Starting phenix.real_space_refine on Sat Jun 21 16:36:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvn_32854/06_2025/7wvn_32854.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 15874 2.51 5 N 4133 2.21 5 O 4684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24805 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Time building chain proxies: 13.72, per 1000 atoms: 0.55 Number of scatterers: 24805 At special positions: 0 Unit cell: (147.555, 144.276, 196.74, 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 4684 8.00 N 4133 7.00 C 15874 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 3.1 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 50 sheets defined 21.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.566A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.217A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.691A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.583A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.914A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.715A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.626A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.772A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.736A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.865A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.766A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.669A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (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 960 removed outlier: 3.720A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.801A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.568A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.774A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.511A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.106A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.580A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.600A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 639' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.666A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.506A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 746 through 752' Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.854A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 782 removed outlier: 3.719A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 4.047A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.684A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.886A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.643A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.796A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.084A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.913A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.590A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.968A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.802A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.623A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.420A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.518A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 410' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.742A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.804A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.803A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.790A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.012A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.601A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.764A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.831A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.518A 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: 3.772A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.661A 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: 3.918A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.591A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.737A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.064A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.885A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.715A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.730A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.578A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.988A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.681A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.681A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 4.094A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 7.962A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.945A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.892A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.667A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.664A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.982A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.728A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN B 188 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 208 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG B 190 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 206 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE B 192 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 204 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE B 194 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS B 202 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN B 196 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.572A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.945A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.874A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.915A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.670A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.688A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.722A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.515A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.384A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.918A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.003A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.917A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.822A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.822A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.658A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.616A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 359 removed outlier: 4.134A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.877A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.286A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.779A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.697A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.653A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 732 hydrogen bonds defined for protein. 2013 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: 11.47 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7885 1.34 - 1.47: 6268 1.47 - 1.59: 11087 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 25384 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.34e-02 1.83e+03 1.73e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.430 -0.096 2.34e-02 1.83e+03 1.68e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.48e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.35e+01 bond pdb=" C VAL A 620 " pdb=" N PRO A 631 " ideal model delta sigma weight residual 1.341 1.383 -0.042 1.60e-02 3.91e+03 6.99e+00 ... (remaining 25379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 33745 2.33 - 4.66: 638 4.66 - 7.00: 102 7.00 - 9.33: 21 9.33 - 11.66: 9 Bond angle restraints: 34515 Sorted by residual: angle pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta sigma weight residual 121.70 133.11 -11.41 1.80e+00 3.09e-01 4.02e+01 angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 133.20 -11.66 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLU C 156 " pdb=" N PHE C 157 " pdb=" CA PHE C 157 " ideal model delta sigma weight residual 121.70 131.25 -9.55 1.80e+00 3.09e-01 2.82e+01 ... (remaining 34510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 14711 15.89 - 31.77: 347 31.77 - 47.66: 86 47.66 - 63.54: 13 63.54 - 79.43: 1 Dihedral angle restraints: 15158 sinusoidal: 5944 harmonic: 9214 Sorted by residual: dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 34.44 -34.44 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 0.00 33.77 -33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA PHE C 86 " pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta harmonic sigma weight residual 180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 15155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3037 0.060 - 0.121: 725 0.121 - 0.181: 111 0.181 - 0.241: 22 0.241 - 0.301: 9 Chirality restraints: 3904 Sorted by residual: chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+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 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3901 not shown) Planarity restraints: 4462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 25 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO B 26 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.057 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO A 295 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 25 