA A 873 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.611A pdb=" N SER B 513 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE B 558 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE B 515 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA B 560 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B 517 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 731 through 732 removed outlier: 4.281A pdb=" N LYS C 927 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 797 through 800 removed outlier: 6.239A pdb=" N ASN B 797 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 834 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN B 799 " --> pdb=" O PHE B 834 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 772 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA B 872 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 774 " --> pdb=" O ALA B 872 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE B 895 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 773 " --> pdb=" O PHE B 895 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 479 through 483 removed outlier: 6.452A pdb=" N THR C 479 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE C 516 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 481 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 518 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG C 483 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE C 558 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 515 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA C 560 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE C 517 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 731 through 732 removed outlier: 4.333A pdb=" N LYS D 927 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 797 through 800 removed outlier: 6.534A pdb=" N ASN C 797 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE C 834 " --> pdb=" O ASN C 797 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN C 799 " --> pdb=" O PHE C 834 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 831 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU C 869 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 833 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU C 871 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 835 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU C 873 " --> pdb=" O ILE C 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 481 through 483 removed outlier: 6.300A pdb=" N PHE D 481 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 518 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG D 483 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 797 through 800 removed outlier: 6.056A pdb=" N ASN D 797 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE D 834 " --> pdb=" O ASN D 797 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN D 799 " --> pdb=" O PHE D 834 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE D 895 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 773 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 515 through 517 Processing sheet with id=AB3, first strand: chain 'E' and resid 797 through 800 removed outlier: 6.515A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN E 799 " --> pdb=" O PHE E 834 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 479 through 483 removed outlier: 6.850A pdb=" N SER F 513 " --> pdb=" O ILE F 556 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE F 558 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 515 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 560 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE F 517 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 450 " --> pdb=" O GLY F 559 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N THR F 561 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE F 452 " --> pdb=" O THR F 561 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 797 through 800 removed outlier: 6.398A pdb=" N LEU F 772 " --> pdb=" O CYS F 870 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA F 872 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 774 " --> pdb=" O ALA F 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1025 through 1027 removed outlier: 4.716A pdb=" N ILE G1032 " --> pdb=" O PHE G1041 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE G1041 " --> pdb=" O ILE G1032 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 1025 through 1027 removed outlier: 4.771A pdb=" N ILE H1032 " --> pdb=" O PHE H1041 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE H1041 " --> pdb=" O ILE H1032 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 1025 through 1027 1476 hydrogen bonds defined for protein. 4281 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: 6.52 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5404 1.30 - 1.43: 8013 1.43 - 1.56: 19411 1.56 - 1.69: 17 1.69 - 1.82: 205 Bond restraints: 33050 Sorted by residual: bond pdb=" C SER F 831 " pdb=" O SER F 831 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.22e-02 6.72e+03 2.28e+01 bond pdb=" C LYS D 491 " pdb=" O LYS D 491 " ideal model delta sigma weight residual 1.235 1.287 -0.051 1.26e-02 6.30e+03 1.66e+01 bond pdb=" N ARG C 627 " pdb=" CA ARG C 627 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CA SER F 831 " pdb=" CB SER F 831 " ideal model delta sigma weight residual 1.534 1.475 0.059 1.76e-02 3.23e+03 1.12e+01 bond pdb=" CA SER F 831 " pdb=" C SER F 831 " ideal model delta sigma weight residual 1.521 1.485 0.036 1.23e-02 6.61e+03 8.52e+00 ... (remaining 33045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 44137 3.13 - 6.25: 417 6.25 - 9.38: 46 9.38 - 12.51: 9 12.51 - 15.64: 2 Bond angle restraints: 44611 Sorted by residual: angle pdb=" N THR I1077 " pdb=" CA THR I1077 " pdb=" C THR I1077 " ideal model delta sigma weight residual 111.28 120.46 -9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" N SER C 528 " pdb=" CA SER C 528 " pdb=" C SER C 528 " ideal model delta sigma weight residual 108.23 118.12 -9.89 1.72e+00 3.38e-01 3.30e+01 angle pdb=" N GLU H1119 " pdb=" CA GLU H1119 " pdb=" C GLU H1119 " ideal model delta sigma weight residual 112.38 106.07 6.31 1.22e+00 6.72e-01 2.67e+01 angle pdb=" N LYS C 508 " pdb=" CA LYS C 508 " pdb=" C LYS C 508 " ideal model delta sigma weight residual 113.12 107.20 5.92 1.25e+00 6.40e-01 2.24e+01 angle pdb=" CA LYS D 593 " pdb=" CB LYS D 593 " pdb=" CG LYS D 593 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 ... (remaining 44606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.24: 18925 27.24 - 54.47: 1351 54.47 - 81.71: 107 81.71 - 108.95: 20 108.95 - 136.18: 2 Dihedral angle restraints: 20405 sinusoidal: 8617 harmonic: 11788 Sorted by residual: dihedral pdb=" C5' ADP E1401 " pdb=" O5' ADP E1401 " pdb=" PA ADP E1401 " pdb=" O2A ADP E1401 " ideal model delta sinusoidal sigma weight residual 300.00 163.82 136.18 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 70.67 -130.67 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" CA ASN G 346 " pdb=" C ASN G 346 " pdb=" N PHE G 347 " pdb=" CA PHE G 347 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 20402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4450 0.068 - 0.137: 547 0.137 - 0.205: 15 0.205 - 0.274: 2 0.274 - 0.342: 4 Chirality restraints: 5018 Sorted by residual: chirality pdb=" CA THR F 716 " pdb=" N THR F 716 " pdb=" C THR F 716 " pdb=" CB THR F 716 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU H1125 " pdb=" CB LEU H1125 " pdb=" CD1 LEU H1125 " pdb=" CD2 LEU H1125 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR I1077 " pdb=" N THR I1077 " pdb=" C THR I1077 " pdb=" CB THR I1077 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 5015 not shown) Planarity restraints: 5713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 924 " 0.106 5.00e-02 4.00e+02 1.58e-01 4.00e+01 pdb=" N PRO A 925 " -0.274 5.00e-02 4.00e+02 pdb=" CA PRO A 925 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 925 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 655 " 0.090 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO B 656 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO B 656 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 656 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 923 " -0.089 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO C 924 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO C 924 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 924 " -0.068 5.00e-02 4.00e+02 ... (remaining 5710 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3864 2.75 - 3.29: 33512 3.29 - 3.82: 54242 3.82 - 4.36: 63304 4.36 - 4.90: 105895 Nonbonded interactions: 260817 Sorted