Starting phenix.real_space_refine on Thu Mar 5 19:56:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk2_32556/03_2026/7wk2_32556.cif" } resolution = 3.1 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= 0.030 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 114 5.16 5 C 15921 2.51 5 N 4146 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 24879 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} 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': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Time building chain proxies: 5.62, per 1000 atoms: 0.23 Number of scatterers: 24879 At special positions: 0 Unit cell: (148.648, 144.276, 178.159, 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 114 16.00 O 4698 8.00 N 4146 7.00 C 15921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.96 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.70 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=2.76 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.90 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 904.2 milliseconds 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 46 sheets defined 21.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.816A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.837A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.867A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.693A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.567A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.735A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.509A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.539A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.668A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.963A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.890A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.502A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.806A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.868A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.650A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.382A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.844A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.936A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.526A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.842A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 763 through 783 removed outlier: 3.669A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.738A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.609A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.821A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.644A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.514A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.827A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.524A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1031 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B1012 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.602A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.509A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.302A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.961A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.535A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.581A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 removed outlier: 3.824A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.896A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.789A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.631A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.753A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (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: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.671A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.665A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.883A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.287A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.516A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.872A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.880A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.580A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 359 removed outlier: 3.793A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.143A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.583A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.713A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.545A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.682A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.185A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.370A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.558A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.673A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.690A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.519A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.879A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.501A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.534A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.201A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.843A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.590A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.506A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.580A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.474A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.037A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.531A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.953A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.788A 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 728 removed outlier: 3.750A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.742A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.978A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 716 hydrogen bonds defined for protein. 1941 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: 5.63 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4060 1.30 - 1.43: 6814 1.43 - 1.56: 14441 1.56 - 1.70: 2 1.70 - 1.83: 144 Bond restraints: 25461 Sorted by residual: bond pdb=" CA ASN A 317 " pdb=" C ASN A 317 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.21e-02 6.83e+03 5.12e+01 bond pdb=" C THR B 573 " pdb=" O THR B 573 " ideal model delta sigma weight residual 1.234 1.166 0.068 1.35e-02 5.49e+03 2.51e+01 bond pdb=" C LYS A 856 " pdb=" O LYS A 856 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.44e-02 4.82e+03 2.49e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.34e-02 1.83e+03 2.40e+01 bond pdb=" C GLY A 857 " pdb=" O GLY A 857 " ideal model delta sigma weight residual 1.238 1.167 0.071 1.45e-02 4.76e+03 2.38e+01 ... (remaining 25456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 33901 2.46 - 4.92: 612 4.92 - 7.39: 86 7.39 - 9.85: 13 9.85 - 12.31: 8 Bond angle restraints: 34620 Sorted by residual: angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.21 102.90 12.31 1.30e+00 5.92e-01 8.97e+01 angle pdb=" N THR B 573 " pdb=" CA THR B 573 " pdb=" C THR B 573 " ideal model delta sigma weight residual 110.53 121.50 -10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" C ASP B 568 " pdb=" N ILE B 569 " pdb=" CA ILE B 569 " ideal model delta sigma weight residual 120.42 129.38 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 132.46 -10.92 1.91e+00 2.74e-01 3.27e+01 ... (remaining 34615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 14918 22.07 - 44.15: 248 44.15 - 66.22: 29 66.22 - 88.30: 0 88.30 - 110.37: 3 Dihedral angle