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 26 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.043 5.00e-02 4.00e+02 ... (remaining 4459 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7799 2.86 - 3.37: 18283 3.37 - 3.88: 39768 3.88 - 4.39: 41398 4.39 - 4.90: 74422 Nonbonded interactions: 181670 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.348 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.366 3.040 nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.372 3.040 nonbonded pdb=" O GLY A1093 " pdb=" OH TYR C 904 " model vdw 2.375 3.040 ... (remaining 181665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.640 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 25423 Z= 0.281 Angle : 0.831 11.661 34593 Z= 0.486 Chirality : 0.055 0.301 3904 Planarity : 0.007 0.102 4462 Dihedral : 8.232 79.427 9105 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.12), residues: 3114 helix: -4.99 (0.05), residues: 576 sheet: -0.31 (0.17), residues: 584 loop : -1.76 (0.11), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.014 0.002 HIS C1048 PHE 0.024 0.003 PHE A 32 TYR 0.021 0.002 TYR A 873 ARG 0.006 0.001 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.33319 ( 710) hydrogen bonds : angle 11.07586 ( 2013) SS BOND : bond 0.00238 ( 39) SS BOND : angle 1.03561 ( 78) covalent geometry : bond 0.00585 (25384) covalent geometry : angle 0.83067 (34515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 833 time to evaluate : 2.831 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 191 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7706 (tt0) REVERT: A 278 LYS cc_start: 0.8209 (tttt) cc_final: 0.7734 (ttmm) REVERT: A 320 VAL cc_start: 0.8332 (t) cc_final: 0.8109 (t) REVERT: A 406 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5028 (mp0) REVERT: A 555 SER cc_start: 0.7863 (t) cc_final: 0.7577 (p) REVERT: A 574 ASP cc_start: 0.6662 (p0) cc_final: 0.5607 (t0) REVERT: A 673 SER cc_start: 0.7862 (t) cc_final: 0.6483 (m) REVERT: A 699 LEU cc_start: 0.6861 (mt) cc_final: 0.6539 (mt) REVERT: A 717 ASN cc_start: 0.7208 (t0) cc_final: 0.6860 (t0) REVERT: A 719 THR cc_start: 0.8057 (m) cc_final: 0.7806 (p) REVERT: A 725 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6822 (mt-10) REVERT: A 736 VAL cc_start: 0.8531 (t) cc_final: 0.8249 (m) REVERT: A 776 LYS cc_start: 0.7889 (mttt) cc_final: 0.7554 (mttt) REVERT: A 780 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 814 LYS cc_start: 0.8399 (mttt) cc_final: 0.8183 (mmmt) REVERT: A 867 ASP cc_start: 0.7896 (m-30) cc_final: 0.7667 (m-30) REVERT: A 887 THR cc_start: 0.9017 (p) cc_final: 0.8645 (t) REVERT: A 947 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7732 (ttmt) REVERT: A 950 ASP cc_start: 0.7753 (m-30) cc_final: 0.7057 (p0) REVERT: A 969 LYS cc_start: 0.8580 (mttt) cc_final: 0.8102 (mttt) REVERT: A 979 ASP cc_start: 0.7495 (m-30) cc_final: 0.6985 (t0) REVERT: A 991 VAL cc_start: 0.8508 (t) cc_final: 0.8054 (p) REVERT: A 1051 SER cc_start: 0.8970 (m) cc_final: 0.8471 (p) REVERT: A 1097 SER cc_start: 0.9107 (t) cc_final: 0.8804 (p) REVERT: B 29 THR cc_start: 0.7859 (t) cc_final: 0.7515 (t) REVERT: B 44 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7719 (mtt90) REVERT: B 45 SER cc_start: 0.9015 (p) cc_final: 0.8693 (t) REVERT: B 49 HIS cc_start: 0.7591 (t70) cc_final: 0.7289 (t70) REVERT: B 62 VAL cc_start: 0.7542 (m) cc_final: 0.7327 (p) REVERT: B 66 HIS cc_start: 0.4817 (p-80) cc_final: 0.4018 (p-80) REVERT: B 80 ASP cc_start: 0.6703 (m-30) cc_final: 0.6239 (m-30) REVERT: B 81 ASN cc_start: 0.7531 (t0) cc_final: 0.7208 (m-40) REVERT: B 191 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 195 LYS cc_start: 0.8530 (pttt) cc_final: 0.7844 (tptt) REVERT: B 206 LYS cc_start: 0.8234 (tptt) cc_final: 0.7995 (tptt) REVERT: B 224 GLU cc_start: 0.6182 (mt-10) cc_final: 0.5869 (mt-10) REVERT: B 267 VAL cc_start: 0.8800 (t) cc_final: 0.8406 (p) REVERT: B 300 LYS cc_start: 0.7970 (mttt) cc_final: 0.7595 (mtmm) REVERT: B 327 VAL cc_start: 0.7495 (t) cc_final: 0.7195 (m) REVERT: B 328 ARG cc_start: 0.5920 (mmm160) cc_final: 0.5714 (mmm160) REVERT: B 386 LYS cc_start: 0.7697 (mttt) cc_final: 0.7376 (mtmt) REVERT: B 439 ASN cc_start: 0.8057 (p0) cc_final: 0.7463 (p0) REVERT: B 455 LEU cc_start: 0.8308 (mt) cc_final: 0.7750 (mt) REVERT: B 528 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7520 (ttpt) REVERT: B 537 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7847 (ttmt) REVERT: B 551 VAL cc_start: 0.8007 (t) cc_final: 0.7728 (m) REVERT: B 553 THR cc_start: 0.8032 (p) cc_final: 0.7717 (m) REVERT: B 675 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6788 (mm-40) REVERT: B 721 SER cc_start: 0.7952 (t) cc_final: 0.7726 (t) REVERT: B 756 TYR cc_start: 0.7910 (m-80) cc_final: 0.7354 (m-80) REVERT: B 759 PHE cc_start: 0.7725 (t80) cc_final: 0.7315 (t80) REVERT: B 780 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 856 LYS cc_start: 0.7427 (mttt) cc_final: 0.7134 (mttm) REVERT: B 884 SER cc_start: 0.8153 (m) cc_final: 0.7571 (t) REVERT: B 888 PHE cc_start: 0.7804 (p90) cc_final: 0.7521 (p90) REVERT: B 935 GLN cc_start: 0.8160 (tt0) cc_final: 0.7957 (tt0) REVERT: B 936 ASP cc_start: 0.7693 (m-30) cc_final: 0.7201 (m-30) REVERT: B 947 LYS cc_start: 0.8029 (mttt) cc_final: 0.7485 (mttm) REVERT: B 969 LYS cc_start: 0.8573 (mttt) cc_final: 0.8348 (mttt) REVERT: B 988 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 1043 CYS cc_start: 0.6233 (m) cc_final: 0.5993 (m) REVERT: B 1055 SER cc_start: 0.7188 (m) cc_final: 0.6845 (t) REVERT: B 1102 TRP cc_start: 0.7708 (m100) cc_final: 0.7368 (m100) REVERT: B 1125 ASN cc_start: 0.8544 (p0) cc_final: 0.8210 (p0) REVERT: C 64 TRP cc_start: 0.6912 (t60) cc_final: 0.6512 (t60) REVERT: C 237 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7173 (mtm-85) REVERT: C 309 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6261 (mt-10) REVERT: C 374 PHE cc_start: 0.5566 (m-10) cc_final: 0.5334 (m-80) REVERT: C 386 LYS cc_start: 0.8317 (mttt) cc_final: 0.7931 (mttt) REVERT: C 553 THR cc_start: 0.7079 (p) cc_final: 0.6661 (t) REVERT: C 558 LYS cc_start: 0.8376 (mttt) cc_final: 0.8103 (tmtt) REVERT: C 654 GLU cc_start: 0.7662 (tt0) cc_final: 0.7371 (tt0) REVERT: C 721 SER cc_start: 0.7733 (t) cc_final: 0.7414 (p) REVERT: C 723 THR cc_start: 0.8522 (p) cc_final: 0.8311 (p) REVERT: C 730 SER cc_start: 0.8753 (p) cc_final: 0.8531 (t) REVERT: C 737 ASP cc_start: 0.7675 (t0) cc_final: 0.7154 (t0) REVERT: C 884 SER cc_start: 0.8670 (m) cc_final: 0.8416 (p) REVERT: C 954 HIS cc_start: 0.7541 (m-70) cc_final: 0.7323 (t70) REVERT: C 969 LYS cc_start: 0.8873 (mttt) cc_final: 0.8412 (mtpp) REVERT: C 1028 LYS cc_start: 0.8000 (mttt) cc_final: 0.7482 (mmtp) outliers start: 3 outliers final: 1 residues processed: 836 average time/residue: 0.3839 time to fit residues: 485.3901 Evaluate side-chains 600 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 599 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 81 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 239 GLN A 245 HIS A 544 ASN A 563 GLN A 613 GLN A 675 GLN A 779 GLN A 787 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 505 HIS B 519 HIS B 544 ASN B 641 ASN B 717 ASN B 751 ASN B 907 ASN B 949 GLN B1023 ASN B1054 GLN B1083 HIS C 61 ASN C 66 HIS C 239 GLN C 422 ASN C 717 ASN C 907 ASN C 954 HIS C 955 ASN C1048 HIS C1054 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.174765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142979 restraints weight = 52520.015| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.82 r_work: 0.3822 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25423 Z= 0.157 Angle : 0.642 11.751 34593 Z= 0.338 Chirality : 0.046 0.289 3904 Planarity : 0.005 0.047 4462 Dihedral : 4.914 44.030 3392 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.38 % Allowed : 9.06 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.12), residues: 3114 helix: -3.00 (0.14), residues: 594 sheet: 0.19 (0.17), residues: 666 loop : -1.37 (0.12), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.008 0.001 HIS A 66 PHE 0.031 0.002 PHE C 192 TYR 0.022 0.002 TYR B 501 ARG 0.010 0.001 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.06239 ( 710) hydrogen bonds : angle 6.56874 ( 2013) SS BOND : bond 0.00593 ( 39) SS BOND : angle 1.82872 ( 78) covalent geometry : bond 0.00343 (25384) covalent geometry : angle 0.63675 (34515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 649 time to evaluate : 2.522 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: A 190 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7745 (ttm-80) REVERT: A 245 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6415 (m170) REVERT: A 269 TYR cc_start: 0.7872 (m-10) cc_final: 0.7636 (m-10) REVERT: A 275 PHE cc_start: 0.8687 (m-10) cc_final: 0.8288 (m-10) REVERT: A 278 LYS cc_start: 0.8780 (tttt) cc_final: 0.8569 (ttmt) REVERT: A 304 LYS cc_start: 0.8868 (mttt) cc_final: 0.8650 (ttmm) REVERT: A 406 GLU cc_start: 0.5861 (mt-10) cc_final: 0.5268 (tp30) REVERT: A 552 LEU cc_start: 0.8304 (mm) cc_final: 0.8019 (mm) REVERT: A 558 LYS cc_start: 0.6552 (tmtt) cc_final: 0.5985 (tmtt) REVERT: A 573 THR cc_start: 0.8326 (m) cc_final: 0.8109 (p) REVERT: A 574 ASP cc_start: 0.7005 (p0) cc_final: 0.6741 (t0) REVERT: A 585 LEU cc_start: 0.7174 (mt) cc_final: 0.6749 (mt) REVERT: A 