by model distance: nonbonded pdb=" OG SER I1059 " pdb=" OD2 ASP I1117 " model vdw 2.210 3.040 nonbonded pdb=" N GLU A 848 " pdb=" OE1 GLU A 848 " model vdw 2.212 3.120 nonbonded pdb=" O ARG C 828 " pdb=" OG SER C 831 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A1361 " pdb=" OG1 THR A1370 " model vdw 2.227 3.040 nonbonded pdb=" O PHE I 990 " pdb=" NH2 ARG I 998 " model vdw 2.233 3.120 ... (remaining 260812 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' and (resid 410 through 487 or resid 496 through 526 or resid 539 thro \ ugh 733 or resid 752 through 1379)) selection = (chain 'B' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'C' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'D' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 1378)) selection = (chain 'E' and (resid 409 through 732 or resid 751 through 1378)) selection = (chain 'F' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.070 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.069 33050 Z= 0.188 Angle : 0.777 15.636 44611 Z= 0.417 Chirality : 0.045 0.342 5018 Planarity : 0.006 0.158 5713 Dihedral : 17.303 136.184 12707 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 0.86 % Allowed : 22.87 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 3965 helix: 0.06 (0.12), residues: 1952 sheet: -1.03 (0.27), residues: 368 loop : -1.69 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 627 TYR 0.041 0.001 TYR B 784 PHE 0.037 0.001 PHE I1042 TRP 0.013 0.001 TRP C 841 HIS 0.004 0.001 HIS E 453 Details of bonding type rmsd covalent geometry : bond 0.00383 (33050) covalent geometry : angle 0.77671 (44611) hydrogen bonds : bond 0.16547 ( 1476) hydrogen bonds : angle 6.28746 ( 4281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 651 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7059 (mp0) cc_final: 0.6758 (mt-10) REVERT: B 881 LYS cc_start: 0.7720 (tppt) cc_final: 0.7341 (mmmm) REVERT: C 435 TYR cc_start: 0.8109 (m-80) cc_final: 0.7806 (m-80) REVERT: D 421 TYR cc_start: 0.7789 (m-80) cc_final: 0.7465 (m-80) REVERT: D 632 GLU cc_start: 0.7206 (tp30) cc_final: 0.6982 (tp30) REVERT: E 764 GLU cc_start: 0.6903 (pp20) cc_final: 0.6589 (pp20) REVERT: E 856 LEU cc_start: 0.8356 (tp) cc_final: 0.8052 (tp) REVERT: E 886 SER cc_start: 0.7899 (m) cc_final: 0.7689 (m) REVERT: F 427 GLU cc_start: 0.7705 (tt0) cc_final: 0.7317 (tm-30) REVERT: F 572 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6987 (mpp-170) REVERT: G 1033 LEU cc_start: 0.7054 (tp) cc_final: 0.6391 (pp) outliers start: 31 outliers final: 13 residues processed: 666 average time/residue: 0.2471 time to fit residues: 247.2691 Evaluate side-chains 659 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 646 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 511 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain H residue 1111 LYS Chi-restraints excluded: chain H residue 1114 ARG Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 1026 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN C 531 GLN C 562 ASN C 699 GLN D 453 HIS D 639 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 727 ASN E 799 GLN F 712 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128722 restraints weight = 50050.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132420 restraints weight = 25407.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134755 restraints weight = 15888.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136410 restraints weight = 11700.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136942 restraints weight = 9424.414| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33050 Z= 0.204 Angle : 0.682 11.815 44611 Z= 0.339 Chirality : 0.044 0.227 5018 Planarity : 0.006 0.112 5713 Dihedral : 6.969 136.862 4397 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 2.34 % Allowed : 20.25 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3965 helix: 0.27 (0.12), residues: 1989 sheet: -1.10 (0.28), residues: 357 loop : -1.64 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 573 TYR 0.025 0.002 TYR B 784 PHE 0.019 0.001 PHE I1042 TRP 0.017 0.001 TRP D 841 HIS 0.005 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00467 (33050) covalent geometry : angle 0.68223 (44611) hydrogen bonds : bond 0.05138 ( 1476) hydrogen bonds : angle 4.80974 ( 4281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 672 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.8224 (tpp) cc_final: 0.7972 (tpt) REVERT: A 581 GLU cc_start: 0.7007 (mp0) cc_final: 0.6695 (mp0) REVERT: A 643 PHE cc_start: 0.7799 (m-80) cc_final: 0.7520 (m-80) REVERT: A 804 LEU cc_start: 0.7859 (mm) cc_final: 0.7590 (mp) REVERT: A 908 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7396 (ttp80) REVERT: B 439 TYR cc_start: 0.7738 (m-80) cc_final: 0.7455 (m-10) REVERT: B 498 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7597 (ttp80) REVERT: B 547 ASP cc_start: 0.6610 (t0) cc_final: 0.6293 (t0) REVERT: B 667 MET cc_start: 0.7469 (mmm) cc_final: 0.7161 (mmm) REVERT: C 410 VAL cc_start: 0.8078 (m) cc_final: 0.7857 (p) REVERT: C 499 GLN cc_start: 0.8168 (tp40) cc_final: 0.7909 (tp40) REVERT: C 665 ASP cc_start: 0.7667 (m-30) cc_final: 0.7389 (m-30) REVERT: C 725 LEU cc_start: 0.8142 (tt) cc_final: 0.7884 (tp) REVERT: C 881 LYS cc_start: 0.7518 (ptpp) cc_final: 0.7187 (ptpp) REVERT: C 925 MET cc_start: 0.5574 (tmm) cc_final: 0.5162 (tmm) REVERT: C 1365 ASP cc_start: 0.6425 (t0) cc_final: 0.6177 (t0) REVERT: D 589 LYS cc_start: 0.8445 (mmmm) cc_final: 0.7900 (mmmm) REVERT: D 593 LYS cc_start: 0.8343 (mmmt) cc_final: 0.8052 (mmtp) REVERT: D 632 GLU cc_start: 0.7229 (tp30) cc_final: 0.6958 (tp30) REVERT: D 667 MET cc_start: 0.7463 (mpp) cc_final: 0.7176 (mpp) REVERT: D 698 ASP cc_start: 0.7654 (p0) cc_final: 0.7412 (p0) REVERT: D 760 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7098 (tm-30) REVERT: D 792 TYR cc_start: 0.7438 (t80) cc_final: 0.7021 (t80) REVERT: D 903 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5989 (tm-30) REVERT: D 914 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6319 (tm-30) REVERT: D 1328 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7613 (ttmm) REVERT: D 1329 LYS cc_start: 0.8142 (tppt) cc_final: 0.7807 (tppt) REVERT: E 708 ASP cc_start: 0.6886 (m-30) cc_final: 0.6371 (m-30) REVERT: E 764 GLU cc_start: 0.6776 (pp20) cc_final: 0.6424 (pp20) REVERT: E 863 ASN cc_start: 0.7800 (p0) cc_final: 0.7100 (p0) REVERT: F 427 GLU cc_start: 0.7745 (tt0) cc_final: 0.7369 (tm-30) REVERT: F 429 VAL cc_start: 0.7954 (t) cc_final: 0.7684 (t) REVERT: F 463 MET cc_start: 0.6616 (tpp) cc_final: 0.6332 (tpp) REVERT: F 519 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5091 (tm-30) REVERT: F 792 TYR cc_start: 0.7838 (t80) cc_final: 0.7445 (t80) REVERT: F 824 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: F 840 ILE cc_start: 0.8267 (mt) cc_final: 0.7977 (mm) REVERT: F 863 ASN cc_start: 0.6876 (p0) cc_final: 0.6665 (p0) REVERT: G 1033 LEU cc_start: 0.6742 (tp) cc_final: 0.6228 (pp) REVERT: H 1116 ARG cc_start: -0.3945 (OUTLIER) cc_final: -0.4726 (tmm-80) outliers start: 85 outliers final: 44 residues processed: 716 average time/residue: 0.2422 time to fit residues: 263.5412 Evaluate side-chains 705 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 658 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 824 GLU Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 987 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 59 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 51 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 531 GLN C 562 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.172348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128652 restraints weight = 50124.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132121 restraints weight = 26397.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133787 restraints weight = 17122.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135881 restraints weight = 13142.