Starting phenix.real_space_refine on Wed Mar 4 21:41:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0e_20995/03_2026/6v0e_20995.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 10542 2.51 5 N 2922 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s 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: 16602 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.61, per 1000 atoms: 0.16 Number of scatterers: 16602 At special positions: 0 Unit cell: (106.11, 108.73, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 3114 8.00 N 2922 7.00 C 10542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 780.7 milliseconds 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 12.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.501A pdb=" N ALA A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR A 744 " --> pdb=" O ASP A 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 745 " --> pdb=" O SER A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 741 through 745' Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.552A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR B 744 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 745 " --> pdb=" O SER B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 867 through 871 Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR C 744 " --> pdb=" O ASP C 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 745 " --> pdb=" O SER C 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 741 through 745' Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 867 through 871 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.554A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 741 through 745 removed outlier: 4.501A pdb=" N TYR D 744 " --> pdb=" O ASP D 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 745 " --> pdb=" O SER D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 867 through 871 Processing helix chain 'E' and resid 560 through 564 Processing helix chain 'E' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA E 598 " --> pdb=" O PRO E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 632 removed outlier: 3.502A pdb=" N ALA E 630 " --> pdb=" O SER E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 715 Processing helix chain 'E' and resid 741 through 745 removed outlier: 4.502A pdb=" N TYR E 744 " --> pdb=" O ASP E 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 745 " --> pdb=" O SER E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 745' Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 867 through 871 Processing helix chain 'F' and resid 560 through 564 Processing helix chain 'F' and resid 594 through 600 removed outlier: 3.521A pdb=" N ALA F 598 " --> pdb=" O PRO F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.553A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 632 removed outlier: 3.501A pdb=" N ALA F 630 " --> pdb=" O SER F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 741 through 745 removed outlier: 4.501A pdb=" N TYR F 744 " --> pdb=" O ASP F 741 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 745 " --> pdb=" O SER F 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 741 through 745' Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 867 through 871 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.610A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 521 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG A 793 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 776 " --> pdb=" O ARG A 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE A 858 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 751 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 860 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU A 753 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL B 517 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 521 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS B 558 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL B 543 " --> pdb=" O HIS B 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N PHE B 858 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 751 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU B 860 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 753 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 521 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS C 558 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 