586 ASP cc_start: 0.7294 (t0) cc_final: 0.6453 (p0) REVERT: A 673 SER cc_start: 0.8187 (t) cc_final: 0.7518 (m) REVERT: A 751 ASN cc_start: 0.8575 (m-40) cc_final: 0.8325 (m110) REVERT: A 816 SER cc_start: 0.8023 (p) cc_final: 0.7477 (m) REVERT: A 887 THR cc_start: 0.9154 (p) cc_final: 0.8749 (t) REVERT: A 947 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8195 (ttmt) REVERT: A 950 ASP cc_start: 0.7652 (m-30) cc_final: 0.7449 (p0) REVERT: A 969 LYS cc_start: 0.8976 (mttt) cc_final: 0.8671 (mtmm) REVERT: A 979 ASP cc_start: 0.8127 (m-30) cc_final: 0.7354 (t0) REVERT: A 1051 SER cc_start: 0.8848 (m) cc_final: 0.8525 (p) REVERT: A 1097 SER cc_start: 0.9222 (t) cc_final: 0.9014 (p) REVERT: B 29 THR cc_start: 0.7975 (t) cc_final: 0.7729 (t) REVERT: B 62 VAL cc_start: 0.8047 (m) cc_final: 0.7763 (p) REVERT: B 81 ASN cc_start: 0.7832 (t0) cc_final: 0.7543 (m-40) REVERT: B 97 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7109 (tptt) REVERT: B 100 ILE cc_start: 0.8933 (mm) cc_final: 0.7989 (mm) REVERT: B 195 LYS cc_start: 0.8379 (pttt) cc_final: 0.8167 (tppt) REVERT: B 203 ILE cc_start: 0.8681 (mm) cc_final: 0.8464 (mm) REVERT: B 224 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6764 (mt-10) REVERT: B 226 LEU cc_start: 0.8625 (tp) cc_final: 0.8400 (tp) REVERT: B 267 VAL cc_start: 0.9012 (t) cc_final: 0.8724 (p) REVERT: B 308 VAL cc_start: 0.8457 (t) cc_final: 0.8162 (p) REVERT: B 324 GLU cc_start: 0.8047 (mp0) cc_final: 0.7525 (pm20) REVERT: B 325 SER cc_start: 0.8836 (m) cc_final: 0.8560 (t) REVERT: B 386 LYS cc_start: 0.8110 (mttt) cc_final: 0.7742 (mtmt) REVERT: B 439 ASN cc_start: 0.8385 (p0) cc_final: 0.7749 (p0) REVERT: B 528 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7582 (ptpt) REVERT: B 537 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8218 (tttt) REVERT: B 547 LYS cc_start: 0.8148 (mttt) cc_final: 0.7635 (mmmm) REVERT: B 574 ASP cc_start: 0.7895 (p0) cc_final: 0.7644 (t0) REVERT: B 607 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7932 (mp10) REVERT: B 695 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6861 (p90) REVERT: B 759 PHE cc_start: 0.7664 (t80) cc_final: 0.7205 (t80) REVERT: B 772 VAL cc_start: 0.8601 (t) cc_final: 0.8355 (p) REVERT: B 884 SER cc_start: 0.8775 (m) cc_final: 0.8173 (t) REVERT: B 888 PHE cc_start: 0.8084 (p90) cc_final: 0.7766 (p90) REVERT: B 936 ASP cc_start: 0.8032 (m-30) cc_final: 0.7612 (m-30) REVERT: B 950 ASP cc_start: 0.6881 (p0) cc_final: 0.6671 (p0) REVERT: B 994 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8117 (t0) REVERT: B 1051 SER cc_start: 0.8834 (t) cc_final: 0.8489 (m) REVERT: B 1073 LYS cc_start: 0.8875 (tttt) cc_final: 0.8483 (tttp) REVERT: B 1084 ASP cc_start: 0.7482 (p0) cc_final: 0.6579 (p0) REVERT: B 1091 ARG cc_start: 0.6351 (tpp-160) cc_final: 0.5736 (ttp80) REVERT: B 1107 ARG cc_start: 0.7219 (mtt180) cc_final: 0.6567 (ttm110) REVERT: B 1125 ASN cc_start: 0.8562 (p0) cc_final: 0.8219 (p0) REVERT: C 104 TRP cc_start: 0.7689 (m-90) cc_final: 0.7459 (m-90) REVERT: C 191 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7710 (mt-10) REVERT: C 192 PHE cc_start: 0.8129 (m-80) cc_final: 0.7766 (m-10) REVERT: C 195 LYS cc_start: 0.6303 (tptt) cc_final: 0.5984 (mmmt) REVERT: C 237 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7226 (mtm-85) REVERT: C 309 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7116 (mt-10) REVERT: C 334 ASN cc_start: 0.5692 (t0) cc_final: 0.5438 (t0) REVERT: C 335 LEU cc_start: 0.3309 (mt) cc_final: 0.2852 (tt) REVERT: C 362 VAL cc_start: 0.7806 (t) cc_final: 0.7470 (p) REVERT: C 374 PHE cc_start: 0.5951 (m-10) cc_final: 0.5203 (m-80) REVERT: C 386 LYS cc_start: 0.8505 (mttt) cc_final: 0.8250 (mttt) REVERT: C 436 TRP cc_start: 0.4486 (t60) cc_final: 0.3783 (t60) REVERT: C 558 LYS cc_start: 0.8567 (mttt) cc_final: 0.8343 (tmtt) REVERT: C 574 ASP cc_start: 0.7002 (m-30) cc_final: 0.6779 (m-30) REVERT: C 607 GLN cc_start: 0.8520 (mp10) cc_final: 0.8101 (mp10) REVERT: C 654 GLU cc_start: 0.8020 (tt0) cc_final: 0.7796 (tt0) REVERT: C 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7484 (t70) REVERT: C 751 ASN cc_start: 0.8489 (m-40) cc_final: 0.7984 (m-40) REVERT: C 884 SER cc_start: 0.8992 (m) cc_final: 0.8627 (t) REVERT: C 898 PHE cc_start: 0.7721 (t80) cc_final: 0.6416 (t80) REVERT: C 969 LYS cc_start: 0.9176 (mttt) cc_final: 0.8784 (mtmm) REVERT: C 1104 VAL cc_start: 0.6520 (p) cc_final: 0.4736 (m) outliers start: 66 outliers final: 37 residues processed: 687 average time/residue: 0.3886 time to fit residues: 408.9156 Evaluate side-chains 598 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 558 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 105 optimal weight: 0.0070 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 675 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1113 GLN B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 280 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN C 505 HIS C 762 GLN C 895 GLN C 901 GLN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1088 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131763 restraints weight = 51146.200| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.65 r_work: 0.3664 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25423 Z= 0.186 Angle : 0.626 9.895 34593 Z= 0.330 Chirality : 0.046 0.227 3904 Planarity : 0.005 0.079 4462 Dihedral : 4.783 49.020 3392 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.03 % Allowed : 11.70 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3114 helix: -1.11 (0.19), residues: 626 sheet: 0.37 (0.19), residues: 612 loop : -1.13 (0.12), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 104 HIS 0.028 0.002 HIS A 245 PHE 0.032 0.002 PHE B 456 TYR 0.019 0.002 TYR B 501 ARG 0.013 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 710) hydrogen bonds : angle 5.72223 ( 2013) SS BOND : bond 0.00437 ( 39) SS BOND : angle 1.51793 ( 78) covalent geometry : bond 0.00415 (25384) covalent geometry : angle 0.62235 (34515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 605 time to evaluate : 2.498 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: A 109 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 190 ARG cc_start: 0.8459 (mtp180) cc_final: 0.8068 (mtm-85) REVERT: A 239 GLN cc_start: 0.8027 (tt0) cc_final: 0.7592 (tp40) REVERT: A 269 TYR cc_start: 0.8075 (m-10) cc_final: 0.7850 (m-80) REVERT: A 278 LYS cc_start: 0.8821 (tttt) cc_final: 0.8584 (ttmt) REVERT: A 304 LYS cc_start: 0.8817 (mttt) cc_final: 0.8510 (ttmm) REVERT: A 552 LEU cc_start: 0.8233 (mm) cc_final: 0.7844 (mm) REVERT: A 558 LYS cc_start: 0.6646 (tmtt) cc_final: 0.5688 (tmtt) REVERT: A 573 THR cc_start: 0.8494 (m) cc_final: 0.8272 (p) REVERT: A 585 LEU cc_start: 0.7429 (mt) cc_final: 0.6977 (mt) REVERT: A 586 ASP cc_start: 0.7201 (t0) cc_final: 0.6267 (p0) REVERT: A 673 SER cc_start: 0.8385 (t) cc_final: 0.8160 (p) REVERT: A 751 ASN cc_start: 0.8681 (m-40) cc_final: 0.8334 (m110) REVERT: A 816 SER cc_start: 0.7963 (p) cc_final: 0.7677 (m) REVERT: A 861 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 969 LYS cc_start: 0.9114 (mttt) cc_final: 0.8872 (mtmm) REVERT: A 979 ASP cc_start: 0.8009 (m-30) cc_final: 0.7664 (t0) REVERT: A 1005 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8181 (tp40) REVERT: A 1045 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8274 (mmmt) REVERT: A 1051 SER cc_start: 0.8891 (m) cc_final: 0.8586 (p) REVERT: B 29 THR cc_start: 0.8100 (t) cc_final: 0.7874 (t) REVERT: B 62 VAL cc_start: 0.8079 (m) cc_final: 0.7725 (p) REVERT: B 80 ASP cc_start: 0.7067 (m-30) cc_final: 0.6486 (m-30) REVERT: B 81 ASN cc_start: 0.8107 (t0) cc_final: 0.7860 (m-40) REVERT: B 96 GLU cc_start: 0.6440 (mm-30) cc_final: 0.6024 (mm-30) REVERT: B 97 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7542 (mmtm) REVERT: B 190 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7141 (mmm-85) REVERT: B 195 LYS cc_start: 0.8513 (pttt) cc_final: 0.8295 (tppt) REVERT: B 203 ILE cc_start: 0.8665 (mm) cc_final: 0.8311 (mm) REVERT: B 223 LEU cc_start: 0.8238 (mt) cc_final: 0.8038 (mm) REVERT: B 224 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7157 (mp0) REVERT: B 267 VAL cc_start: 0.9082 (t) cc_final: 0.8835 (p) REVERT: B 308 VAL cc_start: 0.8739 (t) cc_final: 0.8492 (p) REVERT: B 324 GLU cc_start: 0.8144 (mp0) cc_final: 0.7727 (mp0) REVERT: B 325 SER cc_start: 0.8911 (m) cc_final: 0.8686 (t) REVERT: B 327 VAL cc_start: 0.8232 (m) cc_final: 0.7894 (m) REVERT: B 386 LYS cc_start: 0.8343 (mttt) cc_final: 0.7899 (mtmt) REVERT: B 452 LEU cc_start: 0.7527 (mt) cc_final: 0.7124 (mp) REVERT: B 493 ARG cc_start: 0.5160 (mmt90) cc_final: 0.4381 (mpt180) REVERT: B 528 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8034 (pttt) REVERT: B 537 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8094 (tttt) REVERT: B 547 LYS cc_start: 0.8217 (mttt) cc_final: 0.7825 (mttp) REVERT: B 574 ASP cc_start: 0.7941 (p0) cc_final: 0.7724 (t0) REVERT: B 605 SER cc_start: 0.8725 (t) cc_final: 0.8304 (p) REVERT: B 772 VAL cc_start: 0.8735 (t) cc_final: 0.8483 (p) REVERT: B 787 GLN cc_start: 0.7831 (mp10) cc_final: 0.7622 (mp10) REVERT: B 869 MET cc_start: 0.8240 (mtm) cc_final: 0.8003 (mtm) REVERT: B 884 SER cc_start: 0.8935 (m) cc_final: 0.8322 (t) REVERT: B 888 PHE cc_start: 0.8259 (p90) cc_final: 0.7945 (p90) REVERT: B 900 MET cc_start: 0.8597 (mtm) cc_final: 0.8266 (mtp) REVERT: B 922 LEU cc_start: 0.8794 (mt) cc_final: 0.8425 (tp) REVERT: B 936 ASP cc_start: 0.8198 (m-30) cc_final: 0.7775 (m-30) REVERT: B 950 ASP cc_start: 0.7008 (p0) cc_final: 0.6803 (p0) REVERT: B 988 GLU cc_start: 0.7851 (tp30) cc_final: 0.7509 (tm-30) REVERT: B 994 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7934 (t0) REVERT: B 1051 SER cc_start: 0.8882 (t) cc_final: 0.8627 (m) REVERT: B 1073 LYS cc_start: 0.8831 (tttt) cc_final: 0.8428 (mtpp) REVERT: B 1091 ARG cc_start: 0.6748 (tpp-160) cc_final: 0.6314 (ttp80) REVERT: B 1125 ASN cc_start: 0.8610 (p0) cc_final: 0.8387 (p0) REVERT: C 41 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7455 (mmmt) REVERT: C 52 GLN cc_start: 0.7914 (tp40) cc_final: 0.7658 (tp-100) REVERT: C 56 LEU cc_start: 0.8787 (tp) cc_final: 0.8503 (tt) REVERT: C 190 ARG cc_start: 0.7869 (tpt-90) cc_final: 0.7426 (mmm-85) REVERT: C 195 LYS cc_start: 0.6933 (tptt) cc_final: 0.6712 (tptp) REVERT: C 202 LYS cc_start: 0.8070 (tptt) cc_final: 0.7664 (mmmt) REVERT: C 206 LYS cc_start: 0.8827 (tptp) cc_final: 0.8304 (tptp) REVERT: C 237 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7172 (mtm-85) REVERT: C 299 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8653 (m) REVERT: C 304 LYS cc_start: 0.8958 (mttt) cc_final: 0.8708 (mttt) REVERT: C 309 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 319 ARG cc_start: 0.6819 (ptt90) cc_final: 0.6506 (pmt-80) REVERT: C 357 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7059 (ttt180) REVERT: C 374 PHE cc_start: 0.6007 (m-10) cc_final: 0.5240 (m-80) REVERT: C 386 LYS cc_start: 0.8662 (mttt) cc_final: 0.8141 (mttt) REVERT: C 436 TRP cc_start: 0.4127 (t60) cc_final: 0.3531 (t60) REVERT: C 493 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7208 (mtp85) REVERT: C 607 GLN cc_start: 0.8571 (mp10) cc_final: 0.8299 (mp10) REVERT: C 654 GLU cc_start: 0.7972 (tt0) cc_final: 0.7761 (tt0) REVERT: C 673 SER cc_start: 0.8375 (t) cc_final: 0.8174 (t) REVERT: C 725 GLU cc_start: 0.8112 (tt0) cc_final: 0.7630 (tt0) REVERT: C 737 ASP cc_start: 0.7924 (t0) cc_final: 0.7564 (t70) REVERT: C 748 GLU cc_start: 0.8127 (pt0) cc_final: 0.7861 (pt0) REVERT: C 751 ASN cc_start: 0.8769 (m-40) cc_final: 0.8409 (m-40) REVERT: C 787 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7798 (mm-40) REVERT: C 795 LYS cc_start: 0.8563 (mppt) cc_final: 0.8168 (mptt) REVERT: C 800 PHE cc_start: 0.6723 (m-10) cc_final: 0.6332 (m-80) REVERT: C 884 SER cc_start: 0.9083 (m) cc_final: 0.8673 (t) REVERT: C 894 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 934 ILE cc_start: 0.7609 (tp) cc_final: 0.7378 (tp) REVERT: C 935 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 969 LYS cc_start: 0.9296 (mttt) cc_final: 0.8890 (mtmm) REVERT: C 981 PHE cc_start: 0.7571 (t80) cc_final: 0.7145 (t80) REVERT: C 1005 GLN cc_start: 0.8522 (tp40) cc_final: 0.8185 (tp40) REVERT: C 1030 SER cc_start: 0.8851 (m) cc_final: 0.8560 (t) outliers start: 84 outliers final: 48 residues processed: 649 average time/residue: 0.3868 time to fit residues: 378.4215 Evaluate side-chains 605 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 552 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 764 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 675 GLN B 134 GLN B 239 GLN B 280 ASN B 544 ASN B 895 GLN B 954 HIS B 955 ASN B1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126346 restraints weight = 50717.702| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.59 r_work: 0.3589 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25423 Z= 0.166 Angle : 0.595 9.659 34593 Z= 0.310 Chirality : 0.045 0.229 3904 Planarity : 0.004 0.057 4462 Dihedral : 4.619 54.839 3392 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.82 % Allowed : 13.68 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3114 helix: -0.12 (0.20), residues: 632 sheet: 0.49 (0.19), residues: 621 loop : -1.06 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 104 HIS 0.007 0.001 HIS C1088 PHE 0.045 0.002 PHE B 497 TYR 0.023 0.002 TYR C 365 ARG 0.008 0.001 ARG C1107 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 710) hydrogen bonds : angle 5.38507 ( 2013) SS BOND : bond 0.00361 ( 39) SS BOND : angle 1.68356 ( 78) covalent geometry : bond 0.00370 (25384) covalent geometry : angle 0.58980 (34515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 569 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8061 (mtp85) REVERT: A 205 SER cc_start: 0.8560 (t) cc_final: 0.8328 (p) REVERT: A 206 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8107 (ttpt) REVERT: A 239 GLN cc_start: 0.8234 (tt0) cc_final: 0.7789 (tp40) REVERT: A 269 TYR cc_start: 0.8239 (m-10) cc_final: 0.7826 (m-80) REVERT: A 304 LYS cc_start: 0.8850 (mttt) cc_final: 0.8543 (ttmm) REVERT: A 537 LYS cc_start: 0.8165 (tttp) cc_final: 0.7920 (ttmm) REVERT: A 585 LEU cc_start: 0.7645 (mt) cc_final: 0.7356 (mt) REVERT: A 586 ASP cc_start: 0.7047 (t0) cc_final: 0.6476 (p0) REVERT: A 751 ASN cc_start: 0.8777 (m-40) cc_final: 0.8237 (m-40) REVERT: A 756 TYR cc_start: 0.8912 (m-80) cc_final: 0.8295 (m-80) REVERT: A 896 ILE cc_start: 0.7133 (mt) cc_final: 0.6758 (tp) REVERT: A 969 LYS cc_start: 0.9108 (mttt) cc_final: 0.8855 (mtmm) REVERT: A 979 ASP cc_start: 0.7891 (m-30) cc_final: 0.7687 (t0) REVERT: A 1005 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8371 (tp40) REVERT: A 1038 LYS cc_start: 0.9043 (mttt) cc_final: 0.8829 (mmmm) REVERT: B 29 THR cc_start: 0.8135 (t) cc_final: 0.7899 (t) REVERT: B 62 VAL cc_start: 0.8125 (m) cc_final: 0.7732 (p) REVERT: B 190 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.7117 (mmm-85) REVERT: B 267 VAL cc_start: 0.9131 (t) cc_final: 0.8873 (p) REVERT: B 298 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 315 THR cc_start: 0.8902 (m) cc_final: 0.8377 (m) REVERT: B 386 LYS cc_start: 0.8416 (mttt) cc_final: 0.7948 (mtmt) REVERT: B 493 ARG cc_start: 0.5277 (mmt90) cc_final: 0.4737 (mmt90) REVERT: B 528 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8044 (ptpt) REVERT: B 537 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8075 (tttt) REVERT: B 563 GLN cc_start: 0.4211 (tt0) cc_final: 0.3415 (tt0) REVERT: B 605 SER cc_start: 0.8783 (t) cc_final: 0.8187 (p) REVERT: B 607 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8206 (mt0) REVERT: B 675 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7085 (mm-40) REVERT: B 752 LEU cc_start: 0.8916 (mt) cc_final: 0.8567 (mp) REVERT: B 772 VAL cc_start: 0.8832 (t) cc_final: 0.8595 (p) REVERT: B 884 SER cc_start: 0.9011 (m) cc_final: 0.8489 (t) REVERT: B 888 PHE cc_start: 0.8261 (p90) cc_final: 0.7954 (p90) REVERT: B 904 TYR cc_start: 0.6466 (m-10) cc_final: 0.6194 (m-10) REVERT: B 922 LEU cc_start: 0.8854 (mt) cc_final: 0.8434 (tp) REVERT: B 933 LYS cc_start: 0.8531 (mttt) cc_final: 0.8282 (mttt) REVERT: B 936 ASP cc_start: 0.8200 (m-30) cc_final: 0.7765 (m-30) REVERT: B 988 GLU cc_start: 0.7825 (tp30) cc_final: 0.7515 (tm-30) REVERT: B 994 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 1051 SER cc_start: 0.8882 (t) cc_final: 0.8520 (m) REVERT: B 1073 LYS cc_start: 0.8865 (tttt) cc_final: 0.8417 (mtpp) REVERT: B 1121 PHE cc_start: 0.7039 (t80) cc_final: 0.6812 (t80) REVERT: C 52 GLN cc_start: 0.7859 (tp40) cc_final: 0.7514 (tp-100) REVERT: C 53 ASP cc_start: 0.8057 (m-30) cc_final: 0.7719 (m-30) REVERT: C 56 LEU cc_start: 0.8788 (tp) cc_final: 0.8494 (tt) REVERT: C 190 ARG cc_start: 0.8223 (tpt-90) cc_final: 0.7639 (mmm-85) REVERT: C 195 LYS cc_start: 0.7100 (tptt) cc_final: 0.6651 (mmtt) REVERT: C 206 LYS cc_start: 0.8860 (tptp) cc_final: 0.8383 (tptp) REVERT: C 237 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7249 (mtm-85) REVERT: C 287 ASP cc_start: 0.8180 (t0) cc_final: 0.7828 (t0) REVERT: C 304 LYS cc_start: 0.8986 (mttt) cc_final: 0.8721 (mttt) REVERT: C 309 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 319 ARG cc_start: 0.6850 (ptt90) cc_final: 0.6238 (pmt-80) REVERT: C 357 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7294 (ttt180) REVERT: C 374 PHE cc_start: 0.5936 (m-10) cc_final: 0.4994 (m-80) REVERT: C 386 LYS cc_start: 0.8669 (mttt) cc_final: 0.8221 (mttt) REVERT: C 436 TRP cc_start: 0.4344 (t60) cc_final: 0.3453 (t60) REVERT: C 493 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7308 (mpp80) REVERT: C 508 TYR cc_start: 0.3756 (m-80) cc_final: 0.2530 (m-80) REVERT: C 607 GLN cc_start: 0.8595 (mp10) cc_final: 0.8277 (mp10) REVERT: C 643 PHE cc_start: 0.8409 (t80) cc_final: 0.8206 (t80) REVERT: C 654 GLU cc_start: 0.8020 (tt0) cc_final: 0.7800 (tt0) REVERT: C 725 GLU cc_start: 0.8031 (tt0) cc_final: 0.7540 (tt0) REVERT: C 737 ASP cc_start: 0.8074 (t0) cc_final: 0.7821 (t0) REVERT: C 751 ASN cc_start: 0.8939 (m-40) cc_final: 0.8677 (m-40) REVERT: C 787 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7750 (mm-40) REVERT: C 795 LYS cc_start: 0.8739 (mppt) cc_final: 0.8359 (mptt) REVERT: C 800 PHE cc_start: 0.7485 (m-10) cc_final: 0.7274 (m-80) REVERT: C 884 SER cc_start: 0.9137 (m) cc_final: 0.8744 (t) REVERT: C 933 LYS cc_start: 0.8202 (mttt) cc_final: 0.7711 (mtmm) REVERT: C 934 ILE cc_start: 0.7725 (tp) cc_final: 0.7496 (tp) REVERT: C 969 LYS cc_start: 0.9329 (mttt) cc_final: 0.8943 (mtmm) REVERT: C 981 PHE cc_start: 0.7578 (t80) cc_final: 0.7281 (t80) REVERT: C 1002 GLN cc_start: 0.8667 (tp40) cc_final: 0.8368 (tp40) REVERT: C 1005 GLN cc_start: 0.8503 (tp40) cc_final: 0.8108 (tp40) outliers start: 78 outliers final: 49 residues processed: 612 average time/residue: 0.3925 time to fit residues: 363.7458 Evaluate side-chains 569 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 518 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 140 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 271 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 675 GLN B 66 HIS B 134 GLN B 188 ASN B 245 HIS B 779 GLN B 907 ASN B1005 GLN C 30 ASN C 450 ASN C1054 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.153180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120270 restraints weight = 50187.948| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.47 r_work: 0.3484 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25423 Z= 0.261 Angle : 0.672 10.935 34593 Z= 0.353 Chirality : 0.048 0.243 3904 Planarity : 0.005 0.082 4462 Dihedral : 4.856 24.258 3392 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.94 % Allowed : 13.94 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3114 helix: 0.23 (0.21), residues: 636 sheet: 0.40 (0.19), residues: 640 loop : -1.05 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 104 HIS 0.007 0.001 HIS A1058 PHE 0.034 0.002 PHE B 497 TYR 0.031 0.002 TYR A 91 ARG 0.010 0.001 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 710) hydrogen bonds : angle 5.54024 ( 2013) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.94700 ( 78) covalent geometry : bond 0.00597 (25384) covalent geometry : angle 0.66636 (34515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 562 time to evaluate : 2.896 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: A 92 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 133 PHE cc_start: 0.6776 (m-10) cc_final: 0.6491 (m-10) REVERT: A 158 ARG cc_start: 0.6911 (mmp-170) cc_final: 0.6309 (mmm160) REVERT: A 190 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8249 (mtt-85) REVERT: A 205 SER cc_start: 0.8783 (t) cc_final: 0.8551 (p) REVERT: A 206 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8194 (ttpt) REVERT: A 239 GLN cc_start: 0.8392 (tt0) cc_final: 0.7915 (tp40) REVERT: A 240 THR cc_start: 0.7670 (m) cc_final: 0.7117 (t) REVERT: A 245 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.5722 (m170) REVERT: A 304 LYS cc_start: 0.8834 (mttt) cc_final: 0.8610 (mtpp) REVERT: A 319 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7749 (mtt180) REVERT: A 585 LEU cc_start: 0.7958 (mt) cc_final: 0.7636 (mt) REVERT: A 586 ASP cc_start: 0.7106 (t0) cc_final: 0.6435 (p0) REVERT: A 591 SER cc_start: 0.9106 (t) cc_final: 0.8741 (p) REVERT: A 776 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8400 (ttmm) REVERT: A 896 ILE cc_start: 0.7677 (mt) cc_final: 0.7369 (tp) REVERT: A 969 LYS cc_start: 0.9182 (mttt) cc_final: 0.8969 (mtmm) REVERT: A 1005 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8383 (tp40) REVERT: A 1038 LYS cc_start: 0.9280 (mttt) cc_final: 0.9018 (mmmm) REVERT: B 66 HIS cc_start: 0.5796 (p90) cc_final: 0.4570 (p-80) REVERT: B 190 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.7153 (mmm-85) REVERT: B 195 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: B 304 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8668 (mmmm) REVERT: B 324 GLU cc_start: 0.8111 (mp0) cc_final: 0.7568 (pm20) REVERT: B 386 LYS cc_start: 0.8582 (mttt) cc_final: 0.8125 (mtmt) REVERT: B 452 LEU cc_start: 0.7439 (mt) cc_final: 0.7214 (mp) REVERT: B 537 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8270 (tttt) REVERT: B 605 SER cc_start: 0.8928 (t) cc_final: 0.8609 (p) REVERT: B 675 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7158 (mm-40) REVERT: B 756 TYR cc_start: 0.8613 (m-80) cc_final: 0.8365 (m-80) REVERT: B 884 SER cc_start: 0.8979 (m) cc_final: 0.8628 (t) REVERT: B 888 PHE cc_start: 0.8626 (p90) cc_final: 0.8390 (p90) REVERT: B 900 MET cc_start: 0.8799 (mtm) cc_final: 0.8427 (mtp) REVERT: B 922 LEU cc_start: 0.8881 (mt) cc_final: 0.8462 (tp) REVERT: B 988 GLU cc_start: 0.7932 (tp30) cc_final: 0.7576 (tm-30) REVERT: B 994 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7916 (t0) REVERT: B 1051 SER cc_start: 0.8844 (t) cc_final: 0.8489 (m) REVERT: B 1073 LYS cc_start: 0.8805 (tttt) cc_final: 0.8437 (mtpp) REVERT: B 1092 GLU cc_start: 0.7906 (tp30) cc_final: 0.7111 (tm-30) REVERT: B 1113 GLN cc_start: 0.8017 (mt0) cc_final: 0.7815 (mt0) REVERT: B 1116 THR cc_start: 0.8666 (t) cc_final: 0.8380 (p) REVERT: C 52 GLN cc_start: 0.7921 (tp40) cc_final: 0.7550 (tp-100) REVERT: C 53 ASP cc_start: 0.8043 (m-30) cc_final: 0.7716 (m-30) REVERT: C 56 LEU cc_start: 0.8760 (tp) cc_final: 0.8484 (tt) REVERT: C 190 ARG cc_start: 0.8292 (tpt-90) cc_final: 0.7897 (mmm-85) REVERT: C 206 LYS cc_start: 0.8898 (tptp) cc_final: 0.8398 (tptp) REVERT: C 237 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7443 (mtm-85) REVERT: C 304 LYS cc_start: 0.9105 (mttt) cc_final: 0.8856 (mttt) REVERT: C 306 PHE cc_start: 0.8629 (t80) cc_final: 0.8402 (m-80) REVERT: C 319 ARG cc_start: 0.6891 (ptt90) cc_final: 0.6490 (pmt-80) REVERT: C 357 ARG cc_start: 0.7924 (ttt180) cc_final: 0.7528 (ttt180) REVERT: C 374 PHE cc_start: 0.6171 (m-10) cc_final: 0.5235 (m-80) REVERT: C 386 LYS cc_start: 0.8798 (mttt) cc_final: 0.8408 (mttt) REVERT: C 436 TRP cc_start: 0.4835 (t60) cc_final: 0.4192 (t60) REVERT: C 493 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7352 (mpp80) REVERT: C 539 VAL cc_start: 0.8546 (m) cc_final: 0.8337 (p) REVERT: C 607 GLN cc_start: 0.8620 (mp10) cc_final: 0.8265 (mp10) REVERT: C 737 ASP cc_start: 0.8220 (t0) cc_final: 0.7967 (t0) REVERT: C 751 ASN cc_start: 0.9008 (m-40) cc_final: 0.8744 (m-40) REVERT: C 758 SER cc_start: 0.8207 (p) cc_final: 0.7987 (p) REVERT: C 787 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7710 (mm-40) REVERT: C 790 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7529 (mmmt) REVERT: C 795 LYS cc_start: 0.8883 (mppt) cc_final: 0.8511 (mptt) REVERT: C 884 SER cc_start: 0.9188 (m) cc_final: 0.8798 (t) REVERT: C 894 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 933 LYS cc_start: 0.8432 (mttt) cc_final: 0.8213 (mttt) REVERT: C 934 ILE cc_start: 0.7989 (tp) cc_final: 0.7699 (tp) REVERT: C 969 LYS cc_start: 0.9339 (mttt) cc_final: 0.9048 (mtpp) REVERT: C 976 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 979 ASP cc_start: 0.8372 (p0) cc_final: 0.8161 (p0) REVERT: C 981 PHE cc_start: 0.7765 (t80) cc_final: 0.7451 (t80) REVERT: C 984 LEU cc_start: 0.7829 (mp) cc_final: 0.7563 (tp) REVERT: C 1002 GLN cc_start: 0.8694 (tp40) cc_final: 0.8415 (tp40) REVERT: C 1005 GLN cc_start: 0.8615 (tp40) cc_final: 0.8390 (tp40) outliers start: 109 outliers final: 65 residues processed: 623 average time/residue: 0.3945 time to fit residues: 371.0773 Evaluate side-chains 588 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 515 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 271 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 279 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 314 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1074 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** 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 = 0.4160 r_free = 0.4160 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123115 restraints weight = 49858.334| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.47 r_work: 0.3519 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25423 Z= 0.134 Angle : 0.600 9.763 34593 Z= 0.312 Chirality : 0.045 0.198 3904 Planarity : 0.004 0.083 4462 Dihedral : 4.588 21.703 3391 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.78 % Allowed : 16.46 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3114 helix: 0.77 (0.22), residues: 616 sheet: 0.43 (0.19), residues: 624 loop : -0.99 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 104 HIS 0.018 0.001 HIS A 245 PHE 0.028 0.002 PHE B 456 TYR 0.019 0.001 TYR A 91 ARG 0.008 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 710) hydrogen bonds : angle 5.25333 ( 2013) SS BOND : bond 0.00339 ( 39) SS BOND : angle 1.52839 ( 78) covalent geometry : bond 0.00306 (25384) covalent geometry : angle 0.59605 (34515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 540 time to evaluate : 2.860 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 92 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 104 TRP cc_start: 0.8440 (m-10) cc_final: 0.8174 (m-10) REVERT: A 158 ARG cc_start: 0.6906 (mmp-170) cc_final: 0.6432 (mmm160) REVERT: A 190 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8182 (mtt-85) REVERT: A 205 SER cc_start: 0.8682 (t) cc_final: 0.8480 (p) REVERT: A 206 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8237 (ttpt) REVERT: A 239 GLN cc_start: 0.8384 (tt0) cc_final: 0.7885 (tp40) REVERT: A 240 THR cc_start: 0.7610 (m) cc_final: 0.7086 (t) REVERT: A 271 GLN cc_start: 0.8526 (mt0) cc_final: 0.8178 (mt0) REVERT: A 304 LYS cc_start: 0.8856 (mttt) cc_final: 0.8545 (ttmm) REVERT: A 567 ARG cc_start: 0.7020 (ptp-110) cc_final: 0.6778 (ptp-110) REVERT: A 585 LEU cc_start: 0.7969 (mt) cc_final: 0.7683 (mt) REVERT: A 591 SER cc_start: 0.9100 (t) cc_final: 0.8749 (p) REVERT: A 592 PHE cc_start: 0.8056 (p90) cc_final: 0.7853 (p90) REVERT: A 