restraints: 15198 sinusoidal: 5958 harmonic: 9240 Sorted by residual: dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N ARG A 158 " pdb=" CA ARG A 158 " ideal model delta harmonic sigma weight residual 180.00 69.63 110.37 0 5.00e+00 4.00e-02 4.87e+02 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 180.00 71.18 108.82 0 5.00e+00 4.00e-02 4.74e+02 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 180.00 71.66 108.34 0 5.00e+00 4.00e-02 4.70e+02 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3569 0.099 - 0.197: 323 0.197 - 0.296: 22 0.296 - 0.395: 0 0.395 - 0.493: 1 Chirality restraints: 3915 Sorted by residual: chirality pdb=" CA THR B 573 " pdb=" N THR B 573 " pdb=" C THR B 573 " pdb=" CB THR B 573 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.08e+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 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 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 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3912 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 854 " -0.025 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS A 854 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS A 854 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 855 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 317 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN A 317 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 317 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 318 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 25 " 0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO C 26 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.052 5.00e-02 4.00e+02 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 7 2.31 - 2.96: 10641 2.96 - 3.61: 30789 3.61 - 4.25: 54415 4.25 - 4.90: 87777 Nonbonded interactions: 183629 Sorted by model distance: nonbonded pdb=" CZ PHE B 759 " pdb=" CD1 PHE C 970 " model vdw 1.667 3.640 nonbonded pdb=" CZ PHE B 759 " pdb=" CE1 PHE C 970 " model vdw 1.862 3.640 nonbonded pdb=" O THR B 761 " pdb=" CG GLN B 762 " model vdw 1.864 3.440 nonbonded pdb=" CE1 PHE B 759 " pdb=" CE1 PHE C 970 " model vdw 2.040 3.640 nonbonded pdb=" N ASN A 317 " pdb=" OD1 ASN A 317 " model vdw 2.180 3.120 ... (remaining 183624 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.900 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.012 0.925 25501 Z= 0.591 Angle : 0.924 48.119 34698 Z= 0.524 Chirality : 0.055 0.493 3915 Planarity : 0.007 0.099 4473 Dihedral : 8.836 110.369 9129 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 0.22 % Allowed : 0.65 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.00 (0.12), residues: 3123 helix: -4.95 (0.06), residues: 540 sheet: -0.04 (0.18), residues: 531 loop : -1.76 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 408 TYR 0.020 0.002 TYR C 904 PHE 0.038 0.003 PHE A 855 TRP 0.014 0.002 TRP B 633 HIS 0.016 0.002 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00611 (25461) covalent geometry : angle 0.83659 (34620) SS BOND : bond 0.25708 ( 39) SS BOND : angle 8.32646 ( 78) hydrogen bonds : bond 0.34110 ( 704) hydrogen bonds : angle 10.87116 ( 1941) Misc. bond : bond 0.10105 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 790 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6817 (mtt90) cc_final: 0.6497 (mpt180) REVERT: A 191 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 308 VAL cc_start: 0.7832 (t) cc_final: 0.7571 (p) REVERT: A 356 LYS cc_start: 0.7665 (tptt) cc_final: 0.7426 (ttmt) REVERT: A 399 SER cc_start: 0.7897 (t) cc_final: 0.6911 (m) REVERT: A 537 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7707 (mtpp) REVERT: A 595 VAL cc_start: 0.8145 (t) cc_final: 0.7871 (m) REVERT: A 736 VAL cc_start: 0.9048 (t) cc_final: 0.8821 (p) REVERT: A 776 LYS cc_start: 0.7785 (mttt) cc_final: 0.7453 (mttt) REVERT: A 875 SER cc_start: 0.8619 (p) cc_final: 0.8316 (m) REVERT: A 905 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6277 (mtt90) REVERT: A 969 LYS cc_start: 0.8462 (mttt) cc_final: 0.8132 (mttm) REVERT: A 986 PRO cc_start: 0.7590 (Cg_exo) cc_final: 0.7370 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7922 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1028 LYS cc_start: 0.8017 (mttt) cc_final: 0.7267 (mttm) REVERT: A 1040 VAL cc_start: 0.7300 (t) cc_final: 0.7025 (t) REVERT: A 1041 ASP cc_start: 0.7266 (m-30) cc_final: 0.7060 (m-30) REVERT: A 1075 PHE cc_start: 0.6539 (m-10) cc_final: 0.6266 (m-80) REVERT: B 30 ASN cc_start: 0.8058 (m-40) cc_final: 0.7827 (p0) REVERT: B 54 LEU cc_start: 0.8118 (mt) cc_final: 0.7858 (mt) REVERT: B 125 ASN cc_start: 0.7469 (m-40) cc_final: 0.7048 (t0) REVERT: B 129 LYS cc_start: 0.7531 (mttt) cc_final: 0.7299 (mtmt) REVERT: B 177 MET cc_start: 0.1028 (mtt) cc_final: 0.0743 (mtt) REVERT: B 351 TYR cc_start: 0.7184 (p90) cc_final: 0.6509 (p90) REVERT: B 584 ILE cc_start: 0.8116 (mt) cc_final: 0.7899 (tt) REVERT: B 734 THR cc_start: 0.8121 (p) cc_final: 0.7006 (m) REVERT: B 748 GLU cc_start: 0.7332 (tp30) cc_final: 0.7120 (tt0) REVERT: B 768 THR cc_start: 0.8334 (m) cc_final: 0.8044 (p) REVERT: B 797 PHE cc_start: 0.6301 (m-10) cc_final: 0.6076 (m-10) REVERT: B 952 VAL cc_start: 0.8222 (t) cc_final: 0.8005 (m) REVERT: B 979 ASP cc_start: 0.7615 (m-30) cc_final: 0.7330 (m-30) REVERT: B 981 PHE cc_start: 0.6672 (t80) cc_final: 0.6423 (t80) REVERT: B 1073 LYS cc_start: 0.8047 (tttt) cc_final: 0.7774 (mtpp) REVERT: B 1084 ASP cc_start: 0.6391 (p0) cc_final: 0.5251 (p0) REVERT: B 1122 VAL cc_start: 0.8343 (t) cc_final: 0.8102 (p) REVERT: C 195 LYS cc_start: 0.8581 (pttt) cc_final: 0.7927 (pttp) REVERT: C 300 LYS cc_start: 0.7596 (mttt) cc_final: 0.7256 (mttp) REVERT: C 309 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6745 (mt-10) REVERT: C 323 THR cc_start: 0.8240 (m) cc_final: 0.6801 (p) REVERT: C 358 ILE cc_start: 0.7548 (mt) cc_final: 0.7343 (mt) REVERT: C 386 LYS cc_start: 0.7888 (mttt) cc_final: 0.7334 (mttt) REVERT: C 390 LEU cc_start: 0.8290 (mt) cc_final: 0.7883 (mt) REVERT: C 559 PHE cc_start: 0.6161 (m-10) cc_final: 0.5776 (m-10) REVERT: C 595 VAL cc_start: 0.8305 (t) cc_final: 0.7982 (p) REVERT: C 739 THR cc_start: 0.7770 (m) cc_final: 0.7464 (m) REVERT: C 752 LEU cc_start: 0.8992 (mp) cc_final: 0.8789 (mt) REVERT: C 827 THR cc_start: 0.7626 (p) cc_final: 0.7246 (p) REVERT: C 867 ASP cc_start: 0.7376 (m-30) cc_final: 0.7144 (m-30) REVERT: C 868 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6525 (mm-30) REVERT: C 873 TYR cc_start: 0.8062 (m-80) cc_final: 0.7759 (m-10) REVERT: C 875 SER cc_start: 0.8787 (p) cc_final: 0.8495 (m) REVERT: C 884 SER cc_start: 0.7752 (m) cc_final: 0.7501 (t) REVERT: C 969 LYS cc_start: 0.8758 (mttt) cc_final: 0.8519 (mttt) REVERT: C 984 LEU cc_start: 0.7707 (mt) cc_final: 0.7480 (mp) REVERT: C 988 GLU cc_start: 0.7939 (tp30) cc_final: 0.7352 (tp30) REVERT: C 1028 LYS cc_start: 0.8030 (mttt) cc_final: 0.7324 (mttm) REVERT: C 1073 LYS cc_start: 0.7474 (tttt) cc_final: 0.7102 (tttt) REVERT: C 1075 PHE cc_start: 0.7375 (m-10) cc_final: 0.6980 (m-10) REVERT: C 1084 ASP cc_start: 0.6580 (p0) cc_final: 0.6344 (t70) REVERT: C 1116 THR cc_start: 0.7745 (p) cc_final: 0.7363 (m) outliers start: 6 outliers final: 2 residues processed: 796 average time/residue: 0.1670 time to fit residues: 204.7844 Evaluate side-chains 590 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 588 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 239 GLN A 343 ASN A 422 ASN A 544 ASN A 563 GLN A 564 GLN A 717 ASN A 762 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 957 GLN A1054 GLN B 