543 " --> pdb=" O HIS C 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG C 793 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL C 776 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE C 858 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 751 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU C 860 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU C 753 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL D 517 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 521 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS D 558 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL D 543 " --> pdb=" O HIS D 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N PHE D 858 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE D 751 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU D 860 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU D 753 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA E 521 " --> pdb=" O PHE E 553 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 695 through 698 removed outlier: 6.513A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 749 through 754 removed outlier: 6.392A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE E 858 " --> pdb=" O SER E 749 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE E 751 " --> pdb=" O PHE E 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU E 860 " --> pdb=" O ILE E 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 753 " --> pdb=" O LEU E 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 517 through 521 removed outlier: 3.609A pdb=" N VAL F 517 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 521 " --> pdb=" O PHE F 553 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL F 543 " --> pdb=" O HIS F 558 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 695 through 698 removed outlier: 6.512A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 749 through 754 removed outlier: 6.391A pdb=" N ARG F 793 " --> pdb=" O VAL F 776 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL F 776 " --> pdb=" O ARG F 793 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N PHE F 858 " --> pdb=" O SER F 749 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 751 " --> pdb=" O PHE F 858 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU F 860 " --> pdb=" O ILE F 751 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU F 753 " --> pdb=" O LEU F 860 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 936 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: 2.89 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5468 1.34 - 1.45: 2449 1.45 - 1.57: 8967 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 16932 Sorted by residual: bond pdb=" C VAL E 699 " pdb=" N THR E 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.94e+00 bond pdb=" C VAL C 699 " pdb=" N THR C 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.88e+00 bond pdb=" C VAL D 699 " pdb=" N THR D 700 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.59e-02 3.96e+03 4.78e+00 bond pdb=" C VAL A 699 " pdb=" N THR A 700 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.59e-02 3.96e+03 4.63e+00 bond pdb=" C VAL B 699 " pdb=" N THR B 700 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.59e-02 3.96e+03 4.55e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 22192 2.51 - 5.02: 704 5.02 - 7.53: 60 7.53 - 10.05: 24 10.05 - 12.56: 6 Bond angle restraints: 22986 Sorted by residual: angle pdb=" C GLY A 828 " pdb=" N THR A 829 " pdb=" CA THR A 829 " ideal model delta sigma weight residual 122.82 128.01 -5.19 1.42e+00 4.96e-01 1.34e+01 angle pdb=" C GLY D 828 " pdb=" N THR D 829 " pdb=" CA THR D 829 " ideal model delta sigma weight residual 122.82 128.01 -5.19 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY B 828 " pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 122.82 127.99 -5.17 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY C 828 " pdb=" N THR C 829 " pdb=" CA THR C 829 " ideal model delta sigma weight residual 122.82 127.99 -5.17 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C GLY E 828 " pdb=" N THR E 829 " pdb=" CA THR E 829 " ideal model delta sigma weight residual 122.82 127.98 -5.16 1.42e+00 4.96e-01 1.32e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 9384 14.40 - 28.80: 546 28.80 - 43.19: 138 43.19 - 57.59: 0 57.59 - 71.99: 12 Dihedral angle restraints: 10080 