Starting phenix.real_space_refine on Thu Mar 5 15:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvo_32855/03_2026/7wvo_32855.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 106 5.16 5 C 14829 2.51 5 N 3860 2.21 5 O 4393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 23188 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6676 Classifications: {'peptide': 856} Link IDs: {'CIS': 2, 'PTRANS': 41, 'TRANS': 812} Chain breaks: 8 Time building chain proxies: 4.68, per 1000 atoms: 0.20 Number of scatterers: 23188 At special positions: 0 Unit cell: (147.555, 144.276, 197.833, 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 106 16.00 O 4393 8.00 N 3860 7.00 C 14829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5558 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 47 sheets defined 22.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.545A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.664A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.583A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.912A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.700A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.610A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.787A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.754A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.751A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.723A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.690A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 960 removed outlier: 3.720A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.769A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.599A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.939A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.514A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.171A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.569A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.602A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 639' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.577A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.859A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 782 removed outlier: 3.737A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 4.036A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.503A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.888A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.621A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.767A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.093A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.890A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.681A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.861A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.778A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.682A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.773A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.760A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.794A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.793A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.005A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.526A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.738A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.783A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.768A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.868A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.567A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.727A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.882A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.761A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.568A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.990A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.691A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.691A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.278A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.012A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.934A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.646A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.658A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.936A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.713A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 188 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B 208 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG B 190 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 206 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 192 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR B 204 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 194 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS B 202 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 196 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.570A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.947A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.805A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.923A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.659A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.670A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.745A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.727A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.363A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.895A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.052A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.862A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.773A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.773A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.648A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.565A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.811A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.701A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.700A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 706 hydrogen bonds defined for protein. 1935 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: 5.45 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7394 1.35 - 1.47: 5833 1.47 - 1.59: 10353 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 23716 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" C VAL A 620 " pdb=" N PRO A 631 " ideal model delta sigma weight residual 1.341 1.384 -0.043 1.60e-02 3.91e+03 7.21e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.83e+00 bond pdb=" CA PHE C 157 " pdb=" CB PHE C 157 " ideal model delta sigma weight residual 1.530 1.571 -0.041 2.00e-02 2.50e+03 4.29e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 31529 2.34 - 4.68: 586 4.68 - 7.02: 101 7.02 - 9.36: 16 9.36 - 11.70: 10 Bond angle restraints: 32242 Sorted by residual: angle pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta sigma weight residual 121.70 133.40 -11.70 1.80e+00 3.09e-01 4.22e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.95 -10.41 1.91e+00 2.74e-01 2.97e+01 ... (remaining 32237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 13750 15.96 - 31.92: 320 31.92 - 47.88: 84 47.88 - 63.84: 14 63.84 - 79.80: 1 Dihedral angle restraints: 14169 sinusoidal: 5550 harmonic: 8619 Sorted by residual: dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 33.70 -33.70 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 0.00 33.40 -33.40 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CA PHE C 86 " pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 14166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2881 0.061 - 0.122: 665 0.122 - 0.184: 92 0.184 - 0.245: 22 0.245 - 0.306: 7 Chirality restraints: 3667 Sorted by residual: chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3664 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 25 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 26 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO A 295 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 25 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 26 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.044 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7370 2.86 - 3.37: 17247 3.37 - 3.88: 37117 3.88 - 4.39: 38676 4.39 - 4.90: 69531 Nonbonded interactions: 169941 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.354 