188 ASN B 417 ASN B 505 HIS B 717 ASN B 954 HIS B 965 GLN B1002 GLN B1054 GLN B1083 HIS B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 409 GLN C 422 ASN C 519 HIS C 563 GLN C 717 ASN C 787 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.171279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144173 restraints weight = 47317.586| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.31 r_work: 0.3858 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25501 Z= 0.184 Angle : 0.647 9.351 34698 Z= 0.344 Chirality : 0.047 0.282 3915 Planarity : 0.005 0.053 4473 Dihedral : 5.484 69.599 3405 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.54 % Favored : 98.43 % Rotamer: Outliers : 2.23 % Allowed : 8.28 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.89 (0.12), residues: 3123 helix: -2.46 (0.16), residues: 549 sheet: 0.16 (0.18), residues: 633 loop : -1.41 (0.12), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.017 0.002 TYR B 265 PHE 0.028 0.002 PHE B 759 TRP 0.019 0.002 TRP A 64 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00412 (25461) covalent geometry : angle 0.64293 (34620) SS BOND : bond 0.01379 ( 39) SS BOND : angle 1.59387 ( 78) hydrogen bonds : bond 0.05436 ( 704) hydrogen bonds : angle 5.99774 ( 1941) Misc. bond : bond 0.00754 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 625 time to evaluate : 0.874 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 190 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7223 (mtt90) REVERT: A 269 TYR cc_start: 0.7957 (m-80) cc_final: 0.7314 (m-80) REVERT: A 298 GLU cc_start: 0.8419 (tp30) cc_final: 0.8094 (tp30) REVERT: A 308 VAL cc_start: 0.8010 (t) cc_final: 0.7753 (p) REVERT: A 354 ASN cc_start: 0.7002 (p0) cc_final: 0.6786 (p0) REVERT: A 356 LYS cc_start: 0.7749 (tptt) cc_final: 0.7517 (tptm) REVERT: A 537 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7987 (mtpp) REVERT: A 780 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 926 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6556 (mt0) REVERT: A 950 ASP cc_start: 0.8107 (m-30) cc_final: 0.7776 (m-30) REVERT: A 969 LYS cc_start: 0.9053 (mttt) cc_final: 0.8837 (mttm) REVERT: A 984 LEU cc_start: 0.7515 (mm) cc_final: 0.7307 (mp) REVERT: A 988 GLU cc_start: 0.7934 (tp30) cc_final: 0.7081 (tp30) REVERT: A 1002 GLN cc_start: 0.8302 (tp40) cc_final: 0.7843 (tp40) REVERT: A 1019 ARG cc_start: 0.7805 (tpt170) cc_final: 0.7582 (tpt170) REVERT: A 1118 ASP cc_start: 0.7786 (p0) cc_final: 0.7165 (p0) REVERT: B 177 MET cc_start: 0.0849 (mtt) cc_final: 0.0486 (mtt) REVERT: B 338 PHE cc_start: 0.6493 (m-80) cc_final: 0.6284 (m-80) REVERT: B 351 TYR cc_start: 0.7447 (p90) cc_final: 0.6859 (p90) REVERT: B 451 TYR cc_start: 0.3991 (m-10) cc_final: 0.3719 (m-10) REVERT: B 576 VAL cc_start: 0.8293 (m) cc_final: 0.7934 (t) REVERT: B 586 ASP cc_start: 0.7578 (m-30) cc_final: 0.7354 (m-30) REVERT: B 773 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7460 (tt0) REVERT: B 817 PHE cc_start: 0.8423 (t80) cc_final: 0.7976 (t80) REVERT: B 868 GLU cc_start: 0.6927 (tp30) cc_final: 0.6652 (tp30) REVERT: B 1002 GLN cc_start: 0.8174 (mm110) cc_final: 0.7547 (mm-40) REVERT: C 97 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7190 (mmtm) REVERT: C 115 GLN cc_start: 0.7772 (pm20) cc_final: 0.7532 (pm20) REVERT: C 190 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7373 (mtt180) REVERT: C 354 ASN cc_start: 0.7323 (p0) cc_final: 0.7118 (t0) REVERT: C 390 LEU cc_start: 0.8801 (mt) cc_final: 0.8471 (mt) REVERT: C 401 VAL cc_start: 0.7657 (t) cc_final: 0.7345 (m) REVERT: C 690 GLN cc_start: 0.7847 (mp10) cc_final: 0.7558 (mp10) REVERT: C 780 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 814 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8089 (mmmt) REVERT: C 819 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 868 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 882 ILE cc_start: 0.8587 (mt) cc_final: 0.8268 (mt) REVERT: C 969 LYS cc_start: 0.8915 (mttt) cc_final: 0.8588 (mtmm) REVERT: C 988 GLU cc_start: 0.8188 (tp30) cc_final: 0.7306 (tp30) REVERT: C 1031 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 1073 LYS cc_start: 0.8372 (tttt) cc_final: 0.7897 (mtpp) REVERT: C 1084 ASP cc_start: 0.6768 (p0) cc_final: 0.6384 (t70) outliers start: 62 outliers final: 33 residues processed: 651 average time/residue: 0.1603 time to fit residues: 164.8065 Evaluate side-chains 596 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 561 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 286 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 287 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 184 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 460 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.165033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137075 restraints weight = 47399.349| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.28 r_work: 0.3767 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25501 Z= 0.141 Angle : 0.595 11.958 34698 Z= 0.308 Chirality : 0.046 0.245 3915 Planarity : 0.004 0.052 4473 Dihedral : 4.941 55.200 3403 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 11.30 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.12 (0.13), residues: 3123 helix: -0.70 (0.20), residues: 585 sheet: 0.49 (0.19), residues: 624 loop : -1.22 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 567 TYR 0.023 0.001 TYR B 365 PHE 0.030 0.002 PHE C 855 TRP 0.016 0.001 TRP A 64 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (25461) covalent geometry : angle 0.59019 (34620) SS BOND : bond 0.00747 ( 39) SS BOND : angle 1.73529 ( 78) hydrogen bonds : bond 0.04514 ( 704) hydrogen bonds : angle 5.36689 ( 1941) Misc. bond : bond 0.00483 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 584 time to evaluate : 0.908 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 190 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7595 (mtt90) REVERT: A 237 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7702 (mtp85) REVERT: A 269 TYR cc_start: 0.7996 (m-80) cc_final: 0.7231 (m-80) REVERT: A 298 GLU cc_start: 0.8552 (tp30) cc_final: 0.8179 (tt0) REVERT: A 308 VAL cc_start: 0.8249 (t) cc_final: 0.7975 (p) REVERT: A 356 LYS cc_start: 0.7680 (tptt) cc_final: 0.7452 (tptm) REVERT: A 410 ILE cc_start: 0.6822 (mm) cc_final: 0.6509 (tp) REVERT: A 537 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8109 (mtpp) REVERT: A 541 PHE cc_start: 0.4705 (m-80) cc_final: 0.4181 (m-10) REVERT: A 552 LEU cc_start: 0.8114 (mt) cc_final: 0.7830 (mm) REVERT: A 814 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7988 (mmmt) REVERT: A 926 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6747 (mt0) REVERT: A 988 GLU cc_start: 0.7997 (tp30) cc_final: 0.7202 (tp30) REVERT: A 1019 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7372 (tpt170) REVERT: A 1144 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 99 ASN cc_start: 0.8737 (p0) cc_final: 0.8509 (p0) REVERT: B 177 MET cc_start: 0.0915 (mtt) cc_final: 0.0594 (mtt) REVERT: B 281 GLU cc_start: 0.7450 (pp20) cc_final: 0.7020 (pp20) REVERT: B 338 PHE cc_start: 0.6492 (m-80) cc_final: 0.6127 (m-80) REVERT: B 346 ARG cc_start: 0.7054 (mmt-90) cc_final: 0.6811 (mmt-90) REVERT: B 351 TYR cc_start: 0.7478 (p90) cc_final: 0.6788 (p90) REVERT: B 359 SER cc_start: 0.8143 (p) cc_final: 0.7895 (p) REVERT: B 451 TYR cc_start: 0.4069 (m-10) cc_final: 0.3666 (m-10) REVERT: B 537 LYS cc_start: 0.8443 (tttt) cc_final: 0.7429 (tttm) REVERT: B 539 VAL cc_start: 0.8212 (m) cc_final: 0.7829 (m) REVERT: B 576 VAL