sinusoidal: 3948 harmonic: 6132 Sorted by residual: dihedral pdb=" CA THR D 846 " pdb=" C THR D 846 " pdb=" N PRO D 847 " pdb=" CA PRO D 847 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR E 846 " pdb=" C THR E 846 " pdb=" N PRO E 847 " pdb=" CA PRO E 847 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR B 846 " pdb=" C THR B 846 " pdb=" N PRO B 847 " pdb=" CA PRO B 847 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1658 0.048 - 0.096: 676 0.096 - 0.144: 230 0.144 - 0.192: 28 0.192 - 0.240: 36 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CB VAL C 527 " pdb=" CA VAL C 527 " pdb=" CG1 VAL C 527 " pdb=" CG2 VAL C 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL E 527 " pdb=" CA VAL E 527 " pdb=" CG1 VAL E 527 " pdb=" CG2 VAL E 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 527 " pdb=" CA VAL B 527 " pdb=" CG1 VAL B 527 " pdb=" CG2 VAL B 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2625 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 846 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 847 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 847 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 846 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 847 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 847 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.037 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2418 2.76 - 3.29: 14322 3.29 - 3.83: 26704 3.83 - 4.36: 31260 4.36 - 4.90: 55417 Nonbonded interactions: 130121 Sorted by model distance: nonbonded pdb=" OG SER A 759 " pdb=" O GLY B 828 " model vdw 2.220 3.040 nonbonded pdb=" OG SER D 759 " pdb=" O GLY E 828 " model vdw 2.220 3.040 nonbonded pdb=" OG SER E 759 " pdb=" O GLY F 828 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 759 " pdb=" O GLY C 828 " model vdw 2.247 3.040 nonbonded pdb=" O GLY A 828 " pdb=" OG SER F 759 " model vdw 2.284 3.040 ... (remaining 130116 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.008 0.056 16932 Z= 0.353 Angle : 1.017 12.556 22986 Z= 0.543 Chirality : 0.062 0.240 2628 Planarity : 0.007 0.064 2988 Dihedral : 10.010 71.988 6180 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.15), residues: 2166 helix: -4.75 (0.10), residues: 198 sheet: -1.70 (0.16), residues: 816 loop : -1.82 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 564 TYR 0.018 0.003 TYR A 682 PHE 0.039 0.005 PHE C 605 TRP 0.011 0.002 TRP C 868 HIS 0.007 0.002 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00836 (16932) covalent geometry : angle 1.01740 (22986) hydrogen bonds : bond 0.28177 ( 414) hydrogen bonds : angle 9.68756 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.9108 (ttt) cc_final: 0.8905 (ttt) REVERT: A 817 ASP cc_start: 0.7696 (m-30) cc_final: 0.7014 (p0) REVERT: B 554 ASP cc_start: 0.7481 (t70) cc_final: 0.7243 (m-30) REVERT: B 817 ASP cc_start: 0.7428 (m-30) cc_final: 0.6975 (p0) REVERT: C 580 LYS cc_start: 0.8097 (tttt) cc_final: 0.7171 (mmmt) REVERT: C 792 MET cc_start: 0.8651 (ptp) cc_final: 0.8301 (ptp) REVERT: C 817 ASP cc_start: 0.7644 (m-30) cc_final: 0.7060 (p0) REVERT: D 651 MET cc_start: 0.9094 (ttt) cc_final: 0.8890 (ttt) REVERT: D 817 ASP cc_start: 0.7705 (m-30) cc_final: 0.7018 (p0) REVERT: E 554 ASP cc_start: 0.7454 (t70) cc_final: 0.7216 (m-30) REVERT: E 817 ASP cc_start: 0.7421 (m-30) cc_final: 0.6931 (p0) REVERT: F 792 MET cc_start: 0.8637 (ptp) cc_final: 0.8285 (ptp) REVERT: F 817 ASP cc_start: 0.7641 (m-30) cc_final: 0.7018 (p0) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1478 time to fit residues: 104.1149 Evaluate side-chains 261 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 591 GLN A 720 ASN A 831 ASN C 551 ASN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 591 GLN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN F 551 ASN F 607 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120395 restraints weight = 22941.126| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.54 r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16932 Z= 0.143 Angle : 0.650 8.209 22986 Z= 0.336 Chirality : 0.047 0.157 2628 Planarity : 0.005 0.041 2988 Dihedral : 5.899 19.412 2370 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.66 % Allowed : 11.86 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 2166 helix: -3.75 (0.22), residues: 162 sheet: -1.43 (0.17), residues: 786 loop : -1.14 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 