776 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8428 (ttmm) REVERT: A 814 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8339 (mmmt) REVERT: A 896 ILE cc_start: 0.7737 (mt) cc_final: 0.7434 (tp) REVERT: A 969 LYS cc_start: 0.9164 (mttt) cc_final: 0.8918 (mtmm) REVERT: A 1038 LYS cc_start: 0.9195 (mttt) cc_final: 0.8956 (mmmm) REVERT: B 190 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7144 (mmm-85) REVERT: B 304 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8658 (mmmm) REVERT: B 324 GLU cc_start: 0.7966 (mp0) cc_final: 0.7478 (pm20) REVERT: B 386 LYS cc_start: 0.8523 (mttt) cc_final: 0.8068 (mtmt) REVERT: B 452 LEU cc_start: 0.7259 (mt) cc_final: 0.7014 (mp) REVERT: B 493 ARG cc_start: 0.5666 (mmt90) cc_final: 0.5291 (mmt-90) REVERT: B 537 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8176 (tttt) REVERT: B 605 SER cc_start: 0.8928 (t) cc_final: 0.8335 (p) REVERT: B 607 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8183 (mt0) REVERT: B 675 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7087 (mm-40) REVERT: B 884 SER cc_start: 0.8921 (m) cc_final: 0.8562 (t) REVERT: B 888 PHE cc_start: 0.8606 (p90) cc_final: 0.8386 (p90) REVERT: B 900 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: B 922 LEU cc_start: 0.8788 (mt) cc_final: 0.8361 (tp) REVERT: B 988 GLU cc_start: 0.7931 (tp30) cc_final: 0.7680 (tm-30) REVERT: B 994 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7654 (t0) REVERT: B 1051 SER cc_start: 0.8818 (t) cc_final: 0.8446 (m) REVERT: B 1073 LYS cc_start: 0.8737 (tttt) cc_final: 0.8399 (mtpp) REVERT: B 1092 GLU cc_start: 0.7885 (tp30) cc_final: 0.7148 (tm-30) REVERT: C 52 GLN cc_start: 0.7878 (tp40) cc_final: 0.7491 (tp-100) REVERT: C 53 ASP cc_start: 0.8042 (m-30) cc_final: 0.7668 (m-30) REVERT: C 56 LEU cc_start: 0.8758 (tp) cc_final: 0.8452 (tt) REVERT: C 190 ARG cc_start: 0.8282 (tpt-90) cc_final: 0.7865 (mmm-85) REVERT: C 206 LYS cc_start: 0.8818 (tptp) cc_final: 0.8322 (tptp) REVERT: C 237 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7319 (mtm-85) REVERT: C 304 LYS cc_start: 0.9060 (mttt) cc_final: 0.8812 (mttt) REVERT: C 319 ARG cc_start: 0.6849 (ptt90) cc_final: 0.6449 (pmt-80) REVERT: C 357 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7401 (ttt180) REVERT: C 374 PHE cc_start: 0.6378 (m-10) cc_final: 0.5363 (m-80) REVERT: C 386 LYS cc_start: 0.8778 (mttt) cc_final: 0.8384 (mttt) REVERT: C 436 TRP cc_start: 0.4913 (t60) cc_final: 0.4234 (t60) REVERT: C 607 GLN cc_start: 0.8547 (mp10) cc_final: 0.8271 (mp10) REVERT: C 712 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 737 ASP cc_start: 0.8161 (t0) cc_final: 0.7889 (t0) REVERT: C 751 ASN cc_start: 0.9056 (m-40) cc_final: 0.8785 (m-40) REVERT: C 758 SER cc_start: 0.8131 (p) cc_final: 0.7877 (p) REVERT: C 773 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 795 LYS cc_start: 0.8895 (mppt) cc_final: 0.8510 (mptt) REVERT: C 867 ASP cc_start: 0.8357 (p0) cc_final: 0.8090 (p0) REVERT: C 884 SER cc_start: 0.9126 (m) cc_final: 0.8752 (t) REVERT: C 902 MET cc_start: 0.8572 (mmt) cc_final: 0.8363 (mmt) REVERT: C 933 LYS cc_start: 0.8353 (mttt) cc_final: 0.8129 (mttt) REVERT: C 969 LYS cc_start: 0.9310 (mttt) cc_final: 0.8987 (mtpp) REVERT: C 981 PHE cc_start: 0.7736 (t80) cc_final: 0.7442 (t80) REVERT: C 984 LEU cc_start: 0.7719 (mp) cc_final: 0.7487 (tp) REVERT: C 1002 GLN cc_start: 0.8617 (tp40) cc_final: 0.8348 (tp40) REVERT: C 1005 GLN cc_start: 0.8560 (tp40) cc_final: 0.8359 (tp40) outliers start: 77 outliers final: 57 residues processed: 583 average time/residue: 0.4026 time to fit residues: 354.1652 Evaluate side-chains 572 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 509 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 208 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.152433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119691 restraints weight = 49796.500| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.43 r_work: 0.3474 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25423 Z= 0.202 Angle : 0.642 12.157 34593 Z= 0.332 Chirality : 0.046 0.229 3904 Planarity : 0.004 0.082 4462 Dihedral : 4.641 22.372 3391 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.74 % Allowed : 17.69 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3114 helix: 0.85 (0.22), residues: 616 sheet: 0.27 (0.19), residues: 647 loop : -1.01 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 104 HIS 0.005 0.001 HIS A 207 PHE 0.022 0.002 PHE C 338 TYR 0.023 0.002 TYR A 91 ARG 0.009 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 710) hydrogen bonds : angle 5.27550 ( 2013) SS BOND : bond 0.00491 ( 39) SS BOND : angle 1.62307 ( 78) covalent geometry : bond 0.00467 (25384) covalent geometry : angle 0.63800 (34515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 528 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 158 ARG cc_start: 0.7026 (mmp-170) cc_final: 0.6762 (mmm160) REVERT: A 190 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8250 (mtt90) REVERT: A 205 SER cc_start: 0.8748 (t) cc_final: 0.8542 (p) REVERT: A 206 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8255 (ttpt) REVERT: A 239 GLN cc_start: 0.8377 (tt0) cc_final: 0.7791 (tp40) REVERT: A 240 THR cc_start: 0.7691 (m) cc_final: 0.7203 (t) REVERT: A 271 GLN cc_start: 0.8476 (mt0) cc_final: 0.8051 (mt0) REVERT: A 319 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7523 (mtt180) REVERT: A 567 ARG cc_start: 0.7106 (ptp-110) cc_final: 0.6728 (ptp-110) REVERT: A 751 ASN cc_start: 0.8843 (m-40) cc_final: 0.8278 (m110) REVERT: A 776 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8438 (ttmm) REVERT: A 814 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8342 (mmmt) REVERT: A 896 ILE cc_start: 0.7671 (mt) cc_final: 0.7383 (tp) REVERT: A 933 LYS cc_start: 0.8623 (mttt) cc_final: 0.8266 (mttt) REVERT: A 969 LYS cc_start: 0.9146 (mttt) cc_final: 0.8920 (mtmm) REVERT: A 990 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 1038 LYS cc_start: 0.9238 (mttt) cc_final: 0.8993 (mmmm) REVERT: A 1092 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 41 LYS cc_start: 0.7298 (mmmt) cc_final: 0.7048 (mmmt) REVERT: B 190 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.7249 (mmm-85) REVERT: B 298 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7926 (tp30) REVERT: B 304 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8689 (mmmm) REVERT: B 318 PHE cc_start: 0.7776 (m-10) cc_final: 0.7563 (m-10) REVERT: B 324 GLU cc_start: 0.8053 (mp0) cc_final: 0.7610 (pm20) REVERT: B 386 LYS cc_start: 0.8486 (mttt) cc_final: 0.8137 (mtmt) REVERT: B 420 ASP cc_start: 0.7931 (m-30) cc_final: 0.7729 (m-30) REVERT: B 427 ASP cc_start: 0.8505 (p0) cc_final: 0.8148 (p0) REVERT: B 452 LEU cc_start: 0.7185 (mt) cc_final: 0.6925 (mt) REVERT: B 547 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8269 (mmmm) REVERT: B 605 SER cc_start: 0.8949 (t) cc_final: 0.8370 (p) REVERT: B 607 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8176 (mt0) REVERT: B 646 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7336 (tpt170) REVERT: B 884 SER cc_start: 0.8949 (m) cc_final: 0.8625 (t) REVERT: B 900 MET cc_start: 0.8749 (mtm) cc_final: 0.8393 (mtp) REVERT: B 922 LEU cc_start: 0.8808 (mt) cc_final: 0.8370 (tp) REVERT: B 988 GLU cc_start: 0.7904 (tp30) cc_final: 0.7686 (tm-30) REVERT: B 994 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 1050 MET cc_start: 0.8640 (mtp) cc_final: 0.8386 (mtm) REVERT: B 1051 SER cc_start: 0.8800 (t) cc_final: 0.8471 (m) REVERT: B 1073 LYS cc_start: 0.8759 (tttt) cc_final: 0.8421 (mtpp) REVERT: B 1092 GLU cc_start: 0.7943 (tp30) cc_final: 0.7170 (tm-30) REVERT: C 47 VAL cc_start: 0.9172 (m) cc_final: 0.8893 (p) REVERT: C 52 GLN cc_start: 0.7941 (tp40) cc_final: 0.7550 (tp-100) REVERT: C 53 ASP cc_start: 0.7982 (m-30) cc_final: 0.7624 (m-30) REVERT: C 56 LEU cc_start: 0.8745 (tp) cc_final: 0.8446 (tt) REVERT: C 190 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.7828 (mmm-85) REVERT: C 206 LYS cc_start: 0.8822 (tptp) cc_final: 0.8339 (tptp) REVERT: C 237 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7251 (mtm-85) REVERT: C 304 LYS cc_start: 0.9135 (mttt) cc_final: 0.8818 (mttt) REVERT: C 319 ARG cc_start: 0.6930 (ptt90) cc_final: 0.6599 (pmt-80) REVERT: C 357 ARG cc_start: 0.7898 (ttt180) cc_final: 0.7548 (ttt180) REVERT: C 386 LYS cc_start: 0.8754 (mttt) cc_final: 0.8417 (mttt) REVERT: C 436 TRP cc_start: 0.5010 (t60) cc_final: 0.4615 (t60) REVERT: C 558 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7472 (tptt) REVERT: C 607 GLN cc_start: 0.8558 (mp10) cc_final: 0.8305 (mp10) REVERT: C 712 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8535 (mt) REVERT: C 737 ASP cc_start: 0.8253 (t0) cc_final: 0.7982 (t0) REVERT: C 751 ASN cc_start: 0.9170 (m-40) cc_final: 0.8939 (m-40) REVERT: C 758 SER cc_start: 0.8109 (p) cc_final: 0.7844 (p) REVERT: C 773 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7456 (mm-30) REVERT: C 795 LYS cc_start: 0.8925 (mppt) cc_final: 0.8548 (mptt) REVERT: C 884 SER cc_start: 0.9158 (m) cc_final: 0.8785 (t) REVERT: C 964 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8588 (mmtt) REVERT: C 969 LYS cc_start: 0.9294 (mttt) cc_final: 0.8963 (mtpp) REVERT: C 976 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 981 PHE cc_start: 0.7829 (t80) cc_final: 0.7556 (t80) REVERT: C 984 LEU cc_start: 0.7809 (mp) cc_final: 0.7557 (tp) REVERT: C 1002 GLN cc_start: 0.8629 (tp40) cc_final: 0.8363 (tp40) REVERT: C 1120 THR cc_start: 0.8427 (m) cc_final: 0.8144 (p) outliers start: 76 outliers final: 61 residues processed: 568 average time/residue: 0.4113 time to fit residues: 352.2525 Evaluate side-chains 571 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 504 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 213 optimal weight: 2.9990 chunk 142 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 270 optimal weight: 0.0980 chunk 226 optimal weight: 0.0000 chunk 300 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 252 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 245 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122211 restraints weight = 49724.651| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.44 r_work: 0.3527 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25423 Z= 0.115 Angle : 0.597 11.854 34593 Z= 0.306 Chirality : 0.044 0.247 3904 Planarity : 0.004 0.083 4462 Dihedral : 4.422 25.057 3391 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 18.