cc_start: 0.8428 (m) cc_final: 0.8082 (t) REVERT: B 586 ASP cc_start: 0.7690 (m-30) cc_final: 0.7391 (m-30) REVERT: B 748 GLU cc_start: 0.7297 (pt0) cc_final: 0.7042 (pt0) REVERT: B 751 ASN cc_start: 0.7843 (m-40) cc_final: 0.7558 (m-40) REVERT: B 756 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5736 (t80) REVERT: B 773 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7630 (tt0) REVERT: B 787 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7361 (mm-40) REVERT: B 817 PHE cc_start: 0.8494 (t80) cc_final: 0.8158 (t80) REVERT: B 868 GLU cc_start: 0.7004 (tp30) cc_final: 0.6690 (tp30) REVERT: B 1104 VAL cc_start: 0.8115 (t) cc_final: 0.7829 (p) REVERT: C 97 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7448 (mmtt) REVERT: C 190 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7581 (mtt180) REVERT: C 206 LYS cc_start: 0.8749 (tppt) cc_final: 0.8423 (tppt) REVERT: C 231 ILE cc_start: 0.8501 (mm) cc_final: 0.8212 (mm) REVERT: C 390 LEU cc_start: 0.8827 (mt) cc_final: 0.8540 (mt) REVERT: C 401 VAL cc_start: 0.7755 (t) cc_final: 0.7459 (m) REVERT: C 552 LEU cc_start: 0.7605 (mt) cc_final: 0.7343 (mp) REVERT: C 559 PHE cc_start: 0.8261 (m-10) cc_final: 0.7970 (m-80) REVERT: C 780 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 814 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8151 (mmmt) REVERT: C 819 GLU cc_start: 0.7842 (mt-10) cc_final: 0.6772 (mt-10) REVERT: C 859 THR cc_start: 0.8490 (t) cc_final: 0.8204 (p) REVERT: C 868 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 872 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: C 882 ILE cc_start: 0.8646 (mt) cc_final: 0.8445 (mt) REVERT: C 933 LYS cc_start: 0.8120 (mttt) cc_final: 0.7828 (mttm) REVERT: C 969 LYS cc_start: 0.8910 (mttt) cc_final: 0.8514 (mtpp) REVERT: C 988 GLU cc_start: 0.8091 (tp30) cc_final: 0.7385 (tp30) REVERT: C 1002 GLN cc_start: 0.8104 (tp40) cc_final: 0.7835 (tp40) REVERT: C 1031 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7406 (mt-10) outliers start: 68 outliers final: 32 residues processed: 609 average time/residue: 0.1700 time to fit residues: 161.2821 Evaluate side-chains 577 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 542 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 3 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 98 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 895 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN B 207 HIS B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1119 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 563 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.157428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129394 restraints weight = 45380.651| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.15 r_work: 0.3674 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25501 Z= 0.164 Angle : 0.604 11.145 34698 Z= 0.314 Chirality : 0.046 0.252 3915 Planarity : 0.004 0.055 4473 Dihedral : 4.760 38.714 3402 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 2.74 % Allowed : 12.53 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.78 (0.14), residues: 3123 helix: -0.06 (0.21), residues: 612 sheet: 0.53 (0.18), residues: 678 loop : -1.10 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.020 0.002 TYR A 660 PHE 0.022 0.002 PHE C 718 TRP 0.018 0.001 TRP A 64 HIS 0.053 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00365 (25461) covalent geometry : angle 0.59807 (34620) SS BOND : bond 0.00755 ( 39) SS BOND : angle 1.83800 ( 78) hydrogen bonds : bond 0.04081 ( 704) hydrogen bonds : angle 4.99672 ( 1941) Misc. bond : bond 0.00275 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 589 time to evaluate : 0.883 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 83 VAL cc_start: 0.7160 (t) cc_final: 0.6759 (t) REVERT: A 190 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7691 (mtt90) REVERT: A 269 TYR cc_start: 0.8011 (m-80) cc_final: 0.7154 (m-80) REVERT: A 308 VAL cc_start: 0.8546 (t) cc_final: 0.8275 (p) REVERT: A 410 ILE cc_start: 0.7109 (mm) cc_final: 0.6862 (tp) REVERT: A 537 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8146 (mtpp) REVERT: A 552 LEU cc_start: 0.8262 (mt) cc_final: 0.7854 (mm) REVERT: A 588 THR cc_start: 0.7642 (m) cc_final: 0.7434 (t) REVERT: A 703 ASN cc_start: 0.7083 (m-40) cc_final: 0.6856 (m110) REVERT: A 814 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7962 (mmmt) REVERT: A 896 ILE cc_start: 0.8259 (tp) cc_final: 0.7989 (tt) REVERT: A 960 ASN cc_start: 0.8509 (t0) cc_final: 0.8305 (m-40) REVERT: A 988 GLU cc_start: 0.7814 (tp30) cc_final: 0.7195 (tp30) REVERT: A 1119 ASN cc_start: 0.8317 (m-40) cc_final: 0.8098 (m-40) REVERT: B 177 MET cc_start: 0.0919 (mtt) cc_final: 0.0581 (mtt) REVERT: B 239 GLN cc_start: 0.7303 (tp40) cc_final: 0.6906 (tp40) REVERT: B 281 GLU cc_start: 0.7530 (pp20) cc_final: 0.7160 (pp20) REVERT: B 338 PHE cc_start: 0.6597 (m-80) cc_final: 0.6198 (m-80) REVERT: B 351 TYR cc_start: 0.7651 (p90) cc_final: 0.6989 (p90) REVERT: B 586 ASP cc_start: 0.7666 (m-30) cc_final: 0.7361 (m-30) REVERT: B 613 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: B 751 ASN cc_start: 0.7919 (m-40) cc_final: 0.7668 (m-40) REVERT: B 773 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7667 (tt0) REVERT: B 787 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7345 (mm-40) REVERT: B 929 SER cc_start: 0.8463 (m) cc_final: 0.8202 (m) REVERT: B 1002 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7827 (tp40) REVERT: B 1104 VAL cc_start: 0.8416 (t) cc_final: 0.8176 (p) REVERT: B 1107 ARG cc_start: 0.7670 (mmm160) cc_final: 0.7347 (mmm160) REVERT: C 97 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7438 (mptt) REVERT: C 190 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7658 (mtt180) REVERT: C 191 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 231 ILE cc_start: 0.8575 (mm) cc_final: 0.8318 (mm) REVERT: C 324 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7356 (mm-30) REVERT: C 401 VAL cc_start: 0.7768 (t) cc_final: 0.7561 (m) REVERT: C 508 TYR cc_start: 0.5114 (m-80) cc_final: 0.4854 (m-80) REVERT: C 539 VAL cc_start: 0.8373 (m) cc_final: 0.7662 (p) REVERT: C 572 THR cc_start: 0.8086 (p) cc_final: 0.7658 (p) REVERT: C 655 TYR cc_start: 0.8597 (t80) cc_final: 0.8125 (t80) REVERT: C 658 ASN cc_start: 0.8556 (p0) cc_final: 0.8203 (p0) REVERT: C 691 SER cc_start: 0.8418 (p) cc_final: 0.8175 (m) REVERT: C 773 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 780 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 814 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8205 (mmmt) REVERT: C 859 THR cc_start: 0.8546 (t) cc_final: 0.8327 (p) REVERT: C 969 LYS cc_start: 0.9068 (mttt) cc_final: 0.8804 (mtpp) REVERT: C 988 GLU cc_start: 0.7977 (tp30) cc_final: 0.7410 (tp30) REVERT: C 1005 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8116 (tp40) outliers start: 76 outliers final: 47 residues processed: 619 average time/residue: 0.1700 time to fit residues: 163.3779 Evaluate side-chains 591 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 543 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 140 optimal weight: 2.9990 chunk 145 optimal weight: 0.0870 chunk 130 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 254 optimal weight: 0.0970 chunk 307 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 703 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 = 0.4183 r_free = 0.4183 target = 0.157654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129679 restraints weight = 45378.481| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.14 