536 TYR 0.016 0.001 TYR C 563 PHE 0.011 0.002 PHE E 818 TRP 0.010 0.001 TRP F 868 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00326 (16932) covalent geometry : angle 0.64984 (22986) hydrogen bonds : bond 0.05164 ( 414) hydrogen bonds : angle 6.69723 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7669 (t0) cc_final: 0.7414 (t0) REVERT: A 651 MET cc_start: 0.9320 (ttt) cc_final: 0.9086 (ttt) REVERT: B 554 ASP cc_start: 0.7894 (t70) cc_final: 0.6808 (m-30) REVERT: B 606 ASP cc_start: 0.7605 (t0) cc_final: 0.7343 (t0) REVERT: B 646 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8751 (mtpt) REVERT: B 817 ASP cc_start: 0.7555 (m-30) cc_final: 0.6668 (p0) REVERT: B 862 GLU cc_start: 0.7981 (mp0) cc_final: 0.7772 (mm-30) REVERT: C 580 LYS cc_start: 0.8060 (tttt) cc_final: 0.6853 (mmtt) REVERT: C 792 MET cc_start: 0.9130 (ptp) cc_final: 0.8584 (ptp) REVERT: D 606 ASP cc_start: 0.7619 (t0) cc_final: 0.7364 (t0) REVERT: D 651 MET cc_start: 0.9345 (ttt) cc_final: 0.9134 (ttt) REVERT: E 554 ASP cc_start: 0.7853 (t70) cc_final: 0.6823 (m-30) REVERT: E 646 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8640 (mtpt) REVERT: E 817 ASP cc_start: 0.7537 (m-30) cc_final: 0.6821 (p0) REVERT: F 563 TYR cc_start: 0.6817 (m-10) cc_final: 0.6560 (m-10) REVERT: F 792 MET cc_start: 0.9174 (ptp) cc_final: 0.8631 (ptp) outliers start: 29 outliers final: 12 residues processed: 307 average time/residue: 0.1257 time to fit residues: 58.5506 Evaluate side-chains 230 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 0.0270 chunk 150 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 35 optimal weight: 0.0040 chunk 208 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 0.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 HIS B 676 GLN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 HIS ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 HIS ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 HIS F 676 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119868 restraints weight = 23260.720| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.58 r_work: 0.3277 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16932 Z= 0.119 Angle : 0.592 7.170 22986 Z= 0.304 Chirality : 0.045 0.152 2628 Planarity : 0.004 0.036 2988 Dihedral : 5.393 18.978 2370 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % 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: -1.82 (0.17), residues: 2166 helix: -2.97 (0.30), residues: 162 sheet: -1.18 (0.17), residues: 846 loop : -0.84 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 695 TYR 0.019 0.001 TYR E 563 PHE 0.010 0.002 PHE E 538 TRP 0.008 0.001 TRP C 809 HIS 0.002 0.001 HIS D 640 Details of bonding type rmsd covalent geometry : bond 0.00267 (16932) covalent geometry : angle 0.59157 (22986) hydrogen bonds : bond 0.04249 ( 414) hydrogen bonds : angle 6.14286 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7702 (t0) cc_final: 0.7448 (t0) REVERT: A 651 MET cc_start: 0.9323 (ttt) cc_final: 0.8939 (ttt) REVERT: A 772 GLU cc_start: 0.8340 (tt0) cc_final: 0.8097 (mt-10) REVERT: B 554 ASP cc_start: 0.7790 (t70) cc_final: 0.6756 (m-30) REVERT: B 564 ARG cc_start: 0.7350 (mtt90) cc_final: 0.7124 (mpt-90) REVERT: B 817 ASP cc_start: 0.8074 (m-30) cc_final: 0.6909 (p0) REVERT: C 580 LYS cc_start: 0.8007 (tttt) cc_final: 0.6868 (mmtt) REVERT: C 792 MET cc_start: 0.9171 (ptp) cc_final: 0.8563 (ptp) REVERT: D 606 ASP cc_start: 0.7685 (t0) cc_final: 0.7454 (t0) REVERT: D 651 MET cc_start: 0.9308 (ttt) cc_final: 0.8911 (ttt) REVERT: E 554 ASP cc_start: 0.7767 (t70) cc_final: 0.6732 (m-30) REVERT: E 606 ASP cc_start: 0.7593 (t0) cc_final: 0.7298 (t0) REVERT: E 817 ASP cc_start: 0.8012 (m-30) cc_final: 0.6874 (p0) REVERT: E 862 GLU cc_start: 0.7986 (mp0) cc_final: 0.7738 (mm-30) REVERT: F 545 THR cc_start: 0.8225 (m) cc_final: 0.7979 (m) REVERT: F 792 MET cc_start: 0.9176 (ptp) cc_final: 0.8625 (ptp) outliers start: 36 outliers final: 21 residues processed: 285 average time/residue: 0.1320 time to fit residues: 57.1509 Evaluate side-chains 261 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain E residue 796 LYS Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 GLN D 640 HIS ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116577 restraints weight = 23353.535| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.57 r_work: 0.3243 