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.367 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.368 3.040 nonbonded pdb=" O GLY A1093 " pdb=" OH TYR C 904 " model vdw 2.369 3.040 nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.373 3.040 ... (remaining 169936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.940 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23751 Z= 0.279 Angle : 0.833 11.698 32312 Z= 0.485 Chirality : 0.055 0.306 3667 Planarity : 0.007 0.101 4164 Dihedral : 8.312 79.801 8506 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.17 (0.12), residues: 2911 helix: -4.98 (0.05), residues: 561 sheet: -0.28 (0.18), residues: 543 loop : -1.76 (0.12), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.022 0.002 TYR A 873 PHE 0.025 0.003 PHE A 32 TRP 0.018 0.002 TRP C 64 HIS 0.013 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00578 (23716) covalent geometry : angle 0.83299 (32242) SS BOND : bond 0.00234 ( 35) SS BOND : angle 1.01255 ( 70) hydrogen bonds : bond 0.33124 ( 684) hydrogen bonds : angle 11.08238 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 779 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6404 (ttp80) REVERT: A 133 PHE cc_start: 0.5809 (m-10) cc_final: 0.5558 (m-10) REVERT: A 141 LEU cc_start: 0.5705 (mt) cc_final: 0.5462 (tt) REVERT: A 191 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 298 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 305 SER cc_start: 0.8342 (t) cc_final: 0.8045 (t) REVERT: A 309 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 321 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7624 (pm20) REVERT: A 536 ASN cc_start: 0.8375 (m-40) cc_final: 0.8151 (m-40) REVERT: A 591 SER cc_start: 0.8796 (t) cc_final: 0.8345 (p) REVERT: A 663 ASP cc_start: 0.7296 (m-30) cc_final: 0.7028 (m-30) REVERT: A 752 LEU cc_start: 0.8377 (mt) cc_final: 0.8062 (tt) REVERT: A 764 LYS cc_start: 0.8358 (mttt) cc_final: 0.8060 (ttmm) REVERT: A 773 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 776 LYS cc_start: 0.8075 (mttt) cc_final: 0.7858 (mttt) REVERT: A 917 TYR cc_start: 0.6942 (m-80) cc_final: 0.5874 (m-80) REVERT: A 947 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7462 (mtpp) REVERT: A 969 LYS cc_start: 0.8578 (mttt) cc_final: 0.8216 (mttt) REVERT: A 976 VAL cc_start: 0.8187 (t) cc_final: 0.7942 (t) REVERT: A 1028 LYS cc_start: 0.8278 (mttt) cc_final: 0.7781 (mmtp) REVERT: A 1116 THR cc_start: 0.7594 (p) cc_final: 0.7300 (p) REVERT: B 101 ILE cc_start: 0.8833 (mm) cc_final: 0.8521 (mm) REVERT: B 132 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4321 (tt0) REVERT: B 195 LYS cc_start: 0.7702 (pttt) cc_final: 0.7271 (tppt) REVERT: B 206 LYS cc_start: 0.8185 (tptt) cc_final: 0.7831 (tptm) REVERT: B 315 THR cc_start: 0.9006 (m) cc_final: 0.8691 (p) REVERT: B 425 LEU cc_start: 0.8013 (mt) cc_final: 0.7727 (mm) REVERT: B 524 VAL cc_start: 0.7403 (t) cc_final: 0.7145 (m) REVERT: B 537 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8076 (mtpp) REVERT: B 599 THR cc_start: 0.7052 (t) cc_final: 0.6842 (t) REVERT: B 654 GLU cc_start: 0.7814 (tt0) cc_final: 0.7560 (tt0) REVERT: B 725 GLU cc_start: 0.7574 (tt0) cc_final: 0.7354 (tt0) REVERT: B 737 ASP cc_start: 0.7137 (t0) cc_final: 0.6925 (t0) REVERT: B 759 PHE cc_start: 0.7540 (t80) cc_final: 0.7284 (t80) REVERT: B 776 LYS cc_start: 0.8116 (mttt) cc_final: 0.7741 (mttt) REVERT: B 780 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6968 (mt-10) REVERT: B 884 SER cc_start: 0.8247 (m) cc_final: 0.7769 (t) REVERT: B 898 PHE cc_start: 0.6487 (t80) cc_final: 0.5915 (t80) REVERT: B 953 ASN cc_start: 0.8405 (m-40) cc_final: 0.7938 (m-40) REVERT: B 1004 LEU cc_start: 0.8083 (tp) cc_final: 0.7796 (mt) REVERT: B 1073 LYS cc_start: 0.7810 (tttt) cc_final: 0.7226 (ttmm) REVERT: B 1122 VAL cc_start: 0.7768 (t) cc_final: 0.7550 (p) REVERT: C 49 HIS cc_start: 0.7450 (t70) cc_final: 0.6901 (t70) REVERT: C 62 VAL cc_start: 0.7481 (m) cc_final: 0.7233 (p) REVERT: C 195 LYS cc_start: 0.7358 (pttt) cc_final: 0.6457 (tppt) REVERT: C 294 ASP cc_start: 0.7189 (m-30) cc_final: 0.6959 (t70) REVERT: C 296 LEU cc_start: 0.8423 (tp) cc_final: 0.8195 (tp) REVERT: C 299 THR cc_start: 0.8272 (m) cc_final: 0.7795 (p) REVERT: C 534 VAL cc_start: 0.9080 (t) cc_final: 0.8826 (m) REVERT: C 697 MET cc_start: 0.7834 (ttm) cc_final: 0.7620 (ttm) REVERT: C 721 SER cc_start: 0.7988 (t) cc_final: 0.7582 (p) REVERT: C 736 VAL cc_start: 0.9050 (t) cc_final: 0.8658 (m) REVERT: C 737 ASP cc_start: 0.7924 (t0) cc_final: 0.7479 (t0) REVERT: C 821 LEU cc_start: 0.8959 (mt) cc_final: 0.8669 (mt) REVERT: C 884 SER cc_start: 0.8889 (m) cc_final: 0.8415 (t) REVERT: C 898 PHE cc_start: 0.6387 (t80) cc_final: 0.4736 (t80) REVERT: C 935 GLN cc_start: 0.8073 (tt0) cc_final: 0.7363 (tt0) REVERT: C 947 LYS cc_start: 0.7615 (mttt) cc_final: 0.7378 (ttmm) REVERT: C 1141 LEU cc_start: 0.8111 (mt) cc_final: 0.7866 (mt) outliers start: 2 outliers final: 0 residues processed: 780 average time/residue: 0.1645 time to fit residues: 195.1277 Evaluate side-chains 587 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0020 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 755 GLN A 762 GLN A 895 GLN A 901 GLN A 920 GLN A 955 ASN A1119 ASN B 99 ASN B 134 GLN B 409 GLN B 505 HIS B 519 HIS B 544 ASN B 703 ASN B 717 ASN B 751 ASN B 804 GLN B 935 GLN B 955 ASN B1083 HIS B1142 GLN C 66 HIS C 188 ASN C 239 GLN C 280 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 717 ASN C 949 GLN C1101 HIS C1119 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.142535 restraints weight = 49350.404| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.88 r_work: 0.3813 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23751 Z= 0.146 Angle : 0.619 11.990 32312 Z= 0.326 Chirality : 0.045 0.193 3667 Planarity : 0.005 0.046 4164 Dihedral : 4.797 23.921 3163 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.16 % Allowed : 9.33 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.98 (0.13), residues: 2911 helix: -2.65 (0.15), residues: 583 sheet: 0.22 (0.19), residues: 566 loop : -1.38 (0.12), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 765 TYR 0.020 0.001 TYR B 501 PHE 0.027 0.002 PHE B 342 TRP 0.014 0.001 TRP C1102 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00297 (23716) covalent geometry : angle 0.61741 (32242) SS BOND : bond 0.00755 ( 35) SS BOND : angle 1.13393 ( 70) hydrogen bonds : bond 0.05509 ( 684) hydrogen bonds : angle 6.21849 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 605 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6359 (t-170) cc_final: 0.6022 (t70) REVERT: A 133 PHE cc_start: 0.6313 (m-10) cc_final: 0.5970 (m-10) REVERT: A 191 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 192 PHE cc_start: 0.7449 (m-10) cc_final: 0.7167 (m-10) REVERT: A 290 ASP cc_start: 0.8029 (t0) cc_final: 0.7685 (t0) REVERT: A 305 SER cc_start: 0.8689 (t) cc_final: 0.8431 (m) REVERT: A 321 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7693 (pm20) REVERT: A 644 GLN cc_start: 0.7856 (tp40) cc_final: 0.7494 (tp40) REVERT: A 752 LEU cc_start: 0.8809 (mt) cc_final: 0.8587 (tt) REVERT: A 773 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 780 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 886 TRP cc_start: 0.8674 (p90) cc_final: 0.7875 (p90) REVERT: A 894 LEU cc_start: 0.8566 (mt) cc_final: 0.8342 (mm) REVERT: A 933 LYS cc_start: 0.8514 (mttt) cc_final: 0.8186 (mttm) REVERT: A 964 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8834 (mtpp) REVERT: A 969 LYS cc_start: 0.8953 (mttt) cc_final: 0.8722 (mttt) REVERT: A 984 LEU cc_start: 0.8097 (mp) cc_final: 0.7754 (tp) REVERT: A 1038 LYS cc_start: 0.8554 (mttt) cc_final: 0.8285 (mmmm) REVERT: A 1086 LYS cc_start: 0.8772 (pttt) cc_final: 0.8522 (pttp) REVERT: B 190 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7768 (ptp90) REVERT: B 191 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 195 LYS cc_start: 0.8009 (pttt) cc_final: 0.7243 (tppt) REVERT: B 202 LYS cc_start: 0.7361 (mttp) cc_final: 0.7136 (mptt) REVERT: B 206 LYS cc_start: 0.8655 (tptt) cc_final: 0.8344 (tptp) REVERT: B 271 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8057 (mm-40) REVERT: B 310 LYS cc_start: 0.7480 (tppt) cc_final: 0.7167 (tttt) REVERT: B 315 THR cc_start: 0.8806 (m) cc_final: 0.8499 (p) REVERT: B 351 TYR cc_start: 0.6806 (p90) cc_final: 0.6330 (p90) REVERT: B 425 LEU cc_start: 0.8071 (mt) cc_final: 0.7607 (mm) REVERT: B 556 ASN cc_start: 0.8023 (p0) cc_final: 0.7657 (p0) REVERT: B 582 LEU cc_start: 0.8009 (mm) cc_final: 0.7633 (mm) REVERT: B 642 VAL cc_start: 0.9209 (t) cc_final: 0.8985 (m) REVERT: B 730 SER cc_start: 0.9064 (p) cc_final: 0.8864 (t) REVERT: B 752 LEU cc_start: 0.8957 (mt) cc_final: 0.8431 (mp) REVERT: B 821 LEU cc_start: 0.7984 (mt) cc_final: 0.7663 (mp) REVERT: B 884 SER cc_start: 0.8738 (m) cc_final: 0.8443 (t) REVERT: B 898 PHE cc_start: 0.7172 (t80) cc_final: 0.6706 (t80) REVERT: B 900 MET cc_start: 0.7894 (mmm) cc_final: 0.7321 (mtt) REVERT: B 933 LYS cc_start: 0.8770 (mttt) cc_final: 0.8182 (mtmm) REVERT: B 1010 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8158 (mm-40) REVERT: B 1071 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: B 1073 LYS cc_start: 0.8492 (tttt) cc_final: 0.8026 (ttmm) REVERT: B 1076 THR cc_start: 0.8238 (m) cc_final: 0.7852 (t) REVERT: B 1084 ASP cc_start: 0.7807 (p0) cc_final: 0.7484 (p0) REVERT: C 49 HIS cc_start: 0.7474 (t70) cc_final: 0.7090 (t70) REVERT: C 62 VAL cc_start: 0.7895 (m) cc_final: 0.7555 (p) REVERT: C 104 TRP cc_start: 0.6869 (m-90) cc_final: 0.6641 (m-90) REVERT: C 170 TYR cc_start: 0.8056 (t80) cc_final: 0.7833 (t80) REVERT: C 195 LYS cc_start: 0.7561 (pttt) cc_final: 0.6806 (tppt) REVERT: C 267 VAL cc_start: 0.8322 (p) cc_final: 0.8079 (t) REVERT: C 281 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: C 289 VAL cc_start: 0.8640 (t) cc_final: 0.8331 (p) REVERT: C 294 ASP cc_start: 0.7849 (m-30) cc_final: 0.7499 (t70) REVERT: C 299 THR cc_start: 0.8622 (m) cc_final: 0.8220 (p) REVERT: C 737 ASP cc_start: 0.8138 (t0) cc_final: 0.7897 (t0) REVERT: C 804 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7758 (mm-40) REVERT: C 821 LEU cc_start: 0.8982 (mt) cc_final: 0.8726 (mt) REVERT: C 884 SER cc_start: 0.9106 (m) cc_final: 0.8699 (t) REVERT: C 935 GLN cc_start: 0.7972 (tt0) cc_final: 0.7697 (tt0) REVERT: C 1006 THR cc_start: 0.8762 (m) cc_final: 0.8465 (p) REVERT: C 1073 LYS cc_start: 0.8674 (tttt) cc_final: 0.8474 (tttt) REVERT: C 1086 LYS cc_start: 0.7287 (mtmm) cc_final: 0.7010 (mtmm) outliers start: 56 outliers final: 32 residues processed: 636 average time/residue: 0.1649 time to fit residues: 160.5224 Evaluate side-chains 567 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 533 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 260 optimal weight: 0.9980 chunk 246 optimal weight: 0.0030 chunk 225 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 292 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 787 GLN A 872 GLN A 955 ASN A1023 ASN A1083 HIS B 134 GLN B 935 GLN B 955 ASN B1011 GLN C 239 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 901 GLN C 955 ASN C1083 HIS C1113 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.167536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.135678 restraints weight = 49002.915| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.83 r_work: 0.3746 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23751 Z= 0.131 Angle : 0.599 15.564 32312 Z= 0.302 Chirality : 0.044 0.179 3667 Planarity : 0.004 0.070 4164 Dihedral : 4.453 21.031 3163 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.24 % Allowed : 12.22 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.15 (0.14), residues: 2911 helix: -0.75 (0.20), residues: 584 sheet: 0.41 (0.19), residues: 565 loop : -1.19 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 355 TYR 0.027 0.001 TYR A 91 PHE 0.037 0.001 PHE B 342 TRP 0.023 0.001 TRP A 104 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00288 (23716) covalent geometry : angle 0.59687 (32242) SS BOND : bond 0.00486 ( 35) SS BOND : angle 1.27604 ( 70) hydrogen bonds : bond 0.04504 ( 684) hydrogen bonds : angle 5.55270 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 546 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6330 (m-10) cc_final: 0.5999 (m-10) REVERT: A 141 LEU cc_start: 0.6290 (mm) cc_final: 0.5199 (tt) REVERT: A 192 PHE cc_start: 0.8044 (m-10) cc_final: 0.7801 (m-80) REVERT: A 305 SER cc_start: 0.8810 (t) cc_final: 0.8526 (m) REVERT: A 321 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7692 (pm20) REVERT: A 539 VAL cc_start: 0.8408 (m) cc_final: 0.8141 (p) REVERT: A 644 GLN cc_start: 0.7606 (tp40) cc_final: 0.7210 (tp40) REVERT: A 752 LEU cc_start: 0.8880 (mt) cc_final: 0.8630 (tp) REVERT: A 764 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8600 (ttpp) REVERT: A 773 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 776 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8398 (ttpp) REVERT: A 780 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 819 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6904 (mt-10) REVERT: A 886 TRP cc_start: 0.8897 (p90) cc_final: 0.8114 (p90) REVERT: A 964 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8841 (mtpp) REVERT: A 969 LYS cc_start: 0.9114 (mttt) cc_final: 0.8874 (mttt) REVERT: A 984 LEU cc_start: 0.8230 (mp) cc_final: 0.7907 (tp) REVERT: A 1019 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8336 (tpp-160) REVERT: A 1038 LYS cc_start: 0.8883 (mttt) cc_final: 0.8574 (mmmm) REVERT: A 1084 ASP cc_start: 0.7892 (p0) cc_final: 0.7162 (p0) REVERT: A 1086 LYS cc_start: 0.8789 (pttt) cc_final: 0.8545 (pttp) REVERT: B 190 ARG cc_start: 0.8363 (mtm180) cc_final: 0.7856 (ptp90) REVERT: B 191 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 195 LYS cc_start: 0.8038 (pttt) cc_final: 0.7397 (tppt) REVERT: B 204 TYR cc_start: 0.5758 (m-80) cc_final: 0.5454 (m-10) REVERT: B 315 THR cc_start: 0.8671 (m) cc_final: 0.8280 (p) REVERT: B 338 PHE cc_start: 0.7748 (m-10) cc_final: 0.7187 (m-10) REVERT: B 340 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 425 LEU cc_start: 0.8097 (mt) cc_final: 0.7646 (mm) REVERT: B 451 TYR cc_start: 0.5897 (m-80) cc_final: 0.5538 (m-80) REVERT: B 556 ASN cc_start: 0.8107 (p0) cc_final: 0.7651 (p0) REVERT: B 642 VAL cc_start: 0.9225 (t) cc_final: 0.9009 (m) REVERT: B 675 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6932 (mm110) REVERT: B 690 GLN cc_start: 0.7789 (mp10) cc_final: 0.7497 (mt0) REVERT: B 773 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 796 TYR cc_start: 0.7451 (t80) cc_final: 0.7219 (t80) REVERT: B 884 SER cc_start: 0.8881 (m) cc_final: 0.8591 (t) REVERT: B 898 PHE cc_start: 0.7726 (t80) cc_final: 0.7409 (t80) REVERT: B 900 MET cc_start: 0.7961 (mmm) cc_final: 0.7540 (mtt) REVERT: B 933 LYS cc_start: 0.8705 (mttt) cc_final: 0.8160 (mtmm) REVERT: B 950 ASP cc_start: 0.8074 (m-30) cc_final: 0.7658 (t0) REVERT: B 957 GLN cc_start: 0.7668 (pp30) cc_final: 0.7352 (pp30) REVERT: B 1005 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8263 (tp40) REVERT: B 1010 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8203 (mm-40) REVERT: B 1051 SER cc_start: 0.8603 (t) cc_final: 0.8105 (p) REVERT: B 1073 LYS cc_start: 0.8605 (tttt) cc_final: 0.8151 (ttmm) REVERT: B 1076 THR cc_start: 0.8596 (m) cc_final: 0.8232 (t) REVERT: B 1084 ASP cc_start: 0.7788 (p0) cc_final: 0.7512 (p0) REVERT: C 41 LYS cc_start: 0.5627 (tptt) cc_final: 0.5075 (tptt) REVERT: C 42 VAL cc_start: 0.8588 (t) cc_final: 0.8335 (m) REVERT: C 49 HIS cc_start: 0.7621 (t70) cc_final: 0.7250 (t70) REVERT: C 207 HIS cc_start: 0.8056 (t-90) cc_final: 0.7729 (t-90) REVERT: C 281 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: C 294 ASP cc_start: 0.7924 (m-30) cc_final: 0.7674 (t70) REVERT: C 299 THR cc_start: 0.8680 (m) cc_final: 0.8293 (p) REVERT: C 314 GLN cc_start: 0.8018 (mp10) cc_final: 0.7782 (mp10) REVERT: C 583 GLU cc_start: 0.7822 (pm20) cc_final: 0.7424 (pm20) REVERT: C 655 TYR cc_start: 0.8555 (t80) cc_final: 0.8318 (t80) REVERT: C 737 ASP cc_start: 0.8136 (t0) cc_final: 0.7864 (t0) REVERT: C 751 ASN cc_start: 0.8409 (m-40) cc_final: 0.8013 (m-40) REVERT: C 790 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8108 (ptpp) REVERT: C 804 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7766 (mm-40) REVERT: C 814 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7750 (mmpt) REVERT: C 821 LEU cc_start: 0.8935 (mt) cc_final: 0.8700 (mt) REVERT: C 825 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8403 (mtpp) REVERT: C 884 SER cc_start: 0.9158 (m) cc_final: 0.8754 (t) REVERT: C 1006 THR cc_start: 0.8775 (m) cc_final: 0.8556 (p) REVERT: C 1073 LYS cc_start: 0.8660 (tttt) cc_final: 0.8326 (ptmm) outliers start: 58 outliers final: 39 residues processed: 575 average time/residue: 0.1576 time to fit residues: 139.3914 Evaluate side-chains 551 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 509 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.0370 chunk 258 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 203 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 563 GLN A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 30 ASN B 343 ASN B 895 GLN B 955 ASN C 239 GLN C1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.163164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131122 restraints weight = 47969.174| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.75 r_work: 0.3676 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23751 Z= 0.124 Angle : 0.579 14.595 32312 Z= 0.290 Chirality : 0.044 0.272 3667 Planarity : 0.004 0.055 4164 Dihedral : 4.285 23.643 3163 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.39 % Allowed : 13.15 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 2911 helix: 0.37 (0.21), residues: 605 sheet: 0.54 (0.20), residues: 575 loop : -1.03 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 357 TYR 0.022 0.001 TYR A 91 PHE 0.020 0.001 PHE A 782 TRP 0.037 0.002 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00278 (23716) covalent geometry : angle 0.57705 (32242) SS BOND : bond 0.00304 ( 35) SS BOND : angle 1.24278 ( 70) hydrogen bonds : bond 0.03851 ( 684) hydrogen bonds : angle 5.17053 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 534 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7974 (t0) cc_final: 0.7467 (t0) REVERT: A 105 ILE cc_start: 0.8061 (mt) cc_final: 0.7769 (mm) REVERT: A 133 PHE cc_start: 0.6373 (m-10) cc_final: 0.5973 (m-10) REVERT: A 191 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 305 SER cc_start: 0.8966 (t) cc_final: 0.8752 (m) REVERT: A 321 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7833 (pm20) REVERT: A 539 VAL cc_start: 0.8373 (m) cc_final: 0.8125 (p) REVERT: A 551 VAL cc_start: 0.8204 (m) cc_final: 0.7850 (p) REVERT: A 644 GLN cc_start: 0.7843 (tp40) cc_final: 0.7492 (tp40) REVERT: A 725 GLU cc_start: 0.8085 (tt0) cc_final: 0.7711 (tt0) REVERT: A 752 LEU cc_start: 0.8926 (mt) cc_final: 0.8689 (tp) REVERT: A 773 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 776 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8123 (ttpp) REVERT: A 886 TRP cc_start: 0.9076 (p90) cc_final: 0.8533 (p90) REVERT: A 900 MET cc_start: 0.8342 (mtm) cc_final: 0.8095 (mtp) REVERT: A 969 LYS cc_start: 0.9159 (mttt) cc_final: 0.8918 (mttt) REVERT: A 1019 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8474 (tpp-160) REVERT: A 1038 LYS cc_start: 0.9079 (mttt) cc_final: 0.8767 (mmmm) REVERT: A 1086 LYS cc_start: 0.8648 (pttt) cc_final: 0.8356 (pttp) REVERT: B 190 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7928 (mtm180) REVERT: B 191 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7432 (mt-10) REVERT: B 195 LYS cc_start: 0.8139 (pttt) cc_final: 0.7506 (tppt) REVERT: B 204 TYR cc_start: 0.6207 (m-80) cc_final: 0.5897 (m-80) REVERT: B 206 LYS cc_start: 0.9036 (tppt) cc_final: 0.8637 (tppt) REVERT: B 388 ASN cc_start: 0.8496 (p0) cc_final: 0.7909 (t0) REVERT: B 516 GLU cc_start: 0.5406 (tm-30) cc_final: 0.3895 (tt0) REVERT: B 528 LYS cc_start: 0.7132 (ttpt) cc_final: 0.5916 (ttpt) REVERT: B 556 ASN cc_start: 0.8140 (p0) cc_final: 0.7708 (p0) REVERT: B 563 GLN cc_start: 0.4905 (tm-30) cc_final: 0.4655 (tm-30) REVERT: B 642 VAL cc_start: 0.9231 (t) cc_final: 0.9026 (m) REVERT: B 690 GLN cc_start: 0.7919 (mp10) cc_final: 0.7580 (mt0) REVERT: B 762 GLN cc_start: 0.8080 (pp30) cc_final: 0.7724 (pp30) REVERT: B 773 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 796 TYR cc_start: 0.7542 (t80) cc_final: 0.7242 (t80) REVERT: B 867 ASP cc_start: 0.7748 (p0) cc_final: 0.7541 (p0) REVERT: B 884 SER cc_start: 0.9000 (m) cc_final: 0.8648 (t) REVERT: B 900 MET cc_start: 0.7965 (mmm) cc_final: 0.7602 (mtm) REVERT: B 933 LYS cc_start: 0.8694 (mttt) cc_final: 0.8134 (mtmm) REVERT: B 957 GLN cc_start: 0.7811 (pp30) cc_final: 0.7575 (pp30) REVERT: B 1005 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8189 (tp40) REVERT: B 1073 LYS cc_start: 0.8549 (tttt) cc_final: 0.8314 (mtpp) REVERT: B 1084 ASP cc_start: 0.7895 (p0) cc_final: 0.7589 (p0) REVERT: C 41 LYS cc_start: 0.5889 (tptt) cc_final: 0.5581 (tptt) REVERT: C 49 HIS cc_start: 0.7428 (t70) cc_final: 0.6945 (t70) REVERT: C 55 PHE cc_start: 0.8339 (m-10) cc_final: 0.7959 (m-10) REVERT: C 119 ILE cc_start: 0.5408 (mm) cc_final: 0.5063 (mm) REVERT: C 281 GLU cc_start: 0.7169 (pp20) cc_final: 0.6728 (pp20) REVERT: C 299 THR cc_start: 0.8757 (m) cc_final: 0.8348 (p) REVERT: C 308 VAL cc_start: 0.8798 (t) cc_final: 0.8392 (p) REVERT: C 317 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: C 583 GLU cc_start: 0.7872 (pm20) cc_final: 0.7612 (pm20) REVERT: C 763 LEU cc_start: 0.7950 (mt) cc_final: 0.7731 (mp) REVERT: C 804 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7799 (mm-40) REVERT: C 821 LEU cc_start: 0.8870 (mt) cc_final: 0.8659 (mt) REVERT: C 884 SER cc_start: 0.9128 (m) cc_final: 0.8767 (t) REVERT: C 957 GLN cc_start: 0.8593 (tt0) cc_final: 0.8230 (tm-30) REVERT: C 969 LYS cc_start: 0.8967 (mttt) cc_final: 0.8644 (mmmm) REVERT: C 995 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7803 (mtm180) REVERT: C 1006 THR cc_start: 0.8753 (m) cc_final: 0.8542 (p) REVERT: C 1019 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7209 (tpt170) outliers start: 62 outliers final: 41 residues processed: 566 average time/residue: 0.1630 time to fit residues: 140.8169 Evaluate side-chains 555 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 513 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 200 optimal weight: 0.5980 chunk 187 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 288 optimal weight: 0.0060 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 292 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN B 52 GLN B 563 GLN B 895 GLN B 914 ASN C 914 ASN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129674 restraints weight = 47725.082| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.71 r_work: 0.3652 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23751 Z= 0.113 Angle : 0.551 12.543 32312 Z= 0.276 Chirality : 0.043 0.215 3667 Planarity : 0.003 0.055 4164 Dihedral : 4.095 22.576 3163 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.51 % Allowed : 14.11 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 2911 helix: 0.90 (0.22), residues: 611 sheet: 0.67 (0.19), residues: 601 loop : -0.96 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.017 0.001 TYR C 655 PHE 0.027 0.001 PHE C 133 TRP 0.042 0.001 TRP A 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00255 (23716) covalent geometry : angle 0.55012 (32242) SS BOND : bond 0.00302 ( 35) SS BOND : angle 0.87232 ( 70) hydrogen bonds : bond 0.03621 ( 684) hydrogen bonds : angle 4.95709 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 520 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6099 (mt-10) REVERT: A 133 PHE cc_start: 0.6292 (m-10) cc_final: 0.5925 (m-10) REVERT: A 191 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 305 SER cc_start: 0.9080 (t) cc_final: 0.8841 (m) REVERT: A 321 GLN cc_start: 0.8543 (mm-40) cc_final: 0.7835 (pm20) REVERT: A 537 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8406 (mmtt) REVERT: A 539 VAL cc_start: 0.8247 (m) cc_final: 0.8004 (p) REVERT: A 644 GLN cc_start: 0.7746 (tp40) cc_final: 0.7435 (tp40) REVERT: A 725 GLU cc_start: 0.8060 (tt0) cc_final: 0.7722 (tt0) REVERT: A 752 LEU cc_start: 0.8923 (mt) cc_final: 0.8681 (tp) REVERT: A 762 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: A 773 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 776 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8129 (ttpp) REVERT: A 790 LYS cc_start: 0.8794 (mttt) cc_final: 0.8348 (mttt) REVERT: A 819 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 969 LYS cc_start: 0.9162 (mttt) cc_final: 0.8912 (mttt) REVERT: A 1019 