r_work: 0.3672 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25501 Z= 0.111 Angle : 0.563 12.165 34698 Z= 0.288 Chirality : 0.045 0.229 3915 Planarity : 0.004 0.041 4473 Dihedral : 4.547 31.779 3402 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.38 % Allowed : 14.11 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3123 helix: 0.40 (0.21), residues: 630 sheet: 0.67 (0.19), residues: 657 loop : -1.01 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.041 0.001 TYR C 660 PHE 0.031 0.001 PHE C 855 TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (25461) covalent geometry : angle 0.55781 (34620) SS BOND : bond 0.00305 ( 39) SS BOND : angle 1.65024 ( 78) hydrogen bonds : bond 0.03667 ( 704) hydrogen bonds : angle 4.90147 ( 1941) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 543 time to evaluate : 0.885 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 83 VAL cc_start: 0.7198 (t) cc_final: 0.6848 (t) REVERT: A 190 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7630 (mtt90) REVERT: A 269 TYR cc_start: 0.8047 (m-80) cc_final: 0.7214 (m-80) REVERT: A 410 ILE cc_start: 0.7126 (mm) cc_final: 0.6880 (tp) REVERT: A 537 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8247 (mtpp) REVERT: A 588 THR cc_start: 0.7637 (m) cc_final: 0.7421 (t) REVERT: A 814 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7968 (mmmt) REVERT: A 988 GLU cc_start: 0.7669 (tp30) cc_final: 0.7054 (tp30) REVERT: A 1142 GLN cc_start: 0.8396 (pp30) cc_final: 0.8190 (pp30) REVERT: B 177 MET cc_start: 0.0885 (mtt) cc_final: 0.0607 (mtt) REVERT: B 239 GLN cc_start: 0.7240 (tp40) cc_final: 0.6831 (tp40) REVERT: B 281 GLU cc_start: 0.7528 (pp20) cc_final: 0.7164 (pp20) REVERT: B 338 PHE cc_start: 0.6564 (m-80) cc_final: 0.6235 (m-80) REVERT: B 351 TYR cc_start: 0.7544 (p90) cc_final: 0.6924 (p90) REVERT: B 567 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7386 (mtt-85) REVERT: B 586 ASP cc_start: 0.7616 (m-30) cc_final: 0.7295 (m-30) REVERT: B 599 THR cc_start: 0.8424 (t) cc_final: 0.8201 (t) REVERT: B 751 ASN cc_start: 0.7964 (m-40) cc_final: 0.7732 (m-40) REVERT: B 773 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7389 (tp30) REVERT: B 902 MET cc_start: 0.8526 (mmt) cc_final: 0.8003 (mmm) REVERT: B 929 SER cc_start: 0.8453 (m) cc_final: 0.8201 (m) REVERT: B 1019 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.6918 (ttm-80) REVERT: B 1104 VAL cc_start: 0.8429 (t) cc_final: 0.8189 (p) REVERT: B 1107 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7346 (mmm160) REVERT: C 191 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 231 ILE cc_start: 0.8542 (mm) cc_final: 0.8296 (mm) REVERT: C 298 GLU cc_start: 0.8767 (tp30) cc_final: 0.8104 (tp30) REVERT: C 323 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 324 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 349 SER cc_start: 0.7249 (m) cc_final: 0.6950 (p) REVERT: C 401 VAL cc_start: 0.7830 (t) cc_final: 0.7620 (m) REVERT: C 498 ARG cc_start: 0.6707 (mpt-90) cc_final: 0.6494 (mmt90) REVERT: C 568 ASP cc_start: 0.7804 (p0) cc_final: 0.7585 (p0) REVERT: C 572 THR cc_start: 0.7799 (p) cc_final: 0.7393 (p) REVERT: C 691 SER cc_start: 0.8424 (p) cc_final: 0.8186 (m) REVERT: C 780 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7809 (mt-10) REVERT: C 814 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8159 (mmmt) REVERT: C 859 THR cc_start: 0.8509 (t) cc_final: 0.8301 (p) REVERT: C 933 LYS cc_start: 0.8212 (mttt) cc_final: 0.7934 (mttm) REVERT: C 950 ASP cc_start: 0.8077 (m-30) cc_final: 0.7675 (m-30) REVERT: C 969 LYS cc_start: 0.9112 (mttt) cc_final: 0.8734 (mtpp) REVERT: C 988 GLU cc_start: 0.7880 (tp30) cc_final: 0.7312 (tp30) REVERT: C 1005 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8079 (tp40) REVERT: C 1019 ARG cc_start: 0.7696 (tpp80) cc_final: 0.7335 (ttm-80) outliers start: 66 outliers final: 45 residues processed: 570 average time/residue: 0.1722 time to fit residues: 152.1897 Evaluate side-chains 568 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 522 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 312 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 301 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 703 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125312 restraints weight = 45781.674| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.15 r_work: 0.3606 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25501 Z= 0.153 Angle : 0.586 12.207 34698 Z= 0.302 Chirality : 0.045 0.266 3915 Planarity : 0.004 0.083 4473 Dihedral : 4.565 25.356 3402 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.74 % Allowed : 14.25 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.35 (0.14), residues: 3123 helix: 0.71 (0.21), residues: 615 sheet: 0.95 (0.20), residues: 612 loop : -1.00 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 355 TYR 0.019 0.002 TYR B 904 PHE 0.033 0.002 PHE C 855 TRP 0.016 0.001 TRP C 436 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00358 (25461) covalent geometry : angle 0.58035 (34620) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.73747 ( 78) hydrogen bonds : bond 0.03876 ( 704) hydrogen bonds : angle 4.82878 ( 1941) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 549 time to evaluate : 0.610 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 83 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7049 (t) REVERT: A 158 ARG cc_start: 0.0134 (OUTLIER) cc_final: -0.0416 (mmm-85) REVERT: A 269 TYR cc_start: 0.7897 (m-80) cc_final: 0.7221 (m-80) REVERT: A 346 ARG cc_start: 0.6621 (tpt170) cc_final: 0.6321 (tpt170) REVERT: A 355 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.6571 (ttm-80) REVERT: A 552 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8175 (mt) REVERT: A 574 ASP cc_start: 0.7672 (m-30) cc_final: 0.7305 (m-30) REVERT: A 748 GLU cc_start: 0.7696 (pt0) cc_final: 0.7150 (pt0) REVERT: A 776 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8206 (ttpp) REVERT: A 814 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8129 (mmmt) REVERT: A 988 GLU cc_start: 0.7611 (tp30) cc_final: 0.6991 (tp30) REVERT: A 1120 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (p) REVERT: B 81 ASN cc_start: 0.6916 (m-40) cc_final: 0.6604 (m-40) REVERT: B 177 MET cc_start: 0.0905 (mtt) cc_final: 0.0598 (mtt) REVERT: B 239 GLN cc_start: 0.7275 (tp40) cc_final: 0.6906 (tp40) REVERT: B 281 GLU cc_start: 0.7496 (pp20) cc_final: 0.7150 (pp20) REVERT: B 338 PHE cc_start: 0.6587 (m-80) cc_final: 0.6335 (m-80) REVERT: B 346 ARG cc_start: 0.7049 (mmt-90) cc_final: 0.6800 (mmt-90) REVERT: B 351 TYR cc_start: 0.7601 (p90) cc_final: 0.6746 (p90) REVERT: B 586 ASP cc_start: 0.7650 (m-30) cc_final: 0.7321 (m-30) REVERT: B 613 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8251 (mm-40) REVERT: B 641 ASN cc_start: 0.7089 (m-40) cc_final: 0.6641 (p0) REVERT: B 642 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8984 (t) REVERT: B 702 GLU cc_start: 0.7630 (tp30) cc_final: 0.7383 (tp30) REVERT: B 751 ASN cc_start: 0.8197 (m-40) cc_final: 0.7941 (m-40) REVERT: B 773 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7739 (tt0) REVERT: B 902 MET cc_start: 0.8522 (mmt) cc_final: 0.8037 (mmm) REVERT: B 935 GLN cc_start: 0.7769 (tt0) cc_final: 0.7434 (tp40) REVERT: B 988 GLU cc_start: 0.7838 (tp30) cc_final: 0.7392 (tp30) REVERT: B 1107 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7505 (mmm160) REVERT: C 52 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7861 (tp-100) REVERT: C 191 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 231 