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3114 helix: 1.17 (0.22), residues: 611 sheet: 0.36 (0.20), residues: 615 loop : -0.97 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 64 HIS 0.005 0.001 HIS A 207 PHE 0.026 0.001 PHE C 201 TYR 0.014 0.001 TYR B 904 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 710) hydrogen bonds : angle 5.05492 ( 2013) SS BOND : bond 0.00344 ( 39) SS BOND : angle 1.37539 ( 78) covalent geometry : bond 0.00264 (25384) covalent geometry : angle 0.59438 (34515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 519 time to evaluate : 2.851 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 92 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7245 (t80) REVERT: A 104 TRP cc_start: 0.8434 (m-10) cc_final: 0.7963 (m-10) REVERT: A 170 TYR cc_start: 0.8594 (t80) cc_final: 0.8366 (t80) REVERT: A 190 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8266 (mtt90) REVERT: A 205 SER cc_start: 0.8589 (t) cc_final: 0.8338 (p) REVERT: A 239 GLN cc_start: 0.8333 (tt0) cc_final: 0.7948 (tp40) REVERT: A 240 THR cc_start: 0.7668 (m) cc_final: 0.7277 (t) REVERT: A 245 HIS cc_start: 0.6223 (OUTLIER) cc_final: 0.5879 (m170) REVERT: A 567 ARG cc_start: 0.7094 (ptp-110) cc_final: 0.6871 (ptp-110) REVERT: A 751 ASN cc_start: 0.8852 (m-40) cc_final: 0.8308 (m110) REVERT: A 776 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8359 (ttmm) REVERT: A 787 GLN cc_start: 0.7777 (tp40) cc_final: 0.7482 (tp40) REVERT: A 814 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8325 (mmmt) REVERT: A 896 ILE cc_start: 0.7613 (mt) cc_final: 0.7349 (tp) REVERT: A 900 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8024 (mmp) REVERT: A 969 LYS cc_start: 0.9183 (mttt) cc_final: 0.8942 (mtmm) REVERT: A 990 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 1038 LYS cc_start: 0.9240 (mttt) cc_final: 0.8989 (mmmm) REVERT: B 41 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6791 (mmmt) REVERT: B 168 PHE cc_start: 0.4488 (t80) cc_final: 0.4238 (t80) REVERT: B 190 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: B 298 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7984 (tp30) REVERT: B 304 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8677 (mmmm) REVERT: B 386 LYS cc_start: 0.8471 (mttt) cc_final: 0.8100 (mtpt) REVERT: B 427 ASP cc_start: 0.8426 (p0) cc_final: 0.8032 (p0) REVERT: B 547 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8212 (mmmm) REVERT: B 605 SER cc_start: 0.8911 (t) cc_final: 0.8326 (p) REVERT: B 607 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8150 (mt0) REVERT: B 646 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7254 (tpt170) REVERT: B 787 GLN cc_start: 0.7963 (mp10) cc_final: 0.7743 (mp10) REVERT: B 884 SER cc_start: 0.8805 (m) cc_final: 0.8497 (t) REVERT: B 900 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8387 (mtp) REVERT: B 922 LEU cc_start: 0.8752 (mt) cc_final: 0.8310 (tp) REVERT: B 988 GLU cc_start: 0.7958 (tp30) cc_final: 0.7705 (tm-30) REVERT: B 994 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7617 (t0) REVERT: B 1051 SER cc_start: 0.8703 (t) cc_final: 0.8369 (m) REVERT: B 1073 LYS cc_start: 0.8694 (tttt) cc_final: 0.8311 (mtpp) REVERT: B 1092 GLU cc_start: 0.7921 (tp30) cc_final: 0.7201 (tm-30) REVERT: B 1116 THR cc_start: 0.8462 (t) cc_final: 0.8246 (p) REVERT: C 52 GLN cc_start: 0.7892 (tp40) cc_final: 0.7505 (tp-100) REVERT: C 53 ASP cc_start: 0.7948 (m-30) cc_final: 0.7571 (m-30) REVERT: C 56 LEU cc_start: 0.8713 (tp) cc_final: 0.8330 (tt) REVERT: C 190 ARG cc_start: 0.8271 (tpt-90) cc_final: 0.7680 (mmm-85) REVERT: C 206 LYS cc_start: 0.8767 (tptp) cc_final: 0.8223 (tptp) REVERT: C 237 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7301 (mtm-85) REVERT: C 304 LYS cc_start: 0.9177 (mttt) cc_final: 0.8877 (mttt) REVERT: C 357 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7423 (ttt180) REVERT: C 386 LYS cc_start: 0.8691 (mttt) cc_final: 0.8360 (mttt) REVERT: C 436 TRP cc_start: 0.5311 (t60) cc_final: 0.4688 (t60) REVERT: C 607 GLN cc_start: 0.8527 (mp10) cc_final: 0.8298 (mp10) REVERT: C 712 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 751 ASN cc_start: 0.9199 (m-40) cc_final: 0.8994 (m-40) REVERT: C 758 SER cc_start: 0.7979 (p) cc_final: 0.7662 (p) REVERT: C 773 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7460 (mm-30) REVERT: C 795 LYS cc_start: 0.8949 (mppt) cc_final: 0.8524 (mmtm) REVERT: C 884 SER cc_start: 0.9086 (m) cc_final: 0.8742 (t) REVERT: C 964 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8605 (mmtt) REVERT: C 969 LYS cc_start: 0.9285 (mttt) cc_final: 0.8940 (mtpp) REVERT: C 976 VAL cc_start: 0.8579 (t) cc_final: 0.8312 (m) REVERT: C 981 PHE cc_start: 0.7684 (t80) cc_final: 0.7430 (t80) REVERT: C 1002 GLN cc_start: 0.8545 (tp40) cc_final: 0.8286 (tp40) REVERT: C 1113 GLN cc_start: 0.8424 (mt0) cc_final: 0.8219 (mt0) REVERT: C 1120 THR cc_start: 0.8333 (m) cc_final: 0.8045 (p) outliers start: 69 outliers final: 48 residues processed: 557 average time/residue: 0.4035 time to fit residues: 338.9883 Evaluate side-chains 563 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 508 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 284 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 207 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 267 optimal weight: 0.0010 chunk 210 optimal weight: 1.9990 overall best weight: 0.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 66 HIS B 134 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122702 restraints weight = 49894.162| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.44 r_work: 0.3543 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25423 Z= 0.113 Angle : 0.603 12.684 34593 Z= 0.309 Chirality : 0.044 0.203 3904 Planarity : 0.004 0.085 4462 Dihedral : 4.326 25.072 3391 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.17 % Allowed : 19.13 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3114 helix: 1.36 (0.23), residues: 609 sheet: 0.34 (0.19), residues: 639 loop : -0.92 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 886 HIS 0.011 0.001 HIS A 245 PHE 0.023 0.001 PHE C 643 TYR 0.018 0.001 TYR B 508 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 710) hydrogen bonds : angle 4.93318 ( 2013) SS BOND : bond 0.00295 ( 39) SS BOND : angle 1.20196 ( 78) covalent geometry : bond 0.00260 (25384) covalent geometry : angle 0.60134 (34515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 524 time to evaluate : 2.489 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 92 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 104 TRP cc_start: 0.8423 (m-10) cc_final: 0.7980 (m-10) REVERT: A 190 ARG cc_start: 0.8525 (mtp180) cc_final: 0.8266 (mtt-85) REVERT: A 205 SER cc_start: 0.8546 (t) cc_final: 0.8211 (p) REVERT: A 239 GLN cc_start: 0.8343 (tt0) cc_final: 0.7963 (tp40) REVERT: A 567 ARG cc_start: 0.7070 (ptp-110) cc_final: 0.6851 (ptp-110) REVERT: A 751 ASN cc_start: 0.8875 (m-40) cc_final: 0.8325 (m110) REVERT: A 814 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8311 (mmmt) REVERT: A 896 ILE cc_start: 0.7597 (mt) cc_final: 0.7338 (tp) REVERT: A 900 MET cc_start: 0.8335 (mmt) cc_final: 0.8025 (mmp) REVERT: A 969 LYS cc_start: 0.9180 (mttt) cc_final: 0.8925 (mtmm) REVERT: A 990 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 993 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 1038 LYS cc_start: 0.9212 (mttt) cc_final: 0.8971 (mmmm) REVERT: A 1072 GLU cc_start: 0.7971 (mp0) cc_final: 0.7672 (mp0) REVERT: A 1086 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7574 (pttp) REVERT: B 190 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: B 298 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7992 (tp30) REVERT: B 304 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8678 (mmmm) REVERT: B 386 LYS cc_start: 0.8456 (mttt) cc_final: 0.8088 (mtpt) REVERT: B 427 ASP cc_start: 0.8407 (p0) cc_final: 0.8059 (p0) REVERT: B 452 LEU cc_start: 0.6981 (mt) cc_final: 0.6758 (mp) REVERT: B 605 SER cc_start: 0.8882 (t) cc_final: 0.8284 (p) REVERT: B 607 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8153 (mt0) REVERT: B 646 ARG cc_start: 