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8439 (tpp-160) REVERT: A 1038 LYS cc_start: 0.9085 (mttt) cc_final: 0.8738 (mmmm) REVERT: A 1045 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8428 (tmtt) REVERT: A 1086 LYS cc_start: 0.8632 (pttt) cc_final: 0.8345 (pttp) REVERT: A 1091 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7418 (ttm-80) REVERT: B 190 ARG cc_start: 0.8396 (mtm180) cc_final: 0.7922 (mtm180) REVERT: B 191 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 195 LYS cc_start: 0.8276 (pttt) cc_final: 0.7578 (tppt) REVERT: B 204 TYR cc_start: 0.6216 (m-80) cc_final: 0.5939 (m-80) REVERT: B 386 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7645 (ptpt) REVERT: B 516 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4284 (pt0) REVERT: B 528 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6069 (ttpt) REVERT: B 556 ASN cc_start: 0.8212 (p0) cc_final: 0.7779 (p0) REVERT: B 690 GLN cc_start: 0.7914 (mp10) cc_final: 0.7558 (mt0) REVERT: B 698 SER cc_start: 0.8456 (t) cc_final: 0.7747 (m) REVERT: B 762 GLN cc_start: 0.8105 (pp30) cc_final: 0.7702 (pp30) REVERT: B 796 TYR cc_start: 0.7635 (t80) cc_final: 0.7425 (t80) REVERT: B 797 PHE cc_start: 0.7600 (m-10) cc_final: 0.7264 (m-10) REVERT: B 825 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8661 (mttt) REVERT: B 867 ASP cc_start: 0.7733 (p0) cc_final: 0.7500 (p0) REVERT: B 868 GLU cc_start: 0.8094 (tp30) cc_final: 0.7311 (tp30) REVERT: B 884 SER cc_start: 0.9014 (m) cc_final: 0.8665 (t) REVERT: B 933 LYS cc_start: 0.8538 (mttt) cc_final: 0.7989 (mtmm) REVERT: B 955 ASN cc_start: 0.8283 (m-40) cc_final: 0.7923 (t0) REVERT: B 1005 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8197 (tp40) REVERT: B 1073 LYS cc_start: 0.8535 (tttt) cc_final: 0.8274 (mttm) REVERT: C 41 LYS cc_start: 0.5608 (tptt) cc_final: 0.5134 (tptt) REVERT: C 44 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7310 (mtt180) REVERT: C 49 HIS cc_start: 0.7353 (t70) cc_final: 0.6618 (t70) REVERT: C 55 PHE cc_start: 0.8264 (m-10) cc_final: 0.7879 (m-10) REVERT: C 206 LYS cc_start: 0.8813 (tppt) cc_final: 0.8372 (tptp) REVERT: C 281 GLU cc_start: 0.7133 (pp20) cc_final: 0.6709 (pp20) REVERT: C 299 THR cc_start: 0.8675 (m) cc_final: 0.8246 (p) REVERT: C 308 VAL cc_start: 0.8871 (t) cc_final: 0.8480 (p) REVERT: C 317 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7541 (m-40) REVERT: C 583 GLU cc_start: 0.7941 (pm20) cc_final: 0.7482 (pm20) REVERT: C 670 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8726 (mm) REVERT: C 751 ASN cc_start: 0.8678 (m-40) cc_final: 0.8286 (m-40) REVERT: C 804 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7780 (mm-40) REVERT: C 821 LEU cc_start: 0.8843 (mt) cc_final: 0.8630 (mt) REVERT: C 869 MET cc_start: 0.8764 (mtp) cc_final: 0.8551 (mtp) REVERT: C 884 SER cc_start: 0.9061 (m) cc_final: 0.8719 (t) REVERT: C 957 GLN cc_start: 0.8542 (tt0) cc_final: 0.8198 (tm-30) REVERT: C 969 LYS cc_start: 0.8954 (mttt) cc_final: 0.8608 (mmmm) REVERT: C 995 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7810 (mtm180) REVERT: C 1006 THR cc_start: 0.8716 (m) cc_final: 0.8397 (p) REVERT: C 1086 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7273 (mtmm) REVERT: C 1119 ASN cc_start: 0.7671 (t0) cc_final: 0.7339 (t0) outliers start: 65 outliers final: 45 residues processed: 545 average time/residue: 0.1739 time to fit residues: 143.9029 Evaluate side-chains 553 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 504 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 216 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 136 optimal weight: 0.0000 chunk 242 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 179 optimal weight: 0.2980 chunk 67 optimal weight: 0.2980 chunk 270 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 506 GLN A 613 GLN A 762 GLN B 895 GLN C 544 ASN C 564 GLN C 690 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128744 restraints weight = 47782.481| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.71 r_work: 0.3650 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23751 Z= 0.106 Angle : 0.547 11.532 32312 Z= 0.274 Chirality : 0.043 0.153 3667 Planarity : 0.003 0.048 4164 Dihedral : 4.030 20.316 3163 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.39 % Allowed : 14.92 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2911 helix: 1.20 (0.23), residues: 606 sheet: 0.78 (0.20), residues: 582 loop : -0.90 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1014 TYR 0.017 0.001 TYR C 655 PHE 0.020 0.001 PHE A 201 TRP 0.060 0.002 TRP A 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00241 (23716) covalent geometry : angle 0.54619 (32242) SS BOND : bond 0.00353 ( 35) SS BOND : angle 0.88102 ( 70) hydrogen bonds : bond 0.03448 ( 684) hydrogen bonds : angle 4.81651 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 535 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6292 (mt-10) cc_final: 0.6026 (mt-10) REVERT: A 105 ILE cc_start: 0.8107 (mt) cc_final: 0.7873 (mm) REVERT: A 133 PHE cc_start: 0.6130 (m-80) cc_final: 0.5811 (m-10) REVERT: A 191 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 192 PHE cc_start: 0.8336 (m-80) cc_final: 0.8055 (m-80) REVERT: A 321 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7848 (pm20) REVERT: A 539 VAL cc_start: 0.8177 (m) cc_final: 0.7910 (p) REVERT: A 644 GLN cc_start: 0.7773 (tp40) cc_final: 0.7471 (tp40) REVERT: A 725 GLU cc_start: 0.8060 (tt0) cc_final: 0.7792 (tt0) REVERT: A 752 LEU cc_start: 0.8944 (mt) cc_final: 0.8706 (tp) REVERT: A 773 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 776 LYS cc_start: 0.8658 (ttpp) cc_final: 0.7995 (ttpp) REVERT: A 790 LYS cc_start: 0.8618 (mttt) cc_final: 0.8405 (mttt) REVERT: A 819 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 906 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: A 925 ASN cc_start: 0.8058 (m-40) cc_final: 0.7702 (m-40) REVERT: A 969 LYS cc_start: 0.9185 (mttt) cc_final: 0.8945 (mttt) REVERT: A 1019 ARG cc_start: 0.8715 (tpp-160) cc_final: 0.8423 (tpp-160) REVERT: A 1038 LYS cc_start: 0.9141 (mttt) cc_final: 0.8815 (mmmm) REVERT: A 1086 LYS cc_start: 0.8599 (pttt) cc_final: 0.8359 (pttp) REVERT: B 92 PHE cc_start: 0.7787 (t80) cc_final: 0.7492 (t80) REVERT: B 190 ARG cc_start: 0.8373 (mtm180) cc_final: 0.7895 (mtm180) REVERT: B 195 LYS cc_start: 0.8327 (pttt) cc_final: 0.7746 (tppt) REVERT: B 204 TYR cc_start: 0.6299 (m-80) cc_final: 0.5909 (m-80) REVERT: B 351 TYR cc_start: 0.6706 (p90) cc_final: 0.6255 (p90) REVERT: B 386 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7682 (ptpt) REVERT: B 451 TYR cc_start: 0.5765 (m-80) cc_final: 0.5408 (m-80) REVERT: B 516 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4314 (pt0) REVERT: B 528 LYS cc_start: 0.7369 (ttpt) cc_final: 0.6079 (ttmm) REVERT: B 556 ASN cc_start: 0.8232 (p0) cc_final: 0.7790 (p0) REVERT: B 660 TYR cc_start: 0.8667 (m-10) cc_final: 0.8452 (m-10) REVERT: B 690 GLN cc_start: 0.7909 (mp10) cc_final: 0.7556 (mt0) REVERT: B 698 SER cc_start: 0.8414 (t) cc_final: 0.7748 (m) REVERT: B 762 GLN cc_start: 0.8117 (pp30) cc_final: 0.7691 (pp30) REVERT: B 825 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8637 (mttt) REVERT: B 867 ASP cc_start: 0.7724 (p0) cc_final: 0.7467 (p0) REVERT: B 868 GLU cc_start: 0.8066 (tp30) cc_final: 0.7287 (tp30) REVERT: B 884 SER cc_start: 0.8958 (m) cc_final: 0.8467 (t) REVERT: B 887 THR cc_start: 0.7641 (p) cc_final: 0.6555 (p) REVERT: B 933 LYS cc_start: 0.8593 (mttt) cc_final: 0.8048 (mtmm) REVERT: B 960 ASN cc_start: 0.8920 (m-40) cc_final: 0.8545 (t0) REVERT: B 977 LEU cc_start: 0.9239 (mt) cc_final: 0.9022 (mt) REVERT: B 1005 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8169 (tp40) REVERT: B 1073 LYS cc_start: 0.8504 (tttt) cc_final: 0.8256 (mttm) REVERT: C 41 LYS cc_start: 0.5506 (tptt) cc_final: 0.5070 (tptt) REVERT: C 44 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7799 (mtt-85) REVERT: C 49 HIS cc_start: 0.7445 (t70) cc_final: 0.7150 (t70) REVERT: C 55 PHE cc_start: 0.8280 (m-10) cc_final: 0.7874 (m-10) REVERT: C 119 ILE cc_start: 0.5776 (mm) cc_final: 0.5423 (mm) REVERT: C 135 PHE cc_start: 0.6927 (m-80) cc_final: 0.6710 (m-80) REVERT: C 191 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7083 (mm-30) REVERT: C 299 THR cc_start: 0.8706 (m) cc_final: 