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16932 Z= 0.164 Angle : 0.609 6.912 22986 Z= 0.310 Chirality : 0.046 0.164 2628 Planarity : 0.004 0.036 2988 Dihedral : 5.401 19.624 2370 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.32 % Allowed : 15.52 % Favored : 81.16 % 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: -1.62 (0.18), residues: 2166 helix: -2.46 (0.35), residues: 162 sheet: -1.05 (0.17), residues: 834 loop : -0.76 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 835 TYR 0.015 0.001 TYR E 563 PHE 0.013 0.002 PHE C 689 TRP 0.008 0.001 TRP C 809 HIS 0.003 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00391 (16932) covalent geometry : angle 0.60882 (22986) hydrogen bonds : bond 0.03870 ( 414) hydrogen bonds : angle 6.17714 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.627 Fit side-chains REVERT: A 772 GLU cc_start: 0.8626 (tt0) cc_final: 0.8392 (mt-10) REVERT: B 606 ASP cc_start: 0.7700 (t0) cc_final: 0.7427 (t0) REVERT: B 817 ASP cc_start: 0.8229 (m-30) cc_final: 0.6991 (p0) REVERT: B 824 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7647 (t) REVERT: B 835 ARG cc_start: 0.7084 (ptt-90) cc_final: 0.6865 (ptt-90) REVERT: C 545 THR cc_start: 0.8367 (m) cc_final: 0.8143 (m) REVERT: C 580 LYS cc_start: 0.7921 (tttt) cc_final: 0.6718 (mmtt) REVERT: C 792 MET cc_start: 0.9344 (ptp) cc_final: 0.8759 (ptp) REVERT: D 834 ILE cc_start: 0.7161 (mm) cc_final: 0.6911 (mp) REVERT: E 817 ASP cc_start: 0.8205 (m-30) cc_final: 0.6991 (p0) REVERT: F 545 THR cc_start: 0.8281 (m) cc_final: 0.8063 (m) REVERT: F 606 ASP cc_start: 0.8164 (t0) cc_final: 0.7800 (t0) REVERT: F 792 MET cc_start: 0.9353 (ptp) cc_final: 0.8795 (ptp) outliers start: 58 outliers final: 32 residues processed: 290 average time/residue: 0.1238 time to fit residues: 54.4029 Evaluate side-chains 252 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 205 optimal weight: 0.0770 chunk 120 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117382 restraints weight = 23181.148| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.57 r_work: 0.3245 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16932 Z= 0.124 Angle : 0.575 7.182 22986 Z= 0.294 Chirality : 0.045 0.157 2628 Planarity : 0.004 0.090 2988 Dihedral : 5.202 19.196 2370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.41 % Allowed : 16.32 % Favored : 81.27 % 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: -1.51 (0.18), residues: 2166 helix: -2.01 (0.39), residues: 162 sheet: -1.02 (0.17), residues: 840 loop : -0.71 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 536 TYR 0.016 0.001 TYR E 563 PHE 0.014 0.002 PHE C 818 TRP 0.009 0.001 TRP F 809 HIS 0.001 0.000 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00290 (16932) covalent geometry : angle 0.57528 (22986) hydrogen bonds : bond 0.03564 ( 414) hydrogen bonds : angle 6.00881 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.586 Fit side-chains REVERT: A 583 LEU cc_start: 0.3306 (OUTLIER) cc_final: 0.3090 (tt) REVERT: B 606 ASP cc_start: 0.7456 (t0) cc_final: 0.7181 (t0) REVERT: C 536 ARG cc_start: 0.6817 (mmm-85) cc_final: 0.5990 (mmm-85) REVERT: C 545 THR cc_start: 0.8147 (m) cc_final: 0.7915 (m) REVERT: C 580 LYS cc_start: 0.7842 (tttt) cc_final: 0.6620 (mmtt) REVERT: C 606 ASP cc_start: 0.7893 (t0) cc_final: 0.7632 (t0) REVERT: C 643 ASP cc_start: 0.8534 (t0) cc_final: 0.8189 (t0) REVERT: C 792 MET cc_start: 0.9201 (ptp) cc_final: 0.8685 (ptp) REVERT: D 583 LEU cc_start: 0.3326 (OUTLIER) cc_final: 0.3084 (tt) REVERT: D 835 ARG cc_start: 0.7433 (ptt-90) cc_final: 0.7135 (ptt-90) REVERT: E 606 ASP cc_start: 0.7441 (t0) cc_final: 0.7210 (t0) REVERT: F 545 THR cc_start: 0.8048 (m) cc_final: 0.7814 (m) REVERT: F 643 ASP cc_start: 0.8443 (t0) cc_final: 0.8108 (t0) REVERT: F 792 MET cc_start: 0.9224 (ptp) cc_final: 0.8713 (ptp) outliers start: 42 outliers final: 29 residues processed: 253 average time/residue: 0.1254 time to fit residues: 47.9507 Evaluate side-chains 254 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114484 restraints weight = 23478.943| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.57 r_work: 0.3198 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16932 Z= 0.210 Angle : 0.633 7.734 22986 Z= 0.321 Chirality : 0.047 0.169 2628 Planarity : 0.004 0.087 2988 Dihedral : 5.416 19.952 2370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.09 % Allowed : 17.24 