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136648 restraints weight = 10491.281| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33050 Z= 0.144 Angle : 0.638 9.867 44611 Z= 0.315 Chirality : 0.043 0.301 5018 Planarity : 0.005 0.084 5713 Dihedral : 6.597 139.078 4373 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.90 % Rotamer: Outliers : 2.43 % Allowed : 21.32 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3965 helix: 0.43 (0.12), residues: 1991 sheet: -1.01 (0.28), residues: 366 loop : -1.54 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 812 TYR 0.020 0.001 TYR B 784 PHE 0.020 0.001 PHE D 480 TRP 0.012 0.001 TRP D 841 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00325 (33050) covalent geometry : angle 0.63763 (44611) hydrogen bonds : bond 0.04442 ( 1476) hydrogen bonds : angle 4.54510 ( 4281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 689 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLN cc_start: 0.6597 (tm130) cc_final: 0.6351 (tm-30) REVERT: A 510 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7806 (mtmm) REVERT: A 581 GLU cc_start: 0.7027 (mp0) cc_final: 0.6679 (mp0) REVERT: A 643 PHE cc_start: 0.7771 (m-80) cc_final: 0.7442 (m-80) REVERT: B 439 TYR cc_start: 0.7686 (m-80) cc_final: 0.7412 (m-10) REVERT: B 498 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7526 (ttp80) REVERT: B 547 ASP cc_start: 0.6563 (t0) cc_final: 0.6184 (t0) REVERT: B 881 LYS cc_start: 0.7664 (tppt) cc_final: 0.7449 (tppt) REVERT: C 410 VAL cc_start: 0.8006 (m) cc_final: 0.7722 (p) REVERT: C 499 GLN cc_start: 0.8146 (tp40) cc_final: 0.7882 (tp40) REVERT: C 505 GLU cc_start: 0.6422 (tp30) cc_final: 0.6181 (tp30) REVERT: C 582 TYR cc_start: 0.8123 (t80) cc_final: 0.7389 (t80) REVERT: C 613 LYS cc_start: 0.7873 (tppt) cc_final: 0.7553 (tppt) REVERT: C 621 TYR cc_start: 0.8519 (m-80) cc_final: 0.8218 (m-10) REVERT: C 665 ASP cc_start: 0.7668 (m-30) cc_final: 0.7396 (m-30) REVERT: C 828 ARG cc_start: 0.6462 (mmm160) cc_final: 0.6045 (mmm-85) REVERT: C 881 LYS cc_start: 0.7519 (ptpp) cc_final: 0.7300 (ptpp) REVERT: C 925 MET cc_start: 0.5590 (tmm) cc_final: 0.5266 (tmm) REVERT: D 480 PHE cc_start: 0.7757 (t80) cc_final: 0.7478 (t80) REVERT: D 589 LYS cc_start: 0.8394 (mmmm) cc_final: 0.7716 (mmmm) REVERT: D 593 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8060 (mmtp) REVERT: D 594 ILE cc_start: 0.8331 (mt) cc_final: 0.8114 (tt) REVERT: D 616 PHE cc_start: 0.6800 (t80) cc_final: 0.6598 (t80) REVERT: D 635 LEU cc_start: 0.8468 (mt) cc_final: 0.8168 (mm) REVERT: D 638 ILE cc_start: 0.8465 (mt) cc_final: 0.8238 (mt) REVERT: D 686 GLN cc_start: 0.7611 (pm20) cc_final: 0.6813 (pp30) REVERT: D 698 ASP cc_start: 0.7648 (p0) cc_final: 0.7243 (p0) REVERT: D 760 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7103 (tm-30) REVERT: D 792 TYR cc_start: 0.7567 (t80) cc_final: 0.7203 (t80) REVERT: D 914 GLU cc_start: 0.6533 (tm-30) cc_final: 0.6233 (tm-30) REVERT: D 1328 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7561 (ttmm) REVERT: D 1329 LYS cc_start: 0.8105 (tppt) cc_final: 0.7730 (tppt) REVERT: E 764 GLU cc_start: 0.6724 (pp20) cc_final: 0.6344 (pp20) REVERT: E 824 GLU cc_start: 0.6401 (tp30) cc_final: 0.6084 (tp30) REVERT: E 856 LEU cc_start: 0.8319 (tp) cc_final: 0.8037 (tp) REVERT: E 863 ASN cc_start: 0.7561 (p0) cc_final: 0.6792 (p0) REVERT: E 933 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6664 (pp) REVERT: F 424 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7933 (tm-30) REVERT: F 427 GLU cc_start: 0.7672 (tt0) cc_final: 0.7457 (tm-30) REVERT: F 463 MET cc_start: 0.6497 (tpp) cc_final: 0.6162 (tpp) REVERT: F 614 LEU cc_start: 0.8734 (mm) cc_final: 0.8506 (mt) REVERT: F 667 MET cc_start: 0.6794 (tpp) cc_final: 0.6491 (tpp) REVERT: F 824 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: F 840 ILE cc_start: 0.8242 (mt) cc_final: 0.7973 (mm) REVERT: F 863 ASN cc_start: 0.6889 (p0) cc_final: 0.6659 (p0) REVERT: F 922 ASP cc_start: 0.7782 (m-30) cc_final: 0.7508 (m-30) REVERT: G 1033 LEU cc_start: 0.6696 (tp) cc_final: 0.6209 (pp) REVERT: G 1125 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8292 (pp) REVERT: H 1116 ARG cc_start: -0.3552 (OUTLIER) cc_final: -0.4495 (tmm-80) outliers start: 88 outliers final: 62 residues processed: 739 average time/residue: 0.2486 time to fit residues: 277.5060 Evaluate side-chains 729 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 663 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 914 GLU Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 1328 LYS Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 824 GLU Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 220 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN C 510 HIS C 562 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 ASN E 896 GLN F 712 ASN F 904 ASN F1339 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130664 restraints weight = 49891.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133925 restraints weight = 28353.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134563 restraints weight = 18559.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135354 restraints weight = 16293.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135907 restraints weight = 14496.215| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33050 Z= 0.157 Angle : 0.628 10.758 44611 Z= 0.310 Chirality : 0.043 0.251 5018 Planarity : 0.005 0.073 5713 Dihedral : 6.511 139.887 4372 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 3.34 % Allowed : 21.49 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3965 helix: 0.49 (0.12), residues: 1995 sheet: -0.96 (0.28), residues: 364 loop : -1.52 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 828 TYR 0.018 0.001 TYR A 732 PHE 0.013 0.001 PHE D 480 TRP 0.011 0.001 TRP D 841 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00358 (33050) covalent geometry : angle 0.62784 (44611) hydrogen bonds : bond 0.04274 ( 1476) hydrogen bonds : angle 4.40125 ( 4281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 680 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.6113 (t0) REVERT: A 581 GLU cc_start: 0.7023 (mp0) cc_final: 0.6687 (mp0) REVERT: A 643 PHE cc_start: 0.7831 (m-80) cc_final: 0.7526 (m-80) REVERT: A 888 ASP cc_start: 0.6814 (t0) cc_final: 0.6435 (t0) REVERT: B 439 TYR cc_start: 0.7692 (m-80) cc_final: 0.7452 (m-10) REVERT: B 483 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.7120 (mmm-85) REVERT: B 498 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7532 (ttp80) REVERT: B 547 ASP cc_start: 0.6702 (t0) cc_final: 0.6115 (t0) REVERT: B 601 LYS cc_start: 0.7835 (tmtt) cc_final: 0.7594 (tmtt) REVERT: B 667 MET cc_start: 0.7520 (mmm) cc_final: 0.7154 (mmm) REVERT: B 881 LYS cc_start: 0.7604 (tppt) cc_final: 0.7304 (tppt) REVERT: B 1328 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7587 (ttpp) REVERT: C 410 VAL cc_start: 0.7964 (m) cc_final: 0.7621 (p) REVERT: C 489 LEU cc_start: 0.7460 (pp) cc_final: 0.7172 (pp) REVERT: C 499 GLN cc_start: 0.8156 (tp40) cc_final: 0.7852 (tp40) REVERT: C 582 TYR cc_start: 0.8123 (t80) cc_final: 0.7372 (t80) REVERT: C 613 LYS cc_start: 0.7852 (tppt) cc_final: 0.7502 (tppt) REVERT: C 621 TYR cc_start: 0.8494 (m-80) cc_final: 0.8187 (m-10) REVERT: C 665 ASP cc_start: 0.7680 (m-30) cc_final: 0.7399 (m-30) REVERT: C 725 LEU cc_start: 0.8246 (tp) cc_final: 0.7999 (tt) REVERT: C 828 ARG cc_start: 0.6399 (mmm160) cc_final: 0.6033 (mmm-85) REVERT: C 879 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6440 (tm-30) REVERT: C 925 MET cc_start: 0.5667 (tmm) cc_final: 0.5310 (tmm) REVERT: D 593 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7873 (mmmt) REVERT: D 594 ILE cc_start: 0.8351 (mt) cc_final: 0.8135 (tt) REVERT: D 613 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7332 (ttmt) REVERT: D 616 PHE cc_start: 0.6844 (t80) cc_final: 0.6599 (t80) REVERT: D 635 LEU cc_start: 0.8474 (mt) cc_final: 0.8225 (mm) REVERT: D 643 PRO cc_start: 0.8347 (Cg_endo) cc_final: 0.7915 (Cg_exo) REVERT: D 647 ARG cc_start: 0.7411 (mmp-170) cc_final: 0.7100 (mmp-170) REVERT: D 698 ASP cc_start: 0.7649 (p0) cc_final: 0.7292 (p0) REVERT: D 760 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7055 (tm-30) REVERT: D 792 TYR cc_start: 0.7631 (t80) cc_final: 0.7195 (t80) REVERT: D 914 GLU cc_start: 0.6535 (tm-30) cc_final: 0.6137 (tm-30) REVERT: D 1328 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7541 (ttmm) REVERT: D 1329 LYS cc_start: 0.8142 (tppt) cc_final: 0.7684 (tppt) REVERT: E 508 LYS cc_start: 0.8474 (mtpt) cc_final: 0.7611 (mtmm) REVERT: E 764 GLU cc_start: 0.6704 (pp20) cc_final: 0.6332 (pp20) REVERT: E 812 ARG cc_start: 0.6120 (ttp-110) cc_final: 0.5915 (mtp-110) REVERT: E 824 GLU cc_start: 0.6446 (tp30) cc_final: 0.6216 (tp30) REVERT: E 856 LEU cc_start: 0.8306 (tp) cc_final: 0.8020 (tp) REVERT: E 863 ASN cc_start: 0.7585 (p0) cc_final: 0.6783 (p0) REVERT: E 871 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8281 (mp) REVERT: E 892 LYS cc_start: 0.6599 (tppt) cc_final: 0.6238 (tppt) REVERT: E 933 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6691 (pp) REVERT: E 1377 LEU cc_start: 0.8306 (mp) cc_final: 0.8065 (mt) REVERT: F 426 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7762 (ttpt) REVERT: F 427 GLU cc_start: 0.7660 (tt0) cc_final: 0.7356 (tm-30) REVERT: F 428 MET cc_start: 0.6559 (tpt) cc_final: 0.5970 (tpt) REVERT: F 463 MET cc_start: 0.6731 (tpp) cc_final: 0.6292 (tpp) REVERT: F 519 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.4625 (tm-30) REVERT: F 546 MET cc_start: 0.7528 (mtt) cc_final: 0.7194 (mtt) REVERT: F 549 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.5101 (mpp) REVERT: F 667 MET cc_start: 0.7018 (tpp) cc_final: 0.6542 (tpp) REVERT: F 815 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5918 (mp0) REVERT: F 824 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: F 840 ILE cc_start: 0.8264 (mt) cc_final: 0.7995 (mm) REVERT: F 863 ASN cc_start: 0.6889 (p0) cc_final: 0.6620 (p0) REVERT: F 922 ASP cc_start: 0.7783 (m-30) cc_final: 0.7563 (m-30) REVERT: F 1339 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6683 (tm130) REVERT: G 1062 LYS cc_start: -0.0286 (tptt) cc_final: -0.0549 (tptt) REVERT: G 1125 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8402 (pp) REVERT: H 1116 ARG cc_start: -0.4021 (OUTLIER) cc_final: -0.5114 (tmm-80) outliers start: 121 outliers final: 68 residues processed: 753 average time/residue: 0.2473 time to fit residues: 283.4066 Evaluate side-chains 743 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 666 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1376 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 510 HIS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 824 GLU Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 1339 GLN Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 54 optimal weight: 0.6980 chunk 356 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 287 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 562 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 ASN E 896 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F1326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128470 restraints weight = 49962.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132055 restraints weight = 25942.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134512 restraints weight = 16554.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135697 restraints weight = 12176.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136797 restraints weight = 10232.639| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33050 Z= 0.152 Angle : 0.646 23.772 44611 Z= 0.315 Chirality : 0.043 0.228 5018 Planarity : 0.005 0.072 5713 Dihedral : 6.415 138.767 4369 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.34 % Allowed : 22.34 % Favored : 74.32 % 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: -0.60 (0.14), residues: 3965 helix: 0.59 (0.12), residues: 1993 sheet: -1.00 (0.28), residues: 356 loop : -1.46 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 828 TYR 0.017 0.001 TYR A 732 PHE 0.021 0.001 PHE D 480 TRP 0.012 0.001 TRP A 842 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00349 (33050) covalent geometry : angle 0.64568 (44611) hydrogen bonds : bond 0.04152 ( 1476) hydrogen bonds : angle 4.32645 ( 4281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 670 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7039 (mp0) cc_final: 0.6711 (mp0) REVERT: A 643 PHE cc_start: 0.7838 (m-80) cc_final: 0.7571 (m-80) REVERT: A 883 ASN cc_start: 0.8252 (m-40) cc_final: 0.7656 (t0) REVERT: A 888 ASP cc_start: 0.6739 (t0) cc_final: 0.6164 (t0) REVERT: B 483 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7147 (mmm-85) REVERT: B 495 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6902 (mm-30) REVERT: B 498 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7511 (ttp80) REVERT: B 547 ASP cc_start: 0.6665 (t0) cc_final: 0.6019 (t0) REVERT: B 601 LYS cc_start: 0.7899 (tmtt) cc_final: 0.7574 (tmtt) REVERT: B 667 MET cc_start: 0.7525 (mmm) cc_final: 0.7207 (mmm) REVERT: B 801 LEU cc_start: 0.7955 (mt) cc_final: 0.7658 (mp) REVERT: B 881 LYS cc_start: 0.7614 (tppt) cc_final: 0.7205 (tppt) REVERT: B 1328 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7566 (ttpp) REVERT: C 410 VAL cc_start: 0.7973 (m) cc_final: 0.7563 (p) REVERT: C 428 MET cc_start: 0.7630 (ptm) cc_final: 0.7399 (ttp) REVERT: C 489 LEU cc_start: 0.7509 (pp) cc_final: 0.7208 (pp) REVERT: C 499 GLN cc_start: 0.8144 (tp40) cc_final: 0.7882 (tp40) REVERT: C 582 TYR cc_start: 0.8115 (t80) cc_final: 0.7360 (t80) REVERT: C 665 ASP cc_start: 0.7672 (m-30) cc_final: 0.7407 (m-30) REVERT: C 828 ARG cc_start: 0.6369 (mmm160) cc_final: 0.6005 (mmm-85) REVERT: C 881 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7323 (ptpp) REVERT: C 925 MET cc_start: 0.5669 (tmm) cc_final: 0.5317 (tmm) REVERT: C 1336 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6627 (tm-30) REVERT: D 546 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5160 (ppp) REVERT: D 593 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7801 (mmmt) REVERT: D 594 ILE cc_start: 0.8377 (mt) cc_final: 0.8080 (tt) REVERT: D 613 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7340 (ttmt) REVERT: D 616 PHE cc_start: 0.6793 (t80) cc_final: 0.6563 (t80) REVERT: D 635 LEU cc_start: 0.8456 (mt) cc_final: 0.8188 (mm) REVERT: D 643 PRO cc_start: 0.8326 (Cg_endo) cc_final: 0.7891 (Cg_exo) REVERT: D 686 GLN cc_start: 0.7546 (pm20) cc_final: 0.7162 (pm20) REVERT: D 698 ASP cc_start: 0.7653 (p0) cc_final: 0.7280 (p0) REVERT: D 760 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6841 (tm-30) REVERT: D 792 TYR cc_start: 0.7700 (t80) cc_final: 0.7415 (t80) REVERT: D 847 GLU cc_start: 0.7610 (mp0) cc_final: 0.7392 (mp0) REVERT: D 914 GLU cc_start: 0.6514 (tm-30) cc_final: 0.6206 (tm-30) REVERT: D 1328 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7483 (ttmm) REVERT: D 1329 LYS cc_start: 0.8096 (tppt) cc_final: 0.7712 (tppt) REVERT: E 764 GLU cc_start: 0.6711 (pp20) cc_final: 0.6285 (pp20) REVERT: E 812 ARG cc_start: 0.6000 (ttp-110) cc_final: 0.5787 (mtp-110) REVERT: E 824 GLU cc_start: 0.6446 (tp30) cc_final: 0.6186 (tp30) REVERT: E 856 LEU cc_start: 0.8138 (tp) cc_final: 0.7895 (tp) REVERT: E 863 ASN cc_start: 0.7600 (p0) cc_final: 0.6796 (p0) REVERT: E 871 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8269 (mp) REVERT: E 892 LYS cc_start: 0.6651 (tppt) cc_final: 0.6276 (tppt) REVERT: E 933 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6574 (pp) REVERT: E 1329 LYS cc_start: 0.7950 (pttm) cc_final: 0.7659 (pttm) REVERT: E 1377 LEU cc_start: 0.8257 (mp) cc_final: 0.7991 (mt) REVERT: F 426 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7743 (ttpt) REVERT: F 427 GLU cc_start: 0.7629 (tt0) cc_final: 0.7394 (tm-30) REVERT: F 428 MET cc_start: 0.6451 (tpt) cc_final: 0.5998 (tpt) REVERT: F 463 MET cc_start: 0.6537 (tpp) cc_final: 0.6010 (tpp) REVERT: F 549 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.5324 (mpp) REVERT: F 573 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7739 (mtt90) REVERT: F 667 MET cc_start: 0.6872 (tpp) cc_final: 0.6320 (tpp) REVERT: F 792 TYR cc_start: 0.7755 (t80) cc_final: 0.6996 (t80) REVERT: F 815 GLU cc_start: 0.6408 (mm-30) cc_final: 0.5918 (mp0) REVERT: F 863 ASN cc_start: 0.6907 (p0) cc_final: 0.6605 (p0) REVERT: F 873 GLU cc_start: 0.6779 (mp0) cc_final: 0.6541 (mp0) REVERT: F 922 ASP cc_start: 0.7731 (m-30) cc_final: 0.7410 (m-30) REVERT: F 1339 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: G 1062 LYS cc_start: -0.0321 (tptt) cc_final: -0.0547 (tptt) REVERT: G 1125 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8487 (pp) outliers start: 121 outliers final: 81 residues processed: 739 average time/residue: 0.2423 time to fit residues: 272.0568 Evaluate side-chains 746 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 658 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1375 LYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 591 ARG Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 1339 GLN Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 10 optimal weight: 0.6980 chunk 279 optimal weight: 0.6980 chunk 382 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 329 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 328 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 562 ASN C 797 ASN C 799 GLN C 896 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F1339 GLN H 349 ASN ** I1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128967 restraints weight = 49786.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132384 restraints weight = 25775.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134865 restraints weight = 16748.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136283 restraints weight = 12287.