0.8267 (p) REVERT: C 308 VAL cc_start: 0.8952 (t) cc_final: 0.8581 (p) REVERT: C 317 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (m-40) REVERT: C 670 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8662 (mm) REVERT: C 751 ASN cc_start: 0.8738 (m-40) cc_final: 0.8352 (m-40) REVERT: C 804 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8006 (mm-40) REVERT: C 869 MET cc_start: 0.8770 (mtp) cc_final: 0.8538 (mtp) REVERT: C 884 SER cc_start: 0.9058 (m) cc_final: 0.8719 (t) REVERT: C 906 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: C 957 GLN cc_start: 0.8558 (tt0) cc_final: 0.8201 (tm-30) REVERT: C 969 LYS cc_start: 0.8956 (mttt) cc_final: 0.8613 (mmmm) REVERT: C 995 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7889 (mtm180) REVERT: C 1002 GLN cc_start: 0.8705 (tp40) cc_final: 0.8486 (tp40) REVERT: C 1006 THR cc_start: 0.8679 (m) cc_final: 0.8437 (p) REVERT: C 1119 ASN cc_start: 0.7700 (t0) cc_final: 0.7359 (t0) outliers start: 62 outliers final: 44 residues processed: 566 average time/residue: 0.1675 time to fit residues: 143.7284 Evaluate side-chains 563 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 514 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 233 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 224 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 256 optimal weight: 0.4980 chunk 287 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 613 GLN A 895 GLN A 949 GLN A 965 GLN A 978 ASN B 30 ASN B 239 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 824 ASN B 895 GLN B1106 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119877 restraints weight = 47102.719| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.59 r_work: 0.3505 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23751 Z= 0.225 Angle : 0.674 9.798 32312 Z= 0.348 Chirality : 0.047 0.247 3667 Planarity : 0.004 0.074 4164 Dihedral : 4.685 23.672 3163 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.01 % Allowed : 15.34 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2911 helix: 1.02 (0.22), residues: 606 sheet: 0.60 (0.20), residues: 602 loop : -1.07 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.023 0.002 TYR C 655 PHE 0.033 0.002 PHE C 168 TRP 0.073 0.003 TRP A 104 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00517 (23716) covalent geometry : angle 0.67046 (32242) SS BOND : bond 0.00383 ( 35) SS BOND : angle 1.69571 ( 70) hydrogen bonds : bond 0.04363 ( 684) hydrogen bonds : angle 5.06288 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 550 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8620 (m) cc_final: 0.8158 (p) REVERT: A 191 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 192 PHE cc_start: 0.8380 (m-80) cc_final: 0.8116 (m-80) REVERT: A 207 HIS cc_start: 0.7091 (m170) cc_final: 0.6702 (m170) REVERT: A 239 GLN cc_start: 0.8505 (tt0) cc_final: 0.7728 (tm-30) REVERT: A 321 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8084 (pm20) REVERT: A 539 VAL cc_start: 0.8387 (m) cc_final: 0.8124 (p) REVERT: A 591 SER cc_start: 0.8623 (t) cc_final: 0.8273 (p) REVERT: A 725 GLU cc_start: 0.8172 (tt0) cc_final: 0.7921 (tt0) REVERT: A 752 LEU cc_start: 0.9019 (mt) cc_final: 0.8725 (tp) REVERT: A 773 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 776 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8280 (ttpp) REVERT: A 819 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 861 LEU cc_start: 0.8763 (mm) cc_final: 0.8515 (mt) REVERT: A 935 GLN cc_start: 0.8612 (tt0) cc_final: 0.8304 (tm-30) REVERT: A 969 LYS cc_start: 0.9208 (mttt) cc_final: 0.9007 (mttt) REVERT: A 1019 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8409 (tpp80) REVERT: A 1038 LYS cc_start: 0.9213 (mttt) cc_final: 0.8877 (mmmm) REVERT: B 190 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8283 (ttm110) REVERT: B 191 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 204 TYR cc_start: 0.6755 (m-80) cc_final: 0.6394 (m-80) REVERT: B 309 GLU cc_start: 0.7387 (mp0) cc_final: 0.7049 (mp0) REVERT: B 351 TYR cc_start: 0.6951 (p90) cc_final: 0.6468 (p90) REVERT: B 358 ILE cc_start: 0.8048 (mt) cc_final: 0.7836 (tt) REVERT: B 392 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: B 444 LYS cc_start: 0.8123 (tppt) cc_final: 0.7734 (ttpt) REVERT: B 516 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.3488 (tt0) REVERT: B 528 LYS cc_start: 0.7590 (ttpt) cc_final: 0.6668 (mtmt) REVERT: B 556 ASN cc_start: 0.8409 (p0) cc_final: 0.8085 (p0) REVERT: B 603 ASN cc_start: 0.8662 (p0) cc_final: 0.8431 (p0) REVERT: B 671 CYS cc_start: 0.6887 (t) cc_final: 0.6687 (t) REVERT: B 690 GLN cc_start: 0.7990 (mp10) cc_final: 0.7581 (mt0) REVERT: B 702 GLU cc_start: 0.6641 (tp30) cc_final: 0.6441 (tp30) REVERT: B 762 GLN cc_start: 0.8443 (pp30) cc_final: 0.7996 (pp30) REVERT: B 814 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7824 (mmtt) REVERT: B 867 ASP cc_start: 0.7897 (p0) cc_final: 0.7651 (p0) REVERT: B 868 GLU cc_start: 0.8264 (tp30) cc_final: 0.7523 (tp30) REVERT: B 884 SER cc_start: 0.8955 (m) cc_final: 0.8389 (t) REVERT: B 933 LYS cc_start: 0.8679 (mttt) cc_final: 0.8155 (mtmm) REVERT: B 960 ASN cc_start: 0.8903 (m-40) cc_final: 0.8667 (t0) REVERT: B 1077 THR cc_start: 0.9145 (t) cc_final: 0.8907 (m) REVERT: B 1111 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8094 (mp0) REVERT: C 31 SER cc_start: 0.8238 (t) cc_final: 0.7983 (p) REVERT: C 41 LYS cc_start: 0.5852 (tptt) cc_final: 0.5392 (tptt) REVERT: C 44 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: C 55 PHE cc_start: 0.8390 (m-10) cc_final: 0.8048 (m-10) REVERT: C 191 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7552 (mt-10) REVERT: C 281 GLU cc_start: 0.7066 (pp20) cc_final: 0.6789 (pp20) REVERT: C 289 VAL cc_start: 0.8853 (t) cc_final: 0.8499 (p) REVERT: C 299 THR cc_start: 0.8729 (m) cc_final: 0.8257 (p) REVERT: C 304 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8748 (mmmm) REVERT: C 308 VAL cc_start: 0.9066 (t) cc_final: 0.8665 (p) REVERT: C 317 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7715 (m-40) REVERT: C 613 GLN cc_start: 0.7894 (tp40) cc_final: 0.7309 (mt0) REVERT: C 737 ASP cc_start: 0.8378 (t0) cc_final: 0.7993 (t0) REVERT: C 739 THR cc_start: 0.8626 (m) cc_final: 0.8306 (p) REVERT: C 751 ASN cc_start: 0.8847 (m-40) cc_final: 0.8505 (m-40) REVERT: C 804 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8057 (mm110) REVERT: C 884 SER cc_start: 0.9090 (m) cc_final: 0.8702 (t) REVERT: C 957 GLN cc_start: 0.8621 (tt0) cc_final: 0.8336 (tm-30) REVERT: C 995 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8063 (mtm180) REVERT: C 1006 THR cc_start: 0.8782 (m) cc_final: 0.8500 (p) REVERT: C 1029 MET cc_start: 0.8659 (tpp) cc_final: 0.8358 (ttm) REVERT: C 1081 ILE cc_start: 0.8356 (pt) cc_final: 0.8018 (mt) REVERT: C 1127 ASP cc_start: 0.8282 (p0) cc_final: 0.7954 (p0) outliers start: 78 outliers final: 47 residues processed: 590 average time/residue: 0.1663 time to fit residues: 149.3118 Evaluate side-chains 562 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 512 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 978 ASN B 188 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 957 GLN B1002 GLN B1119 ASN C 239 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.148150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115559 restraints weight = 46728.311| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.53 r_work: 0.3529 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23751 Z= 0.173 Angle : 0.627 11.705 32312 Z= 0.317 Chirality : 0.045 0.193 3667 Planarity : 0.004 0.045 4164 Dihedral : 4.548 22.434 3163 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.31 % Allowed : 17.31 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2911 helix: 1.17 (0.22), residues: 613 sheet: 0.52 (0.19), residues: 609 loop : -1.08 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.019 0.001 TYR C1067 PHE 0.039 0.002 PHE C1103 TRP 0.078 0.002 TRP A 104 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00402 (23716) covalent geometry : angle 0.62456 (32242) SS BOND : bond 0.00336 ( 35) SS BOND : angle 1.29278 ( 70) hydrogen bonds : bond 0.03927 ( 684) hydrogen bonds : angle 4.95314 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 541 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8650 (m) cc_final: 0.8199 (p) REVERT: A 191 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 192 PHE cc_start: 0.8397 (m-80) cc_final: 0.8128 (m-80) REVERT: A 239 GLN cc_start: 0.8397 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 321 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8374 (pm20) REVERT: A 591 SER cc_start: 0.8596 (t) cc_final: 0.8217 (p) REVERT: A 654 GLU cc_start: 0.8384 (tt0) cc_final: 0.8129 (tt0) REVERT: A 725 GLU cc_start: 0.8098 (tt0) cc_final: 0.7661 (tt0) REVERT: A 738 CYS cc_start: 0.6603 (m) cc_final: 0.6402 (m) REVERT: A 752 LEU cc_start: 0.8988 (mt) cc_final: 0.8728 (tp) REVERT: A 773 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 776 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8004 (ttpp) REVERT: A 861 LEU cc_start: 0.8773 (mm) cc_final: 0.8568 (mt) REVERT: A 894 LEU cc_start: 0.8363 (mt) cc_final: 0.8052 (mm) REVERT: A 935 GLN cc_start: 0.8544 (tt0) cc_final: 0.8251 (tm-30) REVERT: A 1019 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8398 (tpp80) REVERT: A 1038 LYS cc_start: 0.9211 (mttt) cc_final: 0.8860 (mmmm) REVERT: B 191 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 309 GLU cc_start: 0.7514 (mp0) cc_final: 0.7151 (mp0) REVERT: B 351 TYR cc_start: 0.7008 (p90) cc_final: 0.6360 (p90) REVERT: B 356 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8390 (mmtt) REVERT: B 358 ILE cc_start: 0.8041 (mt) cc_final: 0.7675 (tt) REVERT: B 396 TYR cc_start: 0.7540 (m-10) cc_final: 0.7220 (m-80) REVERT: B 444 LYS cc_start: 0.7985 (tppt) cc_final: 0.7615 (ttpt) REVERT: B 528 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6366 (mtmt) REVERT: B 556 ASN cc_start: 0.8358 (p0) cc_final: 0.8016 (p0) REVERT: B 584 ILE cc_start: 0.8225 (pt) cc_final: 0.8019 (pt) REVERT: B 660 TYR cc_start: 0.8881 (m-10) cc_final: 0.8436 (m-10) REVERT: B 690 GLN cc_start: 0.7987 (mp10) cc_final: 0.7579 (mt0) REVERT: B 698 SER cc_start: 0.8523 (t) cc_final: 0.7688 (m) REVERT: B 762 GLN cc_start: 0.8404 (pp30) cc_final: 0.7980 (pp30) REVERT: B 814 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7833 (mmtt) REVERT: B 867 ASP cc_start: 0.7827 (p0) cc_final: 0.7550 (p0) REVERT: B 868 GLU cc_start: 0.8168 (tp30) cc_final: 0.7435 (tp30) REVERT: B 884 SER cc_start: 0.8883 (m) cc_final: 0.8442 (p) REVERT: B 935 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8316 (tm-30) REVERT: B 949 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7725 (tm-30) REVERT: B 960 ASN cc_start: 0.8910 (m-40) cc_final: 0.8707 (t0) REVERT: B 1077 THR cc_start: 0.9118 (t) cc_final: 0.8858 (m) REVERT: B 1111 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8014 (pt0) REVERT: C 31 SER cc_start: 0.8339 (t) cc_final: 0.8033 (p) REVERT: C 44 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8128 (mtt-85) REVERT: C 49 HIS cc_start: 0.7796 (t70) cc_final: 0.7587 (t-90) REVERT: C 55 PHE cc_start: 0.8333 (m-10) cc_final: 0.7918 (m-10) REVERT: C 170 TYR cc_start: 0.8336 (t80) cc_final: 0.7757 (t80) REVERT: C 191 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7613 (mt-10) REVERT: C 281 GLU cc_start: 0.7246 (pp20) cc_final: 0.6884 (pp20) REVERT: C 299 THR cc_start: 0.8701 (m) cc_final: 0.8246 (p) REVERT: C 304 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8719 (mmmm) REVERT: C 534 VAL cc_start: 0.8949 (t) cc_final: 0.8728 (m) REVERT: C 583 GLU cc_start: 0.7432 (pm20) cc_final: 0.6711 (mp0) REVERT: C 613 GLN cc_start: 0.7947 (tp40) cc_final: 0.7363 (mt0) REVERT: C 710 ASN cc_start: 0.9011 (p0) cc_final: 0.8734 (p0) REVERT: C 739 THR cc_start: 0.8579 (m) cc_final: 0.8311 (p) REVERT: C 751 ASN cc_start: 0.8872 (m-40) cc_final: 0.8458 (m-40) REVERT: C 816 SER cc_start: 0.8209 (p) cc_final: 0.7864 (m) REVERT: C 884 SER cc_start: 0.9080 (m) cc_final: 0.8725 (t) REVERT: C 906 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: C 957 GLN cc_start: 0.8550 (tt0) cc_final: 0.8279 (tm-30) REVERT: C 995 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.8054 (mtm180) REVERT: C 1006 THR cc_start: 0.8764 (m) cc_final: 0.8501 (p) REVERT: C 1127 ASP cc_start: 0.8321 (p0) cc_final: 0.7995 (p0) outliers start: 60 outliers final: 44 residues processed: 569 average time/residue: 0.1629 time to fit residues: 141.3945 Evaluate side-chains 561 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 516 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 291 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 161 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS A 613 GLN B 895 GLN B 957 GLN C 755 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.150076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117720 restraints weight = 46979.095| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.54 r_work: 0.3572 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23751 Z= 0.126 Angle : 0.611 9.469 32312 Z= 0.309 Chirality : 0.044 0.178 3667 Planarity : 0.004 0.041 4164 Dihedral : 4.397 21.244 3163 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.97 % Allowed : 18.12 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 2911 helix: 1.41 (0.22), residues: 601 sheet: 0.54 (0.20), residues: 610 loop : -1.03 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.023 0.001 TYR C 655 PHE 0.035 0.002 PHE C1103 TRP 0.052 0.002 TRP A 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00295 (23716) covalent geometry : angle 0.60928 (32242) SS BOND : bond 0.00280 ( 35) SS BOND : angle 1.22042 ( 70) hydrogen bonds : bond 0.03599 ( 684) hydrogen bonds : angle 4.82453 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 530 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8647 (m) cc_final: 0.8164 (p) REVERT: A 191 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7858 (mp0) REVERT: A 192 PHE cc_start: 0.8335 (m-80) cc_final: 0.8110 (m-80) REVERT: A 239 GLN cc_start: 0.8375 (tt0) cc_final: 0.7623 (tm-30) REVERT: A 537 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8380 (mmtt) REVERT: A 591 SER cc_start: 0.8629 (t) cc_final: 0.8250 (p) REVERT: A 752 LEU cc_start: 0.8918 (mt) cc_final: 0.8700 (tp) REVERT: A 773 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 776 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8206 (ttpp) REVERT: A 861 LEU cc_start: 0.8727 (mm) cc_final: 0.8519 (mt) REVERT: A 1017 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8079 (mp0) REVERT: A 1019 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8335 (tpp80) REVERT: A 1038 LYS cc_start: 0.9182 (mttt) cc_final: 0.8872 (mmmm) REVERT: A 1045 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8455 (tptt) REVERT: A 1084 ASP cc_start: 0.7986 (p0) cc_final: 0.7369 (p0) REVERT: B 191 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7098 (mt-10) REVERT: B 309 GLU cc_start: 0.7497 (mp0) cc_final: 0.7282 (mp0) REVERT: B 351 TYR cc_start: 0.6737 (p90) cc_final: 0.6165 (p90) REVERT: B 356 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8515 (mmtt) REVERT: B 358 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7584 (tt) REVERT: B 396 TYR cc_start: 0.7583 (m-10) cc_final: 0.7334 (m-80) REVERT: B 444 LYS cc_start: 0.7790 (tppt) cc_final: 0.7472 (ttpt) REVERT: B 528 LYS cc_start: 0.7352 (ttpt) cc_final: 0.6363 (mtmt) REVERT: B 556 ASN cc_start: 0.8247 (p0) cc_final: 0.7973 (p0) REVERT: B 584 ILE cc_start: 0.8137 (pt) cc_final: 0.7931 (pt) REVERT: B 660 TYR cc_start: 0.8869 (m-10) cc_final: 0.8465 (m-10) REVERT: B 674 TYR cc_start: 0.8570 (t80) cc_final: 0.8005 (t80) REVERT: B 690 GLN cc_start: 0.7910 (mp10) cc_final: 0.7489 (mt0) REVERT: B 698 SER cc_start: 0.8505 (t) cc_final: 0.7643 (m) REVERT: B 762 GLN cc_start: 0.8263 (pp30) cc_final: 0.7868 (pp30) REVERT: B 814 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7776 (mmtt) REVERT: B 867 ASP cc_start: 0.7751 (p0) cc_final: 0.7487 (p0) REVERT: B 868 GLU cc_start: 0.8111 (tp30) cc_final: 0.7437 (tp30) REVERT: B 884 SER cc_start: 0.8863 (m) cc_final: 0.8538 (t) REVERT: B 921 LYS cc_start: 0.8481 (tppt) cc_final: 0.8112 (tptm) REVERT: B 935 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 949 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7710 (tm-30) REVERT: B 1111 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8082 (pt0) REVERT: C 31 SER cc_start: 0.8198 (t) cc_final: 0.7895 (p) REVERT: C 55 PHE cc_start: 0.8251 (m-10) cc_final: 0.7853 (m-10) REVERT: C 170 TYR cc_start: 0.8241 (t80) cc_final: 0.7746 (t80) REVERT: C 191 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7480 (mm-30) REVERT: C 281 GLU cc_start: 0.7213 (pp20) cc_final: 0.6891 (pp20) REVERT: C 299 THR cc_start: 0.8766 (m) cc_final: 0.8313 (p) REVERT: C 304 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8691 (mmmm) REVERT: C 536 ASN cc_start: 0.8557 (m110) cc_final: 0.8326 (m110) REVERT: C 583 GLU cc_start: 0.7362 (pm20) cc_final: 0.6673 (mp0) REVERT: C 613 GLN cc_start: 0.7927 (tp40) cc_final: 0.7430 (mt0) REVERT: C 710 ASN cc_start: 0.8967 (p0) cc_final: 0.8684 (p0) REVERT: C 737 ASP cc_start: 0.8182 (t0) cc_final: 0.7854 (t0) REVERT: C 739 THR cc_start: 0.8482 (m) cc_final: 0.8202 (p) REVERT: C 751 ASN cc_start: 0.8879 (m-40) cc_final: 0.8503 (m-40) REVERT: C 817 PHE cc_start: 0.8140 (t80) cc_final: 0.7786 (t80) REVERT: C 884 SER cc_start: 0.9085 (m) cc_final: 0.8758 (t) REVERT: C 906 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: C 955 ASN cc_start: 0.8001 (m110) cc_final: 0.7597 (t0) REVERT: C 957 GLN cc_start: 0.8502 (tt0) cc_final: 0.8273 (tm-30) REVERT: C 995 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7954 (mtm180) REVERT: C 1006 THR cc_start: 0.8726 (m) cc_final: 0.8488 (p) REVERT: C 1127 ASP cc_start: 0.8156 (p0) cc_final: 0.7851 (p0) outliers start: 51 outliers final: 40 residues processed: 557 average time/residue: 0.1753 time to fit residues: 147.4300 Evaluate side-chains 561 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 519 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 275 optimal weight: 1.9990 chunk 193 optimal weight: 0.2980 chunk 287 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 957 GLN C 755 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.116609 restraints weight = 46597.789| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.50 r_work: 0.3535 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23751 Z= 0.154 Angle : 0.640 9.038 32312 Z= 0.323 Chirality : 0.045 0.177 3667 Planarity : 0.004 0.041 4164 Dihedral : 4.431 23.323 3163 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 18.89 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 2911 helix: 1.50 (0.22), residues: 598 sheet: 0.50 (0.19), residues: 621 loop : -1.02 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.023 0.001 TYR C 655 PHE 0.033 0.002 PHE C1103 TRP 0.053 0.002 TRP A 104 HIS 0.008 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (23716) covalent geometry : angle 0.63809 (32242) SS BOND : bond 0.00320 ( 35) SS BOND : angle 1.30543 ( 70) hydrogen bonds : bond 0.03691 ( 684) hydrogen bonds : angle 4.82320 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5822 Ramachandran restraints generated. 2911 Oldfield, 0 Emsley, 2911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 529 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8639 (m) cc_final: 0.8193 (p) REVERT: A 101 ILE cc_start: 0.8407 (pt) cc_final: 0.8152 (mp) REVERT: A 191 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7849 (mp0) REVERT: A 192 PHE cc_start: 0.8362 (m-80) cc_final: 0.8150 (m-80) REVERT: A 239 GLN cc_start: 0.8495 (tt0) cc_final: 0.7684 (tm-30) REVERT: A 537 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8452 (mmtt) REVERT: A 581 THR cc_start: 0.7556 (p) cc_final: 0.6839 (t) REVERT: A 591 SER cc_start: 0.8646 (t) cc_final: 0.8247 (p) REVERT: A 752 LEU cc_start: 0.8925 (mt) cc_final: 0.8723 (tp) REVERT: A 773 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 776 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8065 (ttpp) REVERT: A 1017 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8123 (mp0) REVERT: A 1019 ARG cc_start: 0.8683 (tpp-160) cc_final: 0.8379 (tpp80) REVERT: A 1038 LYS cc_start: 0.9188 (mttt) cc_final: 0.8854 (mmmm) REVERT: A 1084 ASP cc_start: 0.7997 (p0) cc_final: 0.7728 (p0) REVERT: B 141 LEU cc_start: 0.7215 (pt) cc_final: 0.7000 (mm) REVERT: B 191 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 309 GLU cc_start: 0.7602 (mp0) cc_final: 0.7335 (mp0) REVERT: B 339 ASP cc_start: 0.8035 (p0) cc_final: 0.7773 (p0) REVERT: B 351 TYR cc_start: 0.6932 (p90) cc_final: 0.6321 (p90) REVERT: B 356 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8525 (mmtt) REVERT: B 358 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7510 (tt) REVERT: B 444 LYS cc_start: 0.7915 (tppt) cc_final: 0.7536 (ttpt) REVERT: B 528 LYS cc_start: 0.7266 (ttpt) cc_final: 0.6736 (mtmt) REVERT: B 556 ASN cc_start: 0.8327 (p0) cc_final: 0.8045 (p0) REVERT: B 660 TYR cc_start: 0.8945 (m-10) cc_final: 0.8604 (m-10) REVERT: B 674 TYR cc_start: 0.8599 (t80) cc_final: 0.8151 (t80) REVERT: B 690 GLN cc_start: 0.7975 (mp10) cc_final: 0.7439 (mt0) REVERT: B 698 SER cc_start: 0.8527 (t) cc_final: 0.7684 (m) REVERT: B 762 GLN cc_start: 0.8406 (pp30) cc_final: 0.7988 (pp30) REVERT: B 814 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7852 (mmtt) REVERT: B 867 ASP cc_start: 0.7811 (p0) cc_final: 0.7520 (p0) REVERT: B 868 GLU cc_start: 0.8237 (tp30) cc_final: 0.7526 (tp30) REVERT: B 884 SER cc_start: 0.8842 (m) cc_final: 0.8332 (p) REVERT: B 921 LYS cc_start: 0.8560 (tppt) cc_final: 0.8163 (tptm) REVERT: B 935 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 949 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7697 (tm-30) REVERT: B 955 ASN cc_start: 0.8292 (m-40) cc_final: 0.7956 (t0) REVERT: B 1071 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: B 1111 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8064 (pt0) REVERT: C 31 SER cc_start: 0.8229 (t) cc_final: 0.7952 (p) REVERT: C 55 PHE cc_start: 0.8298 (m-10) cc_final: 0.7768 (m-10) REVERT: C 170 TYR cc_start: 0.8368 (t80) cc_final: 0.7810 (t80) REVERT: C 191 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7621 (mm-30) REVERT: C 281 GLU cc_start: 0.7288 (pp20) cc_final: 0.6895 (pp20) REVERT: C 299 THR cc_start: 0.8720 (m) cc_final: 0.8273 (p) REVERT: C 304 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8705 (mmmm) REVERT: C 583 GLU cc_start: 0.7662 (pm20) cc_final: 0.6958 (mp0) REVERT: C 613 GLN cc_start: 0.7997 (tp40) cc_final: 0.7476 (mt0) REVERT: C 737 ASP cc_start: 0.8288 (t0) cc_final: 0.7988 (t0) REVERT: C 739 THR cc_start: 0.8607 (m) cc_final: 0.8357 (p) REVERT: C 751 ASN cc_start: 0.8919 (m-40) cc_final: 0.8545 (m-40) REVERT: C 804 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8086 (mm-40) REVERT: C 884 SER cc_start: 0.9079 (m) cc_final: 0.8715 (t) REVERT: C 955 ASN cc_start: 0.8007 (m110) cc_final: 0.7576 (t0) REVERT: C 957 GLN cc_start: 0.8570 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 995 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8093 (mtm180) REVERT: C 1006 THR cc_start: 0.8675 (m) cc_final: 0.8441 (p) REVERT: C 1127 ASP cc_start: 0.8297 (p0) cc_final: 0.7981 (p0) outliers start: 49 outliers final: 44 residues processed: 554 average time/residue: 0.1657 time to fit residues: 140.2637 Evaluate side-chains 568 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 522 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 258 optimal weight: 0.5980 chunk 189 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** 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 = 0.4104 r_free = 0.4104 target = 0.148487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116358 restraints weight = 46815.209| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.50 r_work: 0.3521 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23751 Z= 0.151 Angle : 0.632 9.054 32312 Z= 0.321 Chirality : 0.045 0.155 3667 Planarity : 0.004 0.053 4164 Dihedral : 4.409 22.294 3163 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.00 % Allowed : 18.97 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 2911 helix: 1.44 (0.22), residues: 606 sheet: 0.51 (0.20), residues: 606 loop : -1.03 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 44 TYR 0.023 0.001 TYR C 655 PHE 0.034 0.002 PHE C1103 TRP 0.049 0.002 TRP A 104 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00352 (23716) covalent geometry : angle 0.63016 (32242) SS BOND : bond 0.00288 ( 35) SS BOND : angle 1.22201 ( 70) hydrogen bonds : bond 0.03667 ( 684) hydrogen bonds : angle 4.80428 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6090.18 seconds wall clock time: 104 minutes 40.53 seconds (6280.53 seconds total)