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 2166 helix: -1.88 (0.40), residues: 162 sheet: -1.03 (0.17), residues: 786 loop : -0.76 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 536 TYR 0.014 0.002 TYR E 563 PHE 0.018 0.002 PHE C 689 TRP 0.010 0.002 TRP A 574 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00509 (16932) covalent geometry : angle 0.63251 (22986) hydrogen bonds : bond 0.03879 ( 414) hydrogen bonds : angle 6.19076 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.711 Fit side-chains REVERT: A 583 LEU cc_start: 0.3564 (OUTLIER) cc_final: 0.3260 (tt) REVERT: B 536 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6522 (mmm160) REVERT: B 603 ILE cc_start: 0.8368 (mt) cc_final: 0.8029 (tt) REVERT: B 606 ASP cc_start: 0.7789 (t0) cc_final: 0.7507 (t0) REVERT: B 817 ASP cc_start: 0.8497 (m-30) cc_final: 0.7065 (p0) REVERT: C 536 ARG cc_start: 0.7025 (mmm-85) cc_final: 0.6129 (mmm160) REVERT: C 545 THR cc_start: 0.8295 (m) cc_final: 0.8082 (m) REVERT: C 580 LYS cc_start: 0.7904 (tttt) cc_final: 0.6731 (mmtt) REVERT: C 583 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.4304 (tp) REVERT: C 643 ASP cc_start: 0.8791 (t0) cc_final: 0.8460 (t0) REVERT: C 792 MET cc_start: 0.9372 (ptp) cc_final: 0.8830 (ptp) REVERT: D 772 GLU cc_start: 0.8583 (tt0) cc_final: 0.8335 (mt-10) REVERT: E 606 ASP cc_start: 0.7824 (t0) cc_final: 0.7582 (t0) REVERT: F 532 VAL cc_start: 0.8266 (p) cc_final: 0.8060 (p) REVERT: F 545 THR cc_start: 0.8255 (m) cc_final: 0.8045 (m) REVERT: F 583 LEU cc_start: 0.4566 (OUTLIER) cc_final: 0.4342 (tp) REVERT: F 643 ASP cc_start: 0.8792 (t0) cc_final: 0.8451 (t0) REVERT: F 792 MET cc_start: 0.9349 (ptp) cc_final: 0.8818 (ptp) outliers start: 54 outliers final: 40 residues processed: 260 average time/residue: 0.1329 time to fit residues: 51.9748 Evaluate side-chains 248 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 704 SER Chi-restraints excluded: chain F residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 142 optimal weight: 0.0050 chunk 197 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 HIS E 710 HIS ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116418 restraints weight = 23138.145| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.56 r_work: 0.3225 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16932 Z= 0.136 Angle : 0.585 7.478 22986 Z= 0.299 Chirality : 0.046 0.154 2628 Planarity : 0.004 0.052 2988 Dihedral : 5.197 19.644 2370 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.69 % Allowed : 17.87 % Favored : 79.44 % 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: -1.39 (0.18), residues: 2166 helix: -1.54 (0.42), residues: 162 sheet: -1.07 (0.17), residues: 798 loop : -0.60 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 835 TYR 0.015 0.001 TYR E 563 PHE 0.015 0.002 PHE C 833 TRP 0.010 0.002 TRP B 574 HIS 0.002 0.000 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00322 (16932) covalent geometry : angle 0.58459 (22986) hydrogen bonds : bond 0.03549 ( 414) hydrogen bonds : angle 6.00461 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 583 LEU cc_start: 0.3548 (OUTLIER) cc_final: 0.3234 (tp) REVERT: A 798 TYR cc_start: 0.9458 (m-80) cc_final: 0.9255 (m-80) REVERT: B 536 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6546 (mmm160) REVERT: B 554 ASP cc_start: 0.7950 (t70) cc_final: 0.6805 (m-30) REVERT: B 817 ASP cc_start: 0.8409 (m-30) cc_final: 0.7098 (p0) REVERT: C 536 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6241 (mmm160) REVERT: C 545 THR cc_start: 0.8261 (m) cc_final: 0.8051 (m) REVERT: C 580 LYS cc_start: 0.7731 (tttt) cc_final: 0.6651 (mmtt) REVERT: C 583 LEU cc_start: 0.4470 (OUTLIER) cc_final: 0.4160 (tp) REVERT: C 606 ASP cc_start: 0.8142 (t0) cc_final: 0.7883 (t0) REVERT: C 792 MET cc_start: 0.9361 (ptp) cc_final: 0.8821 (ptp) REVERT: D 583 LEU cc_start: 0.3539 (OUTLIER) cc_final: 0.3235 (tp) REVERT: D 772 GLU cc_start: 0.8590 (tt0) cc_final: 0.8345 (mt-10) REVERT: E 536 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6454 (mmm160) REVERT: E 554 ASP cc_start: 0.7900 (t70) cc_final: 0.6775 (m-30) REVERT: E 606 ASP cc_start: 0.7806 (t0) cc_final: 0.7519 (t0) REVERT: E 817 ASP cc_start: 0.8368 (m-30) cc_final: 0.7055 (p0) REVERT: F 545 THR cc_start: 0.8244 (m) cc_final: 0.8038 (m) REVERT: F 583 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.4128 (tp) REVERT: F 792 MET cc_start: 0.9359 (ptp) cc_final: 