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136536 restraints weight = 10159.610| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33050 Z= 0.132 Angle : 0.635 17.979 44611 Z= 0.309 Chirality : 0.043 0.262 5018 Planarity : 0.005 0.067 5713 Dihedral : 6.218 136.510 4365 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.28 % Allowed : 22.65 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3965 helix: 0.73 (0.12), residues: 1973 sheet: -0.98 (0.28), residues: 341 loop : -1.44 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 907 TYR 0.016 0.001 TYR D 756 PHE 0.021 0.001 PHE D 480 TRP 0.012 0.001 TRP A 842 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00301 (33050) covalent geometry : angle 0.63490 (44611) hydrogen bonds : bond 0.03981 ( 1476) hydrogen bonds : angle 4.25192 ( 4281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 671 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7033 (mp0) cc_final: 0.6698 (mp0) REVERT: A 733 GLU cc_start: 0.6962 (tp30) cc_final: 0.6727 (tm-30) REVERT: A 883 ASN cc_start: 0.8241 (m-40) cc_final: 0.7646 (t0) REVERT: A 888 ASP cc_start: 0.6725 (t0) cc_final: 0.6425 (t0) REVERT: B 483 ARG cc_start: 0.7362 (mmm-85) cc_final: 0.7119 (mmm-85) REVERT: B 495 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6910 (mm-30) REVERT: B 498 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7622 (ttp80) REVERT: B 547 ASP cc_start: 0.6679 (t0) cc_final: 0.6168 (t0) REVERT: B 667 MET cc_start: 0.7585 (mmm) cc_final: 0.7267 (mmm) REVERT: B 801 LEU cc_start: 0.7959 (mt) cc_final: 0.7665 (mp) REVERT: B 881 LYS cc_start: 0.7602 (tppt) cc_final: 0.7202 (tppt) REVERT: C 410 VAL cc_start: 0.7932 (m) cc_final: 0.7563 (p) REVERT: C 482 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6115 (ttm) REVERT: C 483 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6665 (mmp-170) REVERT: C 489 LEU cc_start: 0.7515 (pp) cc_final: 0.7181 (pp) REVERT: C 499 GLN cc_start: 0.8131 (tp40) cc_final: 0.7849 (tp40) REVERT: C 582 TYR cc_start: 0.8088 (t80) cc_final: 0.7365 (t80) REVERT: C 665 ASP cc_start: 0.7654 (m-30) cc_final: 0.7389 (m-30) REVERT: C 828 ARG cc_start: 0.6393 (mmm160) cc_final: 0.6042 (mmm-85) REVERT: C 881 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7308 (ptpp) REVERT: C 925 MET cc_start: 0.5826 (tmm) cc_final: 0.5455 (tmm) REVERT: C 1336 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6644 (tm-30) REVERT: D 546 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5208 (ppp) REVERT: D 593 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8007 (mmtt) REVERT: D 594 ILE cc_start: 0.8333 (mt) cc_final: 0.8067 (tt) REVERT: D 613 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7349 (ttmt) REVERT: D 616 PHE cc_start: 0.6872 (t80) cc_final: 0.6639 (t80) REVERT: D 635 LEU cc_start: 0.8466 (mt) cc_final: 0.8253 (mm) REVERT: D 643 PRO cc_start: 0.8277 (Cg_endo) cc_final: 0.7882 (Cg_exo) REVERT: D 698 ASP cc_start: 0.7642 (p0) cc_final: 0.7161 (p0) REVERT: D 760 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7010 (tm-30) REVERT: D 792 TYR cc_start: 0.7814 (t80) cc_final: 0.7100 (t80) REVERT: D 914 GLU cc_start: 0.6531 (tm-30) cc_final: 0.6201 (tm-30) REVERT: D 1329 LYS cc_start: 0.8051 (tppt) cc_final: 0.7703 (tppt) REVERT: E 463 MET cc_start: 0.7135 (tpp) cc_final: 0.6907 (tpp) REVERT: E 764 GLU cc_start: 0.6671 (pp20) cc_final: 0.6336 (pp20) REVERT: E 812 ARG cc_start: 0.5977 (ttp-110) cc_final: 0.5766 (mtp-110) REVERT: E 824 GLU cc_start: 0.6501 (tp30) cc_final: 0.6001 (tp30) REVERT: E 856 LEU cc_start: 0.8186 (tp) cc_final: 0.7914 (tp) REVERT: E 892 LYS cc_start: 0.6646 (tppt) cc_final: 0.6315 (tppt) REVERT: E 933 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6554 (pp) REVERT: E 1329 LYS cc_start: 0.7970 (pttm) cc_final: 0.7621 (pttm) REVERT: E 1377 LEU cc_start: 0.8194 (mp) cc_final: 0.7929 (mt) REVERT: F 426 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7769 (ttpp) REVERT: F 427 GLU cc_start: 0.7601 (tt0) cc_final: 0.7330 (tm-30) REVERT: F 428 MET cc_start: 0.6720 (tpt) cc_final: 0.6109 (tpt) REVERT: F 463 MET cc_start: 0.6556 (tpp) cc_final: 0.6092 (tpp) REVERT: F 498 ARG cc_start: 0.7275 (mmp80) cc_final: 0.7029 (mmp80) REVERT: F 519 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.4614 (tm-30) REVERT: F 546 MET cc_start: 0.7499 (mtt) cc_final: 0.7077 (mtt) REVERT: F 549 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.5156 (mpp) REVERT: F 573 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7721 (mtt90) REVERT: F 667 MET cc_start: 0.6888 (tpp) cc_final: 0.6342 (tpp) REVERT: F 753 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: F 815 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5925 (mp0) REVERT: F 863 ASN cc_start: 0.6929 (p0) cc_final: 0.6646 (p0) REVERT: F 881 LYS cc_start: 0.7927 (pttt) cc_final: 0.7551 (pttt) REVERT: F 922 ASP cc_start: 0.7708 (m-30) cc_final: 0.7407 (m-30) REVERT: F 1339 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6774 (tm130) REVERT: G 1125 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8473 (pp) outliers start: 119 outliers final: 84 residues processed: 737 average time/residue: 0.2420 time to fit residues: 271.2645 Evaluate side-chains 747 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 653 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1375 LYS Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 483 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 896 GLN Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 591 ARG Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1339 GLN Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain H residue 1131 ARG Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 208 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN C 562 ASN C 799 GLN D 644 GLN E 775 ASN E 896 GLN F 443 ASN F 712 ASN F1326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.173035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129044 restraints weight = 49948.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132840 restraints weight = 25401.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134994 restraints weight = 15812.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136745 restraints weight = 11796.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136745 restraints weight = 9536.167| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33050 Z= 0.152 Angle : 0.647 16.806 44611 Z= 0.315 Chirality : 0.043 0.255 5018 Planarity : 0.005 0.063 5713 Dihedral : 6.177 134.177 4365 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.48 % Allowed : 22.81 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3965 helix: 0.75 (0.12), residues: 1981 sheet: -1.00 (0.28), residues: 341 loop : -1.42 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 323 TYR 0.027 0.001 TYR B 784 PHE 0.021 0.001 PHE D 642 TRP 0.013 0.001 TRP A 842 HIS 0.005 0.001 HIS H1009 Details of bonding type rmsd covalent geometry : bond 0.00350 (33050) covalent geometry : angle 0.64737 (44611) hydrogen bonds : bond 0.04039 ( 1476) hydrogen bonds : angle 4.24270 ( 4281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 663 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7064 (mp0) cc_final: 0.6734 (mp0) REVERT: A 614 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6668 (ttpp) REVERT: A 883 ASN cc_start: 0.8245 (m-40) cc_final: 0.7656 (t0) REVERT: A 888 ASP cc_start: 0.6746 (t0) cc_final: 0.6443 (t0) REVERT: A 904 GLU cc_start: 0.6581 (tm-30) cc_final: 0.6200 (tm-30) REVERT: A 908 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7382 (ttp80) REVERT: B 483 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.7174 (mmm-85) REVERT: B 498 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7464 (ttp80) REVERT: B 547 ASP cc_start: 0.6706 (t0) cc_final: 0.6202 (t0) REVERT: B 801 LEU cc_start: 0.7945 (mt) cc_final: 0.7652 (mp) REVERT: B 881 LYS cc_start: 0.7603 (tppt) cc_final: 0.7228 (tppt) REVERT: C 410 VAL cc_start: 0.7971 (m) cc_final: 0.7588 (p) REVERT: C 482 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6186 (ttm) REVERT: C 483 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6691 (mmp-170) REVERT: C 489 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7159 (pp) REVERT: C 499 GLN cc_start: 0.8181 (tp40) cc_final: 0.7907 (tp40) REVERT: C 505 GLU cc_start: 0.6371 (tp30) cc_final: 0.6104 (tp30) REVERT: C 665 ASP cc_start: 0.7682 (m-30) cc_final: 0.7418 (m-30) REVERT: C 881 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7338 (ptpp) REVERT: C 925 MET cc_start: 0.5881 (tmm) cc_final: 0.5502 (tmm) REVERT: C 1336 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6686 (tm-30) REVERT: D 501 ARG cc_start: 0.6788 (mmm160) cc_final: 0.6061 (mmm160) REVERT: D 546 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5248 (ppp) REVERT: D 593 LYS cc_start: 0.8377 (mmmt) cc_final: 0.7977 (mmtt) REVERT: D 594 ILE cc_start: 0.8341 (mt) cc_final: 0.8054 (tt) REVERT: D 598 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7323 (mm-40) REVERT: D 613 