0.7680 (ttt180) cc_final: 0.7192 (tpt170) REVERT: B 748 GLU cc_start: 0.8172 (pp20) cc_final: 0.7940 (pm20) REVERT: B 787 GLN cc_start: 0.7971 (mp10) cc_final: 0.7755 (mp10) REVERT: B 884 SER cc_start: 0.8797 (m) cc_final: 0.8486 (t) REVERT: B 900 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: B 988 GLU cc_start: 0.7950 (tp30) cc_final: 0.7683 (tm-30) REVERT: B 994 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7589 (t0) REVERT: B 1051 SER cc_start: 0.8673 (t) cc_final: 0.8377 (m) REVERT: B 1073 LYS cc_start: 0.8677 (tttt) cc_final: 0.8290 (mtpp) REVERT: B 1092 GLU cc_start: 0.7886 (tp30) cc_final: 0.7218 (tm-30) REVERT: B 1116 THR cc_start: 0.8384 (t) cc_final: 0.8168 (p) REVERT: C 52 GLN cc_start: 0.7902 (tp40) cc_final: 0.7500 (tp-100) REVERT: C 53 ASP cc_start: 0.7886 (m-30) cc_final: 0.7532 (m-30) REVERT: C 56 LEU cc_start: 0.8744 (tp) cc_final: 0.8382 (tt) REVERT: C 65 PHE cc_start: 0.7169 (m-10) cc_final: 0.6968 (m-10) REVERT: C 190 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.7748 (mmm-85) REVERT: C 206 LYS cc_start: 0.8794 (tptp) cc_final: 0.8251 (tptp) REVERT: C 237 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7292 (mtm-85) REVERT: C 298 GLU cc_start: 0.8453 (tt0) cc_final: 0.8194 (tt0) REVERT: C 304 LYS cc_start: 0.9153 (mttt) cc_final: 0.8848 (mttt) REVERT: C 357 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7392 (ttt180) REVERT: C 386 LYS cc_start: 0.8637 (mttt) cc_final: 0.8315 (mttt) REVERT: C 436 TRP cc_start: 0.5262 (t60) cc_final: 0.4678 (t60) REVERT: C 607 GLN cc_start: 0.8517 (mp10) cc_final: 0.8310 (mp10) REVERT: C 712 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8510 (mt) REVERT: C 737 ASP cc_start: 0.8067 (t0) cc_final: 0.7823 (t70) REVERT: C 751 ASN cc_start: 0.9213 (m-40) cc_final: 0.8984 (m-40) REVERT: C 795 LYS cc_start: 0.8965 (mppt) cc_final: 0.8630 (mmtm) REVERT: C 884 SER cc_start: 0.9074 (m) cc_final: 0.8746 (t) REVERT: C 964 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8600 (mmtt) REVERT: C 969 LYS cc_start: 0.9208 (mttt) cc_final: 0.8845 (mtpp) REVERT: C 976 VAL cc_start: 0.8572 (t) cc_final: 0.8268 (m) REVERT: C 981 PHE cc_start: 0.7645 (t80) cc_final: 0.7392 (t80) REVERT: C 1113 GLN cc_start: 0.8428 (mt0) cc_final: 0.8222 (mt0) REVERT: C 1120 THR cc_start: 0.8251 (m) cc_final: 0.7963 (p) outliers start: 60 outliers final: 48 residues processed: 556 average time/residue: 0.3908 time to fit residues: 327.3488 Evaluate side-chains 561 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 507 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 243 optimal weight: 0.0980 chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 134 GLN B 563 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN C 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119102 restraints weight = 50096.928| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.43 r_work: 0.3486 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25423 Z= 0.181 Angle : 0.658 13.118 34593 Z= 0.337 Chirality : 0.046 0.216 3904 Planarity : 0.004 0.081 4462 Dihedral : 4.519 23.563 3391 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.38 % Allowed : 19.64 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3114 helix: 1.21 (0.22), residues: 609 sheet: 0.29 (0.19), residues: 639 loop : -0.93 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 886 HIS 0.005 0.001 HIS A 207 PHE 0.033 0.002 PHE B 168 TYR 0.021 0.001 TYR B 508 ARG 0.009 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 710) hydrogen bonds : angle 5.07358 ( 2013) SS BOND : bond 0.00420 ( 39) SS BOND : angle 1.46991 ( 78) covalent geometry : bond 0.00423 (25384) covalent geometry : angle 0.65482 (34515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 531 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7378 (t80) REVERT: A 104 TRP cc_start: 0.8500 (m-10) cc_final: 0.7908 (m-10) REVERT: A 190 ARG cc_start: 0.8513 (mtp180) cc_final: 0.8282 (mtt90) REVERT: A 205 SER cc_start: 0.8686 (t) cc_final: 0.8424 (p) REVERT: A 239 GLN cc_start: 0.8331 (tt0) cc_final: 0.7903 (tp40) REVERT: A 271 GLN cc_start: 0.8612 (mt0) cc_final: 0.8371 (mp10) REVERT: A 751 ASN cc_start: 0.8939 (m-40) cc_final: 0.8386 (m110) REVERT: A 814 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8371 (mmmt) REVERT: A 896 ILE cc_start: 0.7650 (mt) cc_final: 0.7391 (tp) REVERT: A 900 MET cc_start: 0.8387 (mmt) cc_final: 0.8101 (mmp) REVERT: A 969 LYS cc_start: 0.9134 (mttt) cc_final: 0.8917 (mtmm) REVERT: A 1038 LYS cc_start: 0.9178 (mttt) cc_final: 0.8974 (mmmm) REVERT: A 1086 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7589 (pttp) REVERT: B 190 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7169 (mmm-85) REVERT: B 239 GLN cc_start: 0.7913 (pp30) cc_final: 0.7455 (pp30) REVERT: B 298 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8111 (tp30) REVERT: B 304 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8733 (mmmm) REVERT: B 386 LYS cc_start: 0.8492 (mttt) cc_final: 0.8197 (mtmt) REVERT: B 427 ASP cc_start: 0.8426 (p0) cc_final: 0.8118 (p0) REVERT: B 478 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8140 (tppt) REVERT: B 563 GLN cc_start: 0.5508 (pt0) cc_final: 0.5283 (pt0) REVERT: B 605 SER cc_start: 0.8885 (t) cc_final: 0.8413 (p) REVERT: B 607 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8168 (mt0) REVERT: B 646 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7395 (tpt170) REVERT: B 675 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7113 (mm-40) REVERT: B 884 SER cc_start: 0.8909 (m) cc_final: 0.8647 (t) REVERT: B 900 MET cc_start: 0.8730 (mtm) cc_final: 0.8408 (mtp) REVERT: B 988 GLU cc_start: 0.7685 (tp30) cc_final: 0.7449 (tm-30) REVERT: B 994 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7715 (t0) REVERT: B 1017 GLU cc_start: 0.7566 (tp30) cc_final: 0.7116 (tp30) REVERT: B 1051 SER cc_start: 0.8628 (t) cc_final: 0.8304 (m) REVERT: B 1073 LYS cc_start: 0.8744 (tttt) cc_final: 0.8358 (mtpp) REVERT: B 1092 GLU cc_start: 0.7897 (tp30) cc_final: 0.7230 (tm-30) REVERT: B 1116 THR cc_start: 0.8471 (t) cc_final: 0.8247 (p) REVERT: C 52 GLN cc_start: 0.7980 (tp40) cc_final: 0.7586 (tp-100) REVERT: C 53 ASP cc_start: 0.7870 (m-30) cc_final: 0.7523 (m-30) REVERT: C 56 LEU cc_start: 0.8759 (tp) cc_final: 0.8471 (tt) REVERT: C 65 PHE cc_start: 0.7309 (m-10) cc_final: 0.7094 (m-10) REVERT: C 190 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.7885 (mmm-85) REVERT: C 206 LYS cc_start: 0.8821 (tptp) cc_final: 0.8290 (tptp) REVERT: C 237 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7287 (mtm-85) REVERT: C 298 GLU cc_start: 0.8530 (tt0) cc_final: 0.8276 (tt0) REVERT: C 304 LYS cc_start: 0.9112 (mttt) cc_final: 0.8815 (mttt) REVERT: C 338 PHE cc_start: 0.7941 (m-10) cc_final: 0.7686 (m-80) REVERT: C 357 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7506 (ttt180) REVERT: C 386 LYS cc_start: 0.8601 (mttt) cc_final: 0.8307 (mttt) REVERT: C 436 TRP cc_start: 0.5190 (t60) cc_final: 0.4593 (t60) REVERT: C 559 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: C 607 GLN cc_start: 0.8532 (mp10) cc_final: 0.8307 (mp10) REVERT: C 712 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8601 (mt) REVERT: C 751 ASN cc_start: 0.9262 (m-40) cc_final: 0.9057 (m-40) REVERT: C 758 SER cc_start: 0.7978 (p) cc_final: 0.7691 (p) REVERT: C 795 LYS cc_start: 0.8940 (mppt) cc_final: 0.8614 (mmtm) REVERT: C 884 SER cc_start: 0.9145 (m) cc_final: 0.8788 (t) REVERT: C 964 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8591 (mmtt) REVERT: C 969 LYS cc_start: 0.9223 (mttt) cc_final: 0.8935 (mtpp) REVERT: C 976 VAL cc_start: 0.8633 (t) cc_final: 0.8355 (m) REVERT: C 981 PHE cc_start: 0.7752 (t80) cc_final: 0.7530 (t80) REVERT: C 1010 GLN cc_start: 0.8440 (mt0) cc_final: 0.8062 (mp10) REVERT: C 1113 GLN cc_start: 0.8432 (mt0) cc_final: 0.8224 (mt0) REVERT: C 1120 THR cc_start: 0.8326 (m) cc_final: 0.8017 (p) outliers start: 66 outliers final: 54 residues processed: 563 average time/residue: 0.3980 time to fit residues: 336.6025 Evaluate side-chains 576 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 517 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 66 HIS B 134 GLN B 613 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119384 restraints weight = 50064.706| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.44 r_work: 0.3481 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.8057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25423 Z= 0.155 Angle : 0.650 11.420 34593 Z= 0.333 Chirality : 0.045 0.210 3904 Planarity : 0.004 0.089 4462 Dihedral : 4.529 23.224 3391 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.20 % Allowed : 20.58 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3114 helix: 1.17 (0.22), residues: 618 sheet: 0.33 (0.20), residues: 629 loop : -0.92 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 886 HIS 0.005 0.001 HIS A 207 PHE 0.033 0.002 PHE A 981 TYR 0.021 0.001 TYR A 170 ARG 0.008 0.001 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 710) hydrogen bonds : angle 5.03013 ( 2013) SS BOND : bond 0.00326 ( 39) SS BOND : angle 1.49054 ( 78) covalent geometry : bond 0.00362 (25384) covalent geometry : angle 0.64729 (34515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14653.24 seconds wall clock time: 250 minutes 54.76 seconds (15054.76 seconds total)