0.8862 (ptp) outliers start: 47 outliers final: 36 residues processed: 255 average time/residue: 0.1286 time to fit residues: 49.5601 Evaluate side-chains 248 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 536 ARG Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 127 optimal weight: 0.7980 chunk 181 optimal weight: 0.0670 chunk 190 optimal weight: 0.8980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118206 restraints weight = 23152.904| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.57 r_work: 0.3253 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16932 Z= 0.110 Angle : 0.556 7.352 22986 Z= 0.287 Chirality : 0.045 0.150 2628 Planarity : 0.003 0.034 2988 Dihedral : 4.883 19.006 2370 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.58 % Allowed : 17.98 % Favored : 79.44 % 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: -1.34 (0.18), residues: 2166 helix: -1.13 (0.45), residues: 162 sheet: -1.04 (0.17), residues: 798 loop : -0.62 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 835 TYR 0.023 0.001 TYR B 563 PHE 0.013 0.001 PHE C 833 TRP 0.009 0.001 TRP D 809 HIS 0.001 0.000 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00251 (16932) covalent geometry : angle 0.55645 (22986) hydrogen bonds : bond 0.03253 ( 414) hydrogen bonds : angle 5.75626 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.8149 (tt0) cc_final: 0.7695 (tt0) REVERT: A 545 THR cc_start: 0.7960 (m) cc_final: 0.7619 (m) REVERT: A 651 MET cc_start: 0.9362 (ttt) cc_final: 0.9014 (ttt) REVERT: A 798 TYR cc_start: 0.9438 (m-80) cc_final: 0.9077 (m-80) REVERT: B 817 ASP cc_start: 0.8303 (m-30) cc_final: 0.7086 (p0) REVERT: C 536 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6290 (mmm160) REVERT: C 580 LYS cc_start: 0.7726 (tttt) cc_final: 0.6690 (mmtt) REVERT: C 606 ASP cc_start: 0.8125 (t0) cc_final: 0.7856 (t0) REVERT: C 792 MET cc_start: 0.9354 (ptp) cc_final: 0.8838 (ptp) REVERT: C 798 TYR cc_start: 0.9421 (m-80) cc_final: 0.9131 (m-80) REVERT: D 651 MET cc_start: 0.9378 (ttt) cc_final: 0.9038 (ttt) REVERT: D 772 GLU cc_start: 0.8512 (tt0) cc_final: 0.8267 (mt-10) REVERT: D 798 TYR cc_start: 0.9425 (m-80) cc_final: 0.9052 (m-80) REVERT: E 536 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6452 (mmm160) REVERT: E 542 GLU cc_start: 0.8167 (tt0) cc_final: 0.7780 (tt0) REVERT: E 835 ARG cc_start: 0.6950 (ptt-90) cc_final: 0.6724 (ptt-90) REVERT: F 545 THR cc_start: 0.8146 (m) cc_final: 0.7946 (m) REVERT: F 627 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: F 792 MET cc_start: 0.9340 (ptp) cc_final: 0.8859 (ptp) outliers start: 45 outliers final: 31 residues processed: 261 average time/residue: 0.1276 time to fit residues: 50.2077 Evaluate side-chains 260 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 536 ARG Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 84 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117103 restraints weight = 23123.906| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.57 r_work: 0.3239 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16932 Z= 0.130 Angle : 0.582 8.747 22986 Z= 0.295 Chirality : 0.045 0.157 2628 Planarity : 0.004 0.050 2988 Dihedral : 4.890 19.606 2370 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.29 % Allowed : 18.73 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.18), residues: 2166 helix: -0.99 (0.45), residues: 162 sheet: -0.98 (0.17), residues: 786 loop : -0.66 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 835 TYR 0.013 0.001 TYR E 563 PHE 0.013 0.002 PHE C 818 TRP 0.009 0.001 TRP B 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00306 (16932) covalent geometry : angle 0.58207 (22986) hydrogen bonds : bond 0.03349 ( 414) hydrogen bonds : angle 5.79619 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.8165 (tt0) cc_final: 0.7731 (tt0) REVERT: A 545 THR cc_start: 0.8078 (m) cc_final: 0.7750 (m) REVERT: B 536 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6519 (mmm160) REVERT: B 817 ASP cc_start: 0.8333 (m-30) cc_final: 0.7106 (p0) REVERT: C 536 ARG cc_start: 0.7169 (mmm-85) cc_final: 0.6361 (mmm160) REVERT: C 580 LYS cc_start: 0.7907 (tttt) cc_final: 0.6884 (mmtt) REVERT: C 606 ASP cc_start: 0.8149 (t0) cc_final: 0.7851 (t0) REVERT: C 643 ASP cc_start: 0.8724 (t0) cc_final: 0.8522 (t0) REVERT: C 792 MET cc_start: 0.9365 (ptp) cc_final: 0.8839 (ptp) REVERT: D 772 GLU cc_start: 0.8542 (tt0) cc_final: 0.8253 (mt-10) REVERT: E 536 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6485 (mmm160) REVERT: E 542 GLU cc_start: 0.8154 (tt0) cc_final: 0.7700 (tt0) REVERT: E 606 ASP cc_start: 0.7918 (t0) cc_final: 0.7690 (t0) REVERT: F 545 THR cc_start: 0.8184 (m) cc_final: 0.7981 (m) REVERT: F 627 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: F 792 MET cc_start: 0.9356 (ptp) cc_final: 0.8824 (ptp) outliers start: 40 outliers final: 34 residues processed: 260 average time/residue: 0.1222 time to fit residues: 48.1043 Evaluate side-chains 265 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 536 ARG Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 148 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 129 optimal weight: 0.0270 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118336 restraints weight = 23117.264| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.53 r_work: 0.3261 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16932 Z= 0.107 Angle : 0.566 8.737 22986 Z= 0.287 Chirality : 0.045 0.154 2628 Planarity : 0.003 0.045 2988 Dihedral : 4.752 18.541 2370 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.00 % Allowed : 19.07 % Favored : 78.92 % 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: -1.30 (0.18), residues: 2166 helix: -0.77 (0.46), residues: 162 sheet: -0.99 (0.17), residues: 846 loop : -0.64 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 835 TYR 0.014 0.001 TYR E 563 PHE 0.013 0.001 PHE C 818 TRP 0.008 0.001 TRP B 809 HIS 0.001 0.000 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00245 (16932) covalent geometry : angle 0.56631 (22986) hydrogen bonds : bond 0.03155 ( 414) hydrogen bonds : angle 5.66469 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.8186 (tt0) cc_final: 0.7733 (tt0) REVERT: A 545 THR cc_start: 0.7986 (m) cc_final: 0.7680 (m) REVERT: A 651 MET cc_start: 0.9357 (ttt) cc_final: 0.8884 (ttt) REVERT: B 536 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6594 (mmm160) REVERT: B 570 ASN cc_start: 0.8672 (m-40) cc_final: 0.8387 (m-40) REVERT: B 746 ASP cc_start: 0.7817 (p0) cc_final: 0.7591 (p0) REVERT: B 817 ASP cc_start: 0.8313 (m-30) cc_final: 0.7104 (p0) REVERT: C 536 ARG cc_start: 0.7108 (mmm-85) cc_final: 0.6347 (mmm160) REVERT: C 580 LYS cc_start: 0.7883 (tttt) cc_final: 0.6884 (mmtt) REVERT: C 606 ASP cc_start: 0.8121 (t0) cc_final: 0.7804 (t0) REVERT: C 643 ASP cc_start: 0.8736 (t0) cc_final: 0.8530 (t0) REVERT: C 792 MET cc_start: 0.9342 (ptp) cc_final: 0.8807 (ptp) REVERT: D 545 THR cc_start: 0.8051 (m) cc_final: 0.7706 (m) REVERT: D 651 MET cc_start: 0.9373 (ttt) cc_final: 0.8918 (ttt) REVERT: D 772 GLU cc_start: 0.8506 (tt0) cc_final: 0.8233 (mt-10) REVERT: E 542 GLU cc_start: 0.8166 (tt0) cc_final: 0.7749 (tt0) REVERT: E 570 ASN cc_start: 0.8676 (m-40) cc_final: 0.8385 (m-40) REVERT: E 817 ASP cc_start: 0.8262 (m-30) cc_final: 0.7057 (p0) REVERT: F 627 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: F 643 ASP cc_start: 0.8677 (t0) cc_final: 0.8375 (t0) REVERT: F 792 MET cc_start: 0.9340 (ptp) cc_final: 0.8796 (ptp) outliers start: 35 outliers final: 32 residues processed: 273 average time/residue: 0.1277 time to fit residues: 52.7329 Evaluate side-chains 283 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 870 GLU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 870 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115822 restraints weight = 23134.964| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.56 r_work: 0.3227 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16932 Z= 0.162 Angle : 0.608 9.123 22986 Z= 0.307 Chirality : 0.046 0.159 2628 Planarity : 0.004 0.069 2988 Dihedral : 4.957 19.506 2370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.46 % Allowed : 18.84 % Favored : 78.69 % 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: -1.28 (0.18), residues: 2166 helix: -0.81 (0.45), residues: 162 sheet: -0.96 (0.17), residues: 786 loop : -0.67 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 835 TYR 0.021 0.002 TYR B 624 PHE 0.013 0.002 PHE C 818 TRP 0.009 0.001 TRP F 809 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00387 (16932) covalent geometry : angle 0.60760 (22986) hydrogen bonds : bond 0.03509 ( 414) hydrogen bonds : angle 5.92695 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.23 seconds wall clock time: 65 minutes 50.69 seconds (3950.69 seconds total)