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7385 (ttmt) REVERT: D 616 PHE cc_start: 0.6844 (t80) cc_final: 0.6634 (t80) REVERT: D 637 SER cc_start: 0.8256 (m) cc_final: 0.7907 (p) REVERT: D 698 ASP cc_start: 0.7599 (p0) cc_final: 0.7233 (p0) REVERT: D 760 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7019 (tm-30) REVERT: D 792 TYR cc_start: 0.7707 (t80) cc_final: 0.7198 (t80) REVERT: D 800 ASN cc_start: 0.7649 (m-40) cc_final: 0.7359 (t0) REVERT: D 903 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5785 (tm-30) REVERT: D 914 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6274 (tm-30) REVERT: D 1329 LYS cc_start: 0.8062 (tppt) cc_final: 0.7706 (tppt) REVERT: E 463 MET cc_start: 0.7199 (tpp) cc_final: 0.6976 (tpp) REVERT: E 757 GLU cc_start: 0.7047 (pm20) cc_final: 0.6839 (pm20) REVERT: E 764 GLU cc_start: 0.6707 (pp20) cc_final: 0.6220 (pp20) REVERT: E 824 GLU cc_start: 0.6516 (tp30) cc_final: 0.5944 (tp30) REVERT: E 827 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7383 (ttmt) REVERT: E 856 LEU cc_start: 0.8155 (tp) cc_final: 0.7879 (tp) REVERT: E 863 ASN cc_start: 0.7599 (p0) cc_final: 0.6754 (p0) REVERT: E 871 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (mp) REVERT: E 873 GLU cc_start: 0.6857 (mp0) cc_final: 0.6326 (mp0) REVERT: E 892 LYS cc_start: 0.6672 (tppt) cc_final: 0.6327 (tppt) REVERT: E 933 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6547 (pp) REVERT: E 1329 LYS cc_start: 0.7978 (pttm) cc_final: 0.7603 (pttm) REVERT: E 1377 LEU cc_start: 0.8182 (mp) cc_final: 0.7917 (mt) REVERT: F 424 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7914 (tm-30) REVERT: F 426 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7788 (tppp) REVERT: F 427 GLU cc_start: 0.7646 (tt0) cc_final: 0.7349 (tm-30) REVERT: F 428 MET cc_start: 0.6804 (tpt) cc_final: 0.6175 (tpt) REVERT: F 463 MET cc_start: 0.6637 (tpp) cc_final: 0.6055 (tpp) REVERT: F 498 ARG cc_start: 0.7277 (mmp80) cc_final: 0.7039 (mmp80) REVERT: F 519 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.4574 (tm-30) REVERT: F 546 MET cc_start: 0.7553 (mtt) cc_final: 0.7100 (mtt) REVERT: F 549 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.5145 (mpp) REVERT: F 577 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6439 (t80) REVERT: F 667 MET cc_start: 0.6892 (tpp) cc_final: 0.6341 (tpp) REVERT: F 815 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5950 (mp0) REVERT: F 881 LYS cc_start: 0.7950 (pttt) cc_final: 0.7586 (pttt) REVERT: F 922 ASP cc_start: 0.7699 (m-30) cc_final: 0.7400 (m-30) REVERT: G 1125 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8399 (pp) outliers start: 126 outliers final: 95 residues processed: 734 average time/residue: 0.2448 time to fit residues: 273.9104 Evaluate side-chains 760 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 653 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1327 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 483 ARG Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 903 GLU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 820 GLN Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 591 ARG Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1040 LYS Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 121 optimal weight: 1.9990 chunk 363 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 chunk 273 optimal weight: 0.3980 chunk 272 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 287 optimal weight: 0.0980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN C 562 ASN C 896 GLN F 712 ASN F 820 GLN F1326 GLN F1339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.173357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130025 restraints weight = 49847.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133457 restraints weight = 26026.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135847 restraints weight = 15902.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137411 restraints weight = 11496.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138151 restraints weight = 9330.113| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33050 Z= 0.136 Angle : 0.643 15.627 44611 Z= 0.314 Chirality : 0.042 0.261 5018 Planarity : 0.005 0.059 5713 Dihedral : 6.096 133.746 4365 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.26 % Allowed : 23.48 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3965 helix: 0.79 (0.12), residues: 1975 sheet: -0.97 (0.28), residues: 341 loop : -1.34 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 907 TYR 0.023 0.001 TYR B 784 PHE 0.019 0.001 PHE D 442 TRP 0.011 0.001 TRP A 842 HIS 0.003 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00312 (33050) covalent geometry : angle 0.64328 (44611) hydrogen bonds : bond 0.03936 ( 1476) hydrogen bonds : angle 4.19104 ( 4281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 661 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7059 (mp0) cc_final: 0.6724 (mp0) REVERT: A 614 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6920 (ttpt) REVERT: A 883 ASN cc_start: 0.8232 (m-40) cc_final: 0.7627 (t0) REVERT: A 888 ASP cc_start: 0.6754 (t0) cc_final: 0.6417 (t0) REVERT: A 908 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7380 (ttp80) REVERT: B 483 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: B 498 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7495 (ttp80) REVERT: B 547 ASP cc_start: 0.6717 (t0) cc_final: 0.6182 (t0) REVERT: B 601 LYS cc_start: 0.7453 (tmtt) cc_final: 0.7129 (tmtt) REVERT: B 667 MET cc_start: 0.7500 (mmm) cc_final: 0.7222 (mmm) REVERT: B 801 LEU cc_start: 0.7933 (mt) cc_final: 0.7599 (mp) REVERT: B 881 LYS cc_start: 0.7662 (tppt) cc_final: 0.7232 (tppt) REVERT: C 410 VAL cc_start: 0.7978 (m) cc_final: 0.7602 (p) REVERT: C 482 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6188 (ttm) REVERT: C 483 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6677 (mmp-170) REVERT: C 489 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7157 (pp) REVERT: C 499 GLN cc_start: 0.8170 (tp40) cc_final: 0.7888 (tp40) REVERT: C 505 GLU cc_start: 0.6328 (tp30) cc_final: 0.6053 (tp30) REVERT: C 665 ASP cc_start: 0.7661 (m-30) cc_final: 0.7405 (m-30) REVERT: C 828 ARG cc_start: 0.6404 (mmm160) cc_final: 0.6105 (mmm-85) REVERT: C 881 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7239 (ptpp) REVERT: C 925 MET cc_start: 0.5876 (tmm) cc_final: 0.5537 (tmm) REVERT: C 1336 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6668 (tm-30) REVERT: D 546 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5174 (ppp) REVERT: D 593 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8017 (mmtt) REVERT: D 594 ILE cc_start: 0.8346 (mt) cc_final: 0.8060 (tt) REVERT: D 613 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7327 (ttmt) REVERT: D 616 PHE cc_start: 0.6848 (t80) cc_final: 0.6645 (t80) REVERT: D 635 LEU cc_start: 0.8404 (mt) cc_final: 0.8129 (mm) REVERT: D 637 SER cc_start: 0.8297 (m) cc_final: 0.7895 (p) REVERT: D 638 ILE cc_start: 0.8578 (mt) cc_final: 0.8194 (mt) REVERT: D 643 PRO cc_start: 0.8297 (Cg_endo) cc_final: 0.7907 (Cg_exo) REVERT: D 698 ASP cc_start: 0.7616 (p0) cc_final: 0.7227 (p0) REVERT: D 760 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7039 (tm-30) REVERT: D 792 TYR cc_start: 0.7542 (t80) cc_final: 0.7134 (t80) REVERT: D 903 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5635 (tp30) REVERT: D 907 ARG cc_start: 0.6191 (mpp80) cc_final: 0.5885 (ttm-80) REVERT: D 914 GLU cc_start: 0.6573 (tm-30) cc_final: 0.6258 (tm-30) REVERT: D 1329 LYS cc_start: 0.8041 (tppt) cc_final: 0.7668 (tppt) REVERT: E 463 MET cc_start: 0.7279 (tpp) cc_final: 0.6951 (tpp) REVERT: E 757 GLU cc_start: 0.7041 (pm20) cc_final: 0.6832 (pm20) REVERT: E 764 GLU cc_start: 0.6706 (pp20) cc_final: 0.6281 (pp20) REVERT: E 824 GLU cc_start: 0.6560 (tp30) cc_final: 0.5933 (tp30) REVERT: E 827 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7404 (ttmt) REVERT: E 863 ASN cc_start: 0.7572 (p0) cc_final: 0.6347 (p0) REVERT: E 871 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 873 GLU cc_start: 0.6827 (mp0) cc_final: 0.6338 (mp0) REVERT: E 892 LYS cc_start: 0.6654 (tppt) cc_final: 0.6331 (tppt) REVERT: E 933 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6535 (pp) REVERT: E 1329 LYS cc_start: 0.7971 (pttm) cc_final: 0.7593 (pttm) REVERT: E 1377 LEU cc_start: 0.8146 (mp) cc_final: 0.7890 (mt) REVERT: F 424 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7924 (tm-30) REVERT: F 427 GLU cc_start: 0.7628 (tt0) cc_final: 0.7387 (tm-30) REVERT: F 463 MET cc_start: 0.6563 (tpp) cc_final: 0.5985 (tpp) REVERT: F 498 ARG cc_start: 0.7259 (mmp80) cc_final: 0.7002 (mmp80) REVERT: F 519 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.4482 (tm-30) REVERT: F 546 MET cc_start: 0.7530 (mtt) cc_final: 0.7075 (mtt) REVERT: F 549 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.5237 (mpp) REVERT: F 577 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6444 (t80) REVERT: F 667 MET cc_start: 0.6739 (tpp) cc_final: 0.6156 (tpp) REVERT: F 792 TYR cc_start: 0.7732 (t80) cc_final: 0.6949 (t80) REVERT: F 848 ASN cc_start: 0.7959 (m-40) cc_final: 0.7678 (m-40) REVERT: F 881 LYS cc_start: 0.7956 (pttt) cc_final: 0.7614 (pttt) REVERT: F 922 ASP cc_start: 0.7662 (m-30) cc_final: 0.7392 (m-30) REVERT: F 1339 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6756 (tm130) REVERT: G 1051 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8115 (pp20) REVERT: G 1125 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8373 (pp) outliers start: 118 outliers final: 88 residues processed: 725 average time/residue: 0.2452 time to fit residues: 271.7493 Evaluate side-chains 749 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 648 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 483 ARG Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 903 GLU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 775 ASN Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1339 GLN Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1040 LYS Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1049 VAL Chi-restraints excluded: chain G residue 1118 LEU Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1070 LEU Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 154 optimal weight: 0.0370 chunk 279 optimal weight: 0.2980 chunk 358 optimal weight: 30.0000 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 202 optimal weight: 20.0000 chunk 57 optimal weight: 0.2980 chunk 241 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 562 ASN C 896 GLN F 712 ASN F1326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.173439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129746 restraints weight = 49507.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133524 restraints weight = 25008.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135844 restraints weight = 15543.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137106 restraints weight = 11548.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137284 restraints weight = 9506.406| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33050 Z= 0.135 Angle : 0.652 15.653 44611 Z= 0.318 Chirality : 0.043 0.258 5018 Planarity : 0.005 0.060 5713 Dihedral : 6.039 133.730 4365 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.06 % Allowed : 23.83 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3965 helix: 0.79 (0.12), residues: 1981 sheet: -0.97 (0.28), residues: 341 loop : -1.40 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 907 TYR 0.028 0.001 TYR B 784 PHE 0.021 0.001 PHE D 642 TRP 0.010 0.001 TRP A 842 HIS 0.004 0.001 HIS F 898 Details of bonding type rmsd covalent geometry : bond 0.00313 (33050) covalent geometry : angle 0.65211 (44611) hydrogen bonds : bond 0.03899 ( 1476) hydrogen bonds : angle 4.16939 ( 4281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 659 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7077 (mp0) cc_final: 0.6749 (mp0) REVERT: A 614 LYS cc_start: 0.7318 (ttpt) cc_final: 0.7003 (ttpt) REVERT: A 643 PHE cc_start: 0.7772 (m-10) cc_final: 0.7435 (m-10) REVERT: A 669 LEU cc_start: 0.8144 (mt) cc_final: 0.7880 (mp) REVERT: A 883 ASN cc_start: 0.8226 (m-40) cc_final: 0.7613 (t0) REVERT: A 888 ASP cc_start: 0.6755 (t0) cc_final: 0.6440 (t0) REVERT: A 904 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 908 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7387 (ttp80) REVERT: B 420 ASN cc_start: 0.8032 (t0) cc_final: 0.7731 (t0) REVERT: B 483 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.7138 (mmm-85) REVERT: B 498 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7592 (ttp80) REVERT: B 547 ASP cc_start: 0.6742 (t0) cc_final: 0.6210 (t0) REVERT: B 601 LYS cc_start: 0.7501 (tmtt) cc_final: 0.7132 (tmtt) REVERT: B 667 MET cc_start: 0.7487 (mmm) cc_final: 0.7210 (mmm) REVERT: B 691 LEU cc_start: 0.7987 (mt) cc_final: 0.7748 (mt) REVERT: B 701 ASN cc_start: 0.7533 (m-40) cc_final: 0.7245 (m-40) REVERT: B 732 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6699 (tm-30) REVERT: B 801 LEU cc_start: 0.7916 (mt) cc_final: 0.7584 (mp) REVERT: B 881 LYS cc_start: 0.7666 (tppt) cc_final: 0.7231 (tppt) REVERT: C 410 VAL cc_start: 0.8003 (m) cc_final: 0.7620 (p) REVERT: C 443 ASN cc_start: 0.6792 (m-40) cc_final: 0.6466 (m-40) REVERT: C 489 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7114 (pp) REVERT: C 499 GLN cc_start: 0.8170 (tp40) cc_final: 0.7849 (tp40) REVERT: C 505 GLU cc_start: 0.6341 (tp30) cc_final: 0.6063 (tp30) REVERT: C 665 ASP cc_start: 0.7667 (m-30) cc_final: 0.7415 (m-30) REVERT: C 881 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7239 (ptpp) REVERT: C 925 MET cc_start: 0.5908 (tmm) cc_final: 0.5548 (tmm) REVERT: C 1336 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6691 (tm-30) REVERT: D 501 ARG cc_start: 0.6824 (mmm160) cc_final: 0.6079 (mmm160) REVERT: D 546 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5241 (ppp) REVERT: D 593 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7988 (mmtt) REVERT: D 594 ILE cc_start: 0.8338 (mt) cc_final: 0.8101 (tt) REVERT: D 613 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7315 (ttmt) REVERT: D 637 SER cc_start: 0.8289 (m) cc_final: 0.7871 (p) REVERT: D 643 PRO cc_start: 0.8365 (Cg_endo) cc_final: 0.7990 (Cg_exo) REVERT: D 698 ASP cc_start: 0.7628 (p0) cc_final: 0.7246 (p0) REVERT: D 760 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7052 (tm-30) REVERT: D 762 MET cc_start: 0.7727 (mmm) cc_final: 0.7243 (mmm) REVERT: D 792 TYR cc_start: 0.7713 (t80) cc_final: 0.7206 (t80) REVERT: D 903 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5636 (tp30) REVERT: D 907 ARG cc_start: 0.6208 (mpp80) cc_final: 0.5909 (ttm-80) REVERT: D 914 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6305 (tm-30) REVERT: D 1329 LYS cc_start: 0.8057 (tppt) cc_final: 0.7673 (tppt) REVERT: E 463 MET cc_start: 0.7250 (tpp) cc_final: 0.6945 (tpp) REVERT: E 757 GLU cc_start: 0.7033 (pm20) cc_final: 0.6814 (pm20) REVERT: E 764 GLU cc_start: 0.6731 (pp20) cc_final: 0.6316 (pp20) REVERT: E 824 GLU cc_start: 0.6580 (tp30) cc_final: 0.5969 (tp30) REVERT: E 827 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7444 (ttmt) REVERT: E 856 LEU cc_start: 0.8414 (tp) cc_final: 0.8030 (tp) REVERT: E 863 ASN cc_start: 0.7578 (p0) cc_final: 0.6348 (p0) REVERT: E 871 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (mp) REVERT: E 887 ASP cc_start: 0.7038 (p0) cc_final: 0.6714 (p0) REVERT: E 892 LYS cc_start: 0.6717 (tppt) cc_final: 0.6394 (tppt) REVERT: E 933 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6547 (pp) REVERT: E 1329 LYS cc_start: 0.7978 (pttm) cc_final: 0.7646 (pttm) REVERT: E 1377 LEU cc_start: 0.8115 (mp) cc_final: 0.7858 (mt) REVERT: F 424 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 427 GLU cc_start: 0.7609 (tt0) cc_final: 0.7334 (tm-30) REVERT: F 463 MET cc_start: 0.6627 (tpp) cc_final: 0.6103 (tpp) REVERT: F 498 ARG cc_start: 0.7291 (mmp80) cc_final: 0.6996 (mmp80) REVERT: F 519 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4491 (tm-30) REVERT: F 546 MET cc_start: 0.7458 (mtt) cc_final: 0.7231 (mtt) REVERT: F 549 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.5253 (mpp) REVERT: F 577 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6396 (t80) REVERT: F 667 MET cc_start: 0.6904 (tpp) cc_final: 0.6287 (tpp) REVERT: F 863 ASN cc_start: 0.7033 (p0) cc_final: 0.6682 (p0) REVERT: F 881 LYS cc_start: 0.7965 (pttt) cc_final: 0.7629 (pttt) REVERT: F 922 ASP cc_start: 0.7692 (m-30) cc_final: 0.7396 (m-30) REVERT: F 1339 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: G 1062 LYS cc_start: -0.0521 (tptt) cc_final: -0.0924 (tptt) REVERT: G 1125 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8402 (pp) outliers start: 111 outliers final: 92 residues processed: 719 average time/residue: 0.2423 time to fit residues: 266.8192 Evaluate side-chains 748 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 645 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1375 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 896 GLN Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 903 GLU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 775 ASN Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1339 GLN Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1040 LYS Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1049 VAL Chi-restraints excluded: chain G residue 1118 LEU Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1064 PHE Chi-restraints excluded: chain I residue 1070 LEU Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 338 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 350 optimal weight: 30.0000 chunk 312 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 375 optimal weight: 50.0000 chunk 271 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 562 ASN F 712 ASN F1326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129656 restraints weight = 49808.