ILE cc_start: 0.8582 (mm) cc_final: 0.8339 (mm) REVERT: C 281 GLU cc_start: 0.7823 (pm20) cc_final: 0.7584 (pm20) REVERT: C 340 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7519 (mp0) REVERT: C 349 SER cc_start: 0.7788 (m) cc_final: 0.7433 (p) REVERT: C 498 ARG cc_start: 0.6889 (mpt-90) cc_final: 0.6644 (mmt90) REVERT: C 568 ASP cc_start: 0.7924 (p0) cc_final: 0.7664 (p0) REVERT: C 572 THR cc_start: 0.7802 (p) cc_final: 0.7336 (p) REVERT: C 691 SER cc_start: 0.8561 (p) cc_final: 0.8282 (m) REVERT: C 698 SER cc_start: 0.8684 (t) cc_final: 0.8411 (p) REVERT: C 780 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 814 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8165 (mmmt) REVERT: C 900 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: C 933 LYS cc_start: 0.8292 (mttt) cc_final: 0.8023 (mttm) REVERT: C 950 ASP cc_start: 0.8174 (m-30) cc_final: 0.7785 (m-30) REVERT: C 969 LYS cc_start: 0.9193 (mttt) cc_final: 0.8921 (mtpp) REVERT: C 988 GLU cc_start: 0.7798 (tp30) cc_final: 0.7236 (tp30) REVERT: C 1005 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8141 (tp40) outliers start: 76 outliers final: 49 residues processed: 581 average time/residue: 0.1746 time to fit residues: 156.0858 Evaluate side-chains 585 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 529 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 53 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 926 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 949 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.150487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122465 restraints weight = 45611.008| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.12 r_work: 0.3573 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25501 Z= 0.167 Angle : 0.597 12.500 34698 Z= 0.308 Chirality : 0.046 0.277 3915 Planarity : 0.004 0.052 4473 Dihedral : 4.649 23.591 3402 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.81 % Allowed : 15.12 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.32 (0.15), residues: 3123 helix: 0.85 (0.22), residues: 612 sheet: 0.84 (0.19), residues: 636 loop : -0.98 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.022 0.002 TYR B 612 PHE 0.034 0.002 PHE A 643 TRP 0.021 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00394 (25461) covalent geometry : angle 0.59177 (34620) SS BOND : bond 0.00361 ( 39) SS BOND : angle 1.81200 ( 78) hydrogen bonds : bond 0.03893 ( 704) hydrogen bonds : angle 4.80867 ( 1941) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 543 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: A 83 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7134 (t) REVERT: A 269 TYR cc_start: 0.7875 (m-80) cc_final: 0.7264 (m-80) REVERT: A 309 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 319 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7350 (tpp-160) REVERT: A 355 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6747 (ttm-80) REVERT: A 552 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 574 ASP cc_start: 0.7652 (m-30) cc_final: 0.7359 (m-30) REVERT: A 776 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8196 (ttpp) REVERT: A 800 PHE cc_start: 0.7945 (m-10) cc_final: 0.7703 (m-80) REVERT: A 814 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8090 (mmmt) REVERT: A 933 LYS cc_start: 0.8267 (mttt) cc_final: 0.7964 (mtmm) REVERT: A 950 ASP cc_start: 0.8052 (m-30) cc_final: 0.7793 (m-30) REVERT: A 988 GLU cc_start: 0.7595 (tp30) cc_final: 0.7029 (tp30) REVERT: B 81 ASN cc_start: 0.7273 (m-40) cc_final: 0.7004 (m-40) REVERT: B 177 MET cc_start: 0.0895 (mtt) cc_final: 0.0585 (mtt) REVERT: B 239 GLN cc_start: 0.7298 (tp40) cc_final: 0.6972 (tp40) REVERT: B 281 GLU cc_start: 0.7557 (pp20) cc_final: 0.7209 (pp20) REVERT: B 338 PHE cc_start: 0.6623 (m-80) cc_final: 0.6288 (m-80) REVERT: B 351 TYR cc_start: 0.7627 (p90) cc_final: 0.6771 (p90) REVERT: B 567 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: B 585 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7656 (pp) REVERT: B 586 ASP cc_start: 0.7615 (m-30) cc_final: 0.7259 (m-30) REVERT: B 613 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: B 641 ASN cc_start: 0.6974 (m-40) cc_final: 0.6644 (p0) REVERT: B 642 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9051 (t) REVERT: B 751 ASN cc_start: 0.8253 (m-40) cc_final: 0.7938 (m-40) REVERT: B 773 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7751 (tt0) REVERT: B 804 GLN cc_start: 0.8449 (mt0) cc_final: 0.8207 (mt0) REVERT: B 935 GLN cc_start: 0.7934 (tt0) cc_final: 0.7648 (tp40) REVERT: B 1045 LYS cc_start: 0.8415 (tptt) cc_final: 0.8049 (tptt) REVERT: B 1111 GLU cc_start: 0.8268 (pt0) cc_final: 0.8041 (pm20) REVERT: C 133 PHE cc_start: 0.8033 (m-10) cc_final: 0.7763 (m-10) REVERT: C 231 ILE cc_start: 0.8676 (mm) cc_final: 0.8449 (mm) REVERT: C 281 GLU cc_start: 0.7946 (pm20) cc_final: 0.7694 (pm20) REVERT: C 349 SER cc_start: 0.8085 (m) cc_final: 0.7667 (p) REVERT: C 498 ARG cc_start: 0.6976 (mpt-90) cc_final: 0.6710 (mmt90) REVERT: C 568 ASP cc_start: 0.7988 (p0) cc_final: 0.7367 (p0) REVERT: C 691 SER cc_start: 0.8617 (p) cc_final: 0.8321 (m) REVERT: C 698 SER cc_start: 0.8737 (t) cc_final: 0.8481 (p) REVERT: C 747 THR cc_start: 0.8362 (p) cc_final: 0.8135 (m) REVERT: C 748 GLU cc_start: 0.8672 (mp0) cc_final: 0.8268 (pt0) REVERT: C 780 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 814 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8141 (mmmt) REVERT: C 900 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7996 (mtm) REVERT: C 933 LYS cc_start: 0.8330 (mttt) cc_final: 0.8061 (mttm) REVERT: C 950 ASP cc_start: 0.8191 (m-30) cc_final: 0.7845 (m-30) REVERT: C 969 LYS cc_start: 0.9220 (mttt) cc_final: 0.9004 (mttm) REVERT: C 1005 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8068 (tp40) REVERT: C 1142 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7428 (mm110) outliers start: 78 outliers final: 57 residues processed: 575 average time/residue: 0.1732 time to fit residues: 152.5497 Evaluate side-chains 580 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 517 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 280 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 224 optimal weight: 0.6980 chunk 256 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 151 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 675 GLN A 703 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS B 563 GLN B 613 GLN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 751 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121325 restraints weight = 45431.169| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.13 r_work: 0.3555 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25501 Z= 0.136 Angle : 0.593 12.682 34698 Z= 0.305 Chirality : 0.046 0.269 3915 Planarity : 0.004 0.054 4473 Dihedral : 4.567 22.239 3402 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.74 % Allowed : 16.16 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.29 (0.15), residues: 3123 helix: 0.92 (0.22), residues: 612 sheet: 0.88 (0.19), residues: 645 loop : -1.01 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.014 0.001 TYR B 28 PHE 0.050 0.002 PHE B 559 TRP 0.014 0.001 TRP C 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (25461) covalent geometry : angle 0.58748 (34620) SS BOND : bond 0.00302 ( 39) SS BOND : angle 1.79614 ( 78) hydrogen bonds : bond 0.03734 ( 704) hydrogen bonds : angle 4.77881 ( 1941) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 513 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.6969 (t) REVERT: A 237 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7810 (mtp-110) REVERT: A 269 TYR cc_start: 0.7919 (m-80) cc_final: 0.7288 (m-80) REVERT: A 319 ARG cc_start: 0.7628 (mmt-90) cc_final: 0.7416 (tpp-160) REVERT: A 355 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6492 (ttm-80) REVERT: A 421 TYR cc_start: 0.7549 (m-10) cc_final: 0.7160 (m-80) REVERT: A 552 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 574 ASP cc_start: 0.7705 (m-30) cc_final: 0.7399 (m-30) REVERT: A 576 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7669 (t) REVERT: A 697 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8311 (ptm) REVERT: A 776 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8053 (ttpp) REVERT: A 814 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8093 (mmmt) REVERT: A 933 LYS cc_start: 0.8244 (mttt) cc_final: 0.7940 (mtmm) REVERT: A 988 GLU cc_start: 0.7631 (tp30) cc_final: 0.6980 (tp30) REVERT: A 1019 ARG cc_start: 0.7881 (tpt170) cc_final: 0.6747 (tpt170) REVERT: A 1050 MET cc_start: 0.8644 (ptt) cc_final: 0.8403 (ptm) REVERT: B 81 ASN cc_start: 0.7303 (m-40) cc_final: 0.7077 (m-40) REVERT: B 177 MET cc_start: 0.0877 (mtt) cc_final: 0.0589 (mtt) REVERT: B 238 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7830 (p90) REVERT: B 239 GLN cc_start: 0.7225 (tp40) cc_final: 0.6639 (tp-100) REVERT: B 281 GLU cc_start: 0.7637 (pp20) cc_final: 0.7272 (pp20) REVERT: B 338 PHE cc_start: 0.6680 (m-80) cc_final: 0.6363 (m-80) REVERT: B 351 TYR cc_start: 0.7622 (p90) cc_final: 0.6746 (p90) REVERT: B 567 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7505 (mtt-85) REVERT: B 586 ASP cc_start: 0.7576 (m-30) cc_final: 0.7226 (m-30) REVERT: B 641 ASN cc_start: 0.7041 (m-40) cc_final: 0.6747 (p0) REVERT: B 642 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9092 (t) REVERT: B 751 ASN cc_start: 0.8274 (m-40) cc_final: 0.7946 (m-40) REVERT: B 773 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 804 GLN cc_start: 0.8470 (mt0) cc_final: 0.8224 (mt0) REVERT: B 935 GLN cc_start: 0.7931 (tt0) cc_final: 0.7633 (tp40) REVERT: B 1045 LYS cc_start: 0.8450 (tptt) cc_final: 0.8084 (tptt) REVERT: B 1111 GLU cc_start: 0.8283 (pt0) cc_final: 0.8077 (pm20) REVERT: C 133 PHE cc_start: 0.8111 (m-10) cc_final: 0.7888 (m-10) REVERT: C 231 ILE cc_start: 0.8629 (mm) cc_final: 0.8403 (mm) REVERT: C 281 GLU cc_start: 0.7996 (pm20) cc_final: 0.7696 (pm20) REVERT: C 349 SER cc_start: 0.8092 (m) cc_final: 0.7650 (p) REVERT: C 498 ARG cc_start: 0.7025 (mpt-90) cc_final: 0.6756 (mmt90) REVERT: C 568 ASP cc_start: 0.8053 (p0) cc_final: 0.7583 (p0) REVERT: C 691 SER cc_start: 0.8587 (p) cc_final: 0.8298 (m) REVERT: C 780 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 814 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8143 (mmmt) REVERT: C 900 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: C 933 LYS cc_start: 0.8289 (mttt) cc_final: 0.8035 (mttm) REVERT: C 950 ASP cc_start: 0.8135 (m-30) cc_final: 0.7797 (m-30) REVERT: C 969 LYS cc_start: 0.9222 (mttt) cc_final: 0.8989 (mttm) REVERT: C 1005 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8014 (tp40) REVERT: C 1019 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7522 (ttp80) outliers start: 76 outliers final: 58 residues processed: 544 average time/residue: 0.1745 time to fit residues: 145.0592 Evaluate side-chains 560 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 494 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 65 optimal weight: 0.9990 chunk 284 optimal weight: 0.0570 chunk 14 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 248 optimal weight: 0.0570 chunk 263 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 675 GLN A 703 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS B 563 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.149372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121215 restraints weight = 45417.662| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.13 r_work: 0.3555 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25501 Z= 0.124 Angle : 0.599 12.569 34698 Z= 0.305 Chirality : 0.045 0.255 3915 Planarity : 0.004 0.062 4473 Dihedral : 4.497 23.087 3402 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 16.88 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.21 (0.15), residues: 3123 helix: 1.05 (0.22), residues: 612 sheet: 0.90 (0.20), residues: 645 loop : -0.97 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 567 TYR 0.016 0.001 TYR A1138 PHE 0.039 0.002 PHE C 855 TRP 0.018 0.001 TRP C 436 HIS 0.015 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00290 (25461) covalent geometry : angle 0.59525 (34620) SS BOND : bond 0.00301 ( 39) SS BOND : angle 1.54523 ( 78) hydrogen bonds : bond 0.03639 ( 704) hydrogen bonds : angle 4.72150 ( 1941) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 517 time to evaluate : 0.890 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 83 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 269 TYR cc_start: 0.7898 (m-80) cc_final: 0.7243 (m-80) REVERT: A 319 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7368 (tpp-160) REVERT: A 355 ARG cc_start: 0.7020 (ttm-80) cc_final: 0.6535 (ttm-80) REVERT: A 421 TYR cc_start: 0.7534 (m-10) cc_final: 0.7163 (m-80) REVERT: A 552 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 574 ASP cc_start: 0.7680 (m-30) cc_final: 0.7397 (m-30) REVERT: A 576 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 697 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8353 (ptm) REVERT: A 776 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8057 (ttpp) REVERT: A 804 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8216 (mt0) REVERT: A 814 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8189 (mmmt) REVERT: A 933 LYS cc_start: 0.8216 (mttt) cc_final: 0.7928 (mtmm) REVERT: A 988 GLU cc_start: 0.7554 (tp30) cc_final: 0.6897 (tp30) REVERT: A 1019 ARG cc_start: 0.7928 (tpt170) cc_final: 0.6981 (tpt170) REVERT: A 1038 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8336 (mmmm) REVERT: A 1050 MET cc_start: 0.8660 (ptt) cc_final: 0.8424 (ptm) REVERT: A 1144 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7802 (mp0) REVERT: B 81 ASN cc_start: 0.7303 (m-40) cc_final: 0.7076 (m-40) REVERT: B 177 MET cc_start: 0.0868 (mtt) cc_final: 0.0584 (mtt) REVERT: B 191 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 239 GLN cc_start: 0.7179 (tp40) cc_final: 0.6697 (tp-100) REVERT: B 281 GLU cc_start: 0.7762 (pp20) cc_final: 0.7383 (pp20) REVERT: B 338 PHE cc_start: 0.6615 (m-80) cc_final: 0.6318 (m-80) REVERT: B 351 TYR cc_start: 0.7600 (p90) cc_final: 0.6731 (p90) REVERT: B 567 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7440 (mtt-85) REVERT: B 586 ASP cc_start: 0.7565 (m-30) cc_final: 0.7217 (m-30) REVERT: B 641 ASN cc_start: 0.6983 (m-40) cc_final: 0.6713 (p0) REVERT: B 642 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9086 (t) REVERT: B 751 ASN cc_start: 0.8212 (m-40) cc_final: 0.7918 (m-40) REVERT: B 773 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7749 (tt0) REVERT: B 804 GLN cc_start: 0.8484 (mt0) cc_final: 0.8247 (mt0) REVERT: B 902 MET cc_start: 0.8433 (mmt) cc_final: 0.8096 (mmp) REVERT: B 935 GLN cc_start: 0.8029 (tt0) cc_final: 0.7775 (tp40) REVERT: B 1045 LYS cc_start: 0.8467 (tptt) cc_final: 0.8097 (tptt) REVERT: C 133 PHE cc_start: 0.8131 (m-10) cc_final: 0.7901 (m-10) REVERT: C 196 ASN cc_start: 0.8284 (p0) cc_final: 0.8023 (p0) REVERT: C 231 ILE cc_start: 0.8607 (mm) cc_final: 0.8396 (mm) REVERT: C 281 GLU cc_start: 0.8002 (pm20) cc_final: 0.7699 (pm20) REVERT: C 340 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7506 (mp0) REVERT: C 349 SER cc_start: 0.8108 (m) cc_final: 0.7664 (p) REVERT: C 498 ARG cc_start: 0.7020 (mpt-90) cc_final: 0.6758 (mmt90) REVERT: C 568 ASP cc_start: 0.8041 (p0) cc_final: 0.7492 (p0) REVERT: C 691 SER cc_start: 0.8581 (p) cc_final: 0.8285 (m) REVERT: C 748 GLU cc_start: 0.8685 (mp0) cc_final: 0.8228 (pt0) REVERT: C 814 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8139 (mmmt) REVERT: C 900 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: C 918 GLU cc_start: 0.8099 (mp0) cc_final: 0.7739 (mp0) REVERT: C 933 LYS cc_start: 0.8279 (mttt) cc_final: 0.8023 (mttm) REVERT: C 950 ASP cc_start: 0.8131 (m-30) cc_final: 0.7808 (m-30) REVERT: C 969 LYS cc_start: 0.9223 (mttt) cc_final: 0.9006 (mttp) REVERT: C 1005 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8047 (tp40) outliers start: 73 outliers final: 61 residues processed: 549 average time/residue: 0.1853 time to fit residues: 154.8057 Evaluate side-chains 569 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 502 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 981 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 298 optimal weight: 0.2980 chunk 102 optimal weight: 0.2980 chunk 251 optimal weight: 0.3980 chunk 217 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 206 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 675 GLN A 703 ASN A 717 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 563 GLN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 580 GLN C 913 GLN C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.122224 restraints weight = 45445.079| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.14 r_work: 0.3571 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25501 Z= 0.109 Angle : 0.595 12.573 34698 Z= 0.302 Chirality : 0.045 0.228 3915 Planarity : 0.004 0.055 4473 Dihedral : 4.382 23.250 3402 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.30 % Allowed : 17.57 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.13 (0.15), residues: 3123 helix: 1.18 (0.22), residues: 612 sheet: 0.95 (0.20), residues: 645 loop : -0.94 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 567 TYR 0.013 0.001 TYR B 660 PHE 0.041 0.001 PHE C 855 TRP 0.019 0.001 TRP C 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (25461) covalent geometry : angle 0.59192 (34620) SS BOND : bond 0.00287 ( 39) SS BOND : angle 1.37380 ( 78) hydrogen bonds : bond 0.03451 ( 704) hydrogen bonds : angle 4.66552 ( 1941) Misc. bond : bond 0.00032 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6246 Ramachandran restraints generated. 3123 Oldfield, 0 Emsley, 3123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 512 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7065 (t) REVERT: A 269 TYR cc_start: 0.7924 (m-80) cc_final: 0.7241 (m-80) REVERT: A 319 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7332 (tpp-160) REVERT: A 355 ARG cc_start: 0.7049 (ttm-80) cc_final: 0.6464 (ttm-80) REVERT: A 421 TYR cc_start: 0.7518 (m-10) cc_final: 0.7148 (m-80) REVERT: A 552 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 574 ASP cc_start: 0.7639 (m-30) cc_final: 0.7275 (t70) REVERT: A 576 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7752 (t) REVERT: A 697 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8381 (ptm) REVERT: A 776 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8095 (ttpp) REVERT: A 804 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8249 (mt0) REVERT: A 814 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8189 (mmmt) REVERT: A 933 LYS cc_start: 0.8210 (mttt) cc_final: 0.7922 (mtmm) REVERT: A 988 GLU cc_start: 0.7577 (tp30) cc_final: 0.6927 (tp30) REVERT: A 1019 ARG cc_start: 0.7927 (tpt170) cc_final: 0.6984 (tpt170) REVERT: A 1050 MET cc_start: 0.8632 (ptt) cc_final: 0.8397 (ptm) REVERT: A 1144 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7782 (mp0) REVERT: B 81 ASN cc_start: 0.7253 (m-40) cc_final: 0.7021 (m-40) REVERT: B 177 MET cc_start: 0.0843 (mtt) cc_final: 0.0560 (mtt) REVERT: B 191 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 239 GLN cc_start: 0.7176 (tp40) cc_final: 0.6702 (tp-100) REVERT: B 338 PHE cc_start: 0.6666 (m-80) cc_final: 0.6355 (m-80) REVERT: B 351 TYR cc_start: 0.7592 (p90) cc_final: 0.6715 (p90) REVERT: B 567 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7628 (mtt-85) REVERT: B 586 ASP cc_start: 0.7535 (m-30) cc_final: 0.7177 (m-30) REVERT: B 641 ASN cc_start: 0.6879 (m-40) cc_final: 0.6611 (p0) REVERT: B 642 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9111 (t) REVERT: B 751 ASN cc_start: 0.8199 (m-40) cc_final: 0.7892 (m-40) REVERT: B 773 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7752 (tt0) REVERT: B 804 GLN cc_start: 0.8501 (mt0) cc_final: 0.8270 (mt0) REVERT: B 902 MET cc_start: 0.8427 (mmt) cc_final: 0.8053 (mmp) REVERT: B 935 GLN cc_start: 0.7992 (tt0) cc_final: 0.7695 (tp40) REVERT: B 950 ASP cc_start: 0.7501 (t70) cc_final: 0.7214 (t70) REVERT: B 1045 LYS cc_start: 0.8466 (tptt) cc_final: 0.8101 (tptt) REVERT: C 133 PHE cc_start: 0.8168 (m-10) cc_final: 0.7966 (m-10) REVERT: C 281 GLU cc_start: 0.7978 (pm20) cc_final: 0.7695 (pm20) REVERT: C 349 SER cc_start: 0.8025 (m) cc_final: 0.7582 (p) REVERT: C 498 ARG cc_start: 0.6955 (mpt-90) cc_final: 0.6707 (mmt90) REVERT: C 568 ASP cc_start: 0.8036 (p0) cc_final: 0.7588 (p0) REVERT: C 691 SER cc_start: 0.8572 (p) cc_final: 0.8272 (m) REVERT: C 698 SER cc_start: 0.8673 (t) cc_final: 0.8401 (p) REVERT: C 814 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8160 (mmmt) REVERT: C 900 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8070 (mtm) REVERT: C 918 GLU cc_start: 0.8110 (mp0) cc_final: 0.7750 (mp0) REVERT: C 933 LYS cc_start: 0.8263 (mttt) cc_final: 0.8009 (mtmm) REVERT: C 950 ASP cc_start: 0.8102 (m-30) cc_final: 0.7790 (m-30) REVERT: C 969 LYS cc_start: 0.9237 (mttt) cc_final: 0.9022 (mttp) REVERT: C 988 GLU cc_start: 0.8013 (mp0) cc_final: 0.7706 (mp0) REVERT: C 1005 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8092 (tp40) outliers start: 64 outliers final: 52 residues processed: 542 average time/residue: 0.1780 time to fit residues: 148.4707 Evaluate side-chains 559 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 501 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 14 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 675 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 580 GLN C 762 GLN C 913 GLN C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121953 restraints weight = 45348.327| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.13 r_work: 0.3566 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 25501 Z= 0.192 Angle : 0.901 59.196 34698 Z= 0.516 Chirality : 0.054 1.267 3915 Planarity : 0.005 0.126 4473 Dihedral : 4.450 33.079 3402 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 2.20 % Allowed : 17.89 % Favored : 79.91 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.13 (0.15), residues: 3123 helix: 1.17 (0.22), residues: 612 sheet: 0.96 (0.20), residues: 645 loop : -0.94 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 509 TYR 0.012 0.001 TYR C 421 PHE 0.039 0.001 PHE C 855 TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00439 (25461) covalent geometry : angle 0.89307 (34620) SS BOND : bond 0.00368 ( 39) SS BOND : angle 2.66661 ( 78) hydrogen bonds : bond 0.03485 ( 704) hydrogen bonds : angle 4.66225 ( 1941) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6241.32 seconds wall clock time: 107 minutes 30.35 seconds (6450.35 seconds total)