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133350 restraints weight = 25109.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135757 restraints weight = 15648.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137274 restraints weight = 11421.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137563 restraints weight = 9306.900| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33050 Z= 0.150 Angle : 0.674 15.581 44611 Z= 0.328 Chirality : 0.043 0.260 5018 Planarity : 0.005 0.073 5713 Dihedral : 6.042 134.335 4365 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.95 % Allowed : 24.22 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3965 helix: 0.77 (0.12), residues: 1981 sheet: -0.94 (0.28), residues: 339 loop : -1.39 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 907 TYR 0.016 0.001 TYR D 756 PHE 0.045 0.001 PHE G1042 TRP 0.012 0.001 TRP A 842 HIS 0.003 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00351 (33050) covalent geometry : angle 0.67359 (44611) hydrogen bonds : bond 0.03940 ( 1476) hydrogen bonds : angle 4.18612 ( 4281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 649 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7029 (mp0) cc_final: 0.6689 (mp0) REVERT: A 614 LYS cc_start: 0.7340 (ttpt) cc_final: 0.7008 (ttpt) REVERT: A 643 PHE cc_start: 0.7788 (m-10) cc_final: 0.7455 (m-10) REVERT: A 883 ASN cc_start: 0.8209 (m-40) cc_final: 0.7616 (t0) REVERT: A 888 ASP cc_start: 0.6708 (t0) cc_final: 0.6379 (t0) REVERT: A 904 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6341 (tm-30) REVERT: A 908 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7322 (ttp80) REVERT: B 420 ASN cc_start: 0.7993 (t0) cc_final: 0.7699 (t0) REVERT: B 427 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: B 483 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.7136 (mmm-85) REVERT: B 498 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7593 (ttp80) REVERT: B 547 ASP cc_start: 0.6739 (t0) cc_final: 0.6209 (t0) REVERT: B 601 LYS cc_start: 0.7573 (tmtt) cc_final: 0.7350 (tmtt) REVERT: B 701 ASN cc_start: 0.7539 (m-40) cc_final: 0.7257 (m-40) REVERT: B 732 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 801 LEU cc_start: 0.7914 (mt) cc_final: 0.7592 (mp) REVERT: B 881 LYS cc_start: 0.7655 (tppt) cc_final: 0.7215 (tppt) REVERT: C 410 VAL cc_start: 0.8020 (m) cc_final: 0.7648 (p) REVERT: C 443 ASN cc_start: 0.6710 (m-40) cc_final: 0.6405 (m-40) REVERT: C 489 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7158 (pp) REVERT: C 499 GLN cc_start: 0.8151 (tp40) cc_final: 0.7832 (tp40) REVERT: C 505 GLU cc_start: 0.6322 (tp30) cc_final: 0.6079 (tp30) REVERT: C 665 ASP cc_start: 0.7632 (m-30) cc_final: 0.7358 (m-30) REVERT: C 925 MET cc_start: 0.5876 (tmm) cc_final: 0.5531 (tmm) REVERT: C 1336 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6645 (tm-30) REVERT: D 501 ARG cc_start: 0.6798 (mmm160) cc_final: 0.6092 (mmm160) REVERT: D 546 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5588 (ppp) REVERT: D 593 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7750 (mmmt) REVERT: D 613 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7310 (ttmt) REVERT: D 637 SER cc_start: 0.8279 (m) cc_final: 0.7855 (p) REVERT: D 643 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.7966 (Cg_exo) REVERT: D 698 ASP cc_start: 0.7605 (p0) cc_final: 0.7200 (p0) REVERT: D 760 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 792 TYR cc_start: 0.7723 (t80) cc_final: 0.7305 (t80) REVERT: D 903 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5658 (tp30) REVERT: D 907 ARG cc_start: 0.6200 (mpp80) cc_final: 0.5911 (ttm-80) REVERT: D 914 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6233 (tm-30) REVERT: D 1329 LYS cc_start: 0.8041 (tppt) cc_final: 0.7665 (tppt) REVERT: E 463 MET cc_start: 0.7248 (tpp) cc_final: 0.6899 (tpp) REVERT: E 662 LYS cc_start: 0.6926 (mppt) cc_final: 0.6579 (mmtm) REVERT: E 757 GLU cc_start: 0.7005 (pm20) cc_final: 0.6785 (pm20) REVERT: E 764 GLU cc_start: 0.6708 (pp20) cc_final: 0.6430 (pp20) REVERT: E 824 GLU cc_start: 0.6497 (tp30) cc_final: 0.5928 (tp30) REVERT: E 827 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7474 (ttmt) REVERT: E 856 LEU cc_start: 0.8395 (tp) cc_final: 0.8046 (tp) REVERT: E 871 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8291 (mp) REVERT: E 873 GLU cc_start: 0.6838 (mp0) cc_final: 0.6624 (mp0) REVERT: E 887 ASP cc_start: 0.7042 (p0) cc_final: 0.6683 (p0) REVERT: E 892 LYS cc_start: 0.6702 (tppt) cc_final: 0.6376 (tppt) REVERT: E 907 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6391 (ttm-80) REVERT: E 933 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6545 (pp) REVERT: E 1329 LYS cc_start: 0.7983 (pttm) cc_final: 0.7585 (pttm) REVERT: E 1377 LEU cc_start: 0.8159 (mp) cc_final: 0.7933 (mt) REVERT: F 424 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7891 (tm-30) REVERT: F 427 GLU cc_start: 0.7585 (tt0) cc_final: 0.7358 (tm-30) REVERT: F 463 MET cc_start: 0.6532 (tpp) cc_final: 0.6007 (tpp) REVERT: F 498 ARG cc_start: 0.7221 (mmp80) cc_final: 0.6942 (mmp80) REVERT: F 519 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.4472 (tm-30) REVERT: F 549 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.5344 (mpp) REVERT: F 577 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.6428 (t80) REVERT: F 667 MET cc_start: 0.6802 (tpp) cc_final: 0.6203 (tpp) REVERT: F 863 ASN cc_start: 0.7036 (p0) cc_final: 0.6683 (p0) REVERT: F 881 LYS cc_start: 0.7857 (pttt) cc_final: 0.7526 (pttt) REVERT: F 922 ASP cc_start: 0.7571 (m-30) cc_final: 0.7327 (m-30) REVERT: G 1031 MET cc_start: -0.1715 (tpp) cc_final: -0.2253 (tpp) REVERT: G 1062 LYS cc_start: -0.0317 (tptt) cc_final: -0.0739 (tptt) REVERT: G 1125 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8383 (pp) outliers start: 107 outliers final: 89 residues processed: 709 average time/residue: 0.2455 time to fit residues: 265.7045 Evaluate side-chains 742 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 643 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 903 GLU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 775 ASN Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 519 GLU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1049 VAL Chi-restraints excluded: chain G residue 1118 LEU Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1040 LYS Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1010 LEU Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1059 SER Chi-restraints excluded: chain I residue 1070 LEU Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 201 optimal weight: 1.9990 chunk 139 optimal weight: 0.0000 chunk 361 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 335 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 499 GLN C 562 ASN C 896 GLN E 775 ASN E 896 GLN F 712 ASN F 799 GLN F1326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.173695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130097 restraints weight = 49578.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133764 restraints weight = 25005.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136015 restraints weight = 15650.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137689 restraints weight = 11644.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138323 restraints weight = 9425.635| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33050 Z= 0.150 Angle : 0.668 15.536 44611 Z= 0.325 Chirality : 0.043 0.260 5018 Planarity : 0.005 0.058 5713 Dihedral : 6.009 135.399 4365 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.81 % Allowed : 24.39 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3965 helix: 0.76 (0.12), residues: 1988 sheet: -0.93 (0.28), residues: 339 loop : -1.37 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 828 TYR 0.016 0.001 TYR D 756 PHE 0.032 0.001 PHE G1042 TRP 0.013 0.001 TRP A 842 HIS 0.004 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00349 (33050) covalent geometry : angle 0.66790 (44611) hydrogen bonds : bond 0.03957 ( 1476) hydrogen bonds : angle 4.18515 ( 4281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6314.13 seconds wall clock time: 109 minutes 52.63 seconds (6592.63 seconds total)