Starting phenix.real_space_refine on Sat Jun 21 19:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w94_32360/06_2025/7w94_32360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w94_32360/06_2025/7w94_32360.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/7w94_32360/06_2025/7w94_32360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w94_32360/06_2025/7w94_32360.map" model { file = "/net/cci-nas-00/data/ceres_data/7w94_32360/06_2025/7w94_32360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w94_32360/06_2025/7w94_32360.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= 0.035 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 15993 2.51 5 N 4214 2.21 5 O 4761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25082 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8356 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 6 Chain: "C" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8356 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 6 Chain: "A" Number of atoms: 8370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8370 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 6 Time building chain proxies: 16.77, per 1000 atoms: 0.67 Number of scatterers: 25082 At special positions: 0 Unit cell: (157.168, 144.666, 181.279, 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 4761 8.00 N 4214 7.00 C 15993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.04 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=2.03 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=2.04 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 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=2.04 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 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: 6.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5992 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 49 sheets defined 21.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.233A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.524A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.004A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 4.100A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.636A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.662A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.809A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.820A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.504A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.870A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.608A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.678A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (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 965 removed outlier: 3.587A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 954 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.609A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.181A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 4.149A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1142 through 1147' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.838A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.944A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.512A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.575A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.571A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.597A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.506A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.504A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.180A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.584A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.507A pdb=" N ILE C 931 " --> pdb=" O PHE C 927 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (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 965 removed outlier: 3.910A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.787A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.663A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.808A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.729A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.553A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.994A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 410' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 removed outlier: 3.641A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.812A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 782 removed outlier: 3.683A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.907A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.763A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.612A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.812A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.585A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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 965 removed outlier: 3.921A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.816A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.693A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.901A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 68 removed outlier: 4.125A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.921A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.921A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.298A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.792A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.112A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.540A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.528A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.993A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.535A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.684A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 212 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.684A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.566A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.705A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.653A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.707A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.176A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.518A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.725A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.504A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.978A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.278A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.752A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.539A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.151A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.633A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.656A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AF3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.806A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1094 through 1097 676 hydrogen bonds defined for protein. 1848 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: 10.81 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8122 1.35 - 1.47: 6304 1.47 - 1.59: 11092 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 25662 Sorted by residual: bond pdb=" CA ILE B 210 " pdb=" CB ILE B 210 " ideal model delta sigma weight residual 1.544 1.566 -0.022 1.42e-02 4.96e+03 2.40e+00 bond pdb=" N TRP B 152 " pdb=" CA TRP B 152 " ideal model delta sigma weight residual 1.460 1.480 -0.020 1.54e-02 4.22e+03 1.72e+00 bond pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 1.462 1.482 -0.020 1.54e-02 4.22e+03 1.69e+00 bond pdb=" C GLY B 744 " pdb=" N ASP B 745 " ideal model delta sigma weight residual 1.328 1.344 -0.016 1.30e-02 5.92e+03 1.53e+00 bond pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 1.460 1.477 -0.017 1.42e-02 4.96e+03 1.45e+00 ... (remaining 25657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 34718 3.25 - 6.51: 163 6.51 - 9.76: 16 9.76 - 13.01: 1 13.01 - 16.27: 4 Bond angle restraints: 34902 Sorted by residual: angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 132.57 -16.27 3.50e+00 8.16e-02 2.16e+01 angle pdb=" CA LEU B 517 " pdb=" CB LEU B 517 " pdb=" CG LEU B 517 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU A 110 " pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 116.30 131.05 -14.75 3.50e+00 8.16e-02 1.78e+01 angle pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta sigma weight residual 122.08 127.83 -5.75 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C LYS A 150 " pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 ... (remaining 34897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 13916 18.09 - 36.18: 1119 36.18 - 54.27: 187 54.27 - 72.35: 42 72.35 - 90.44: 31 Dihedral angle restraints: 15295 sinusoidal: 5977 harmonic: 9318 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -0.46 -85.54 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.32 -84.68 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 15292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3229 0.061 - 0.122: 619 0.122 - 0.183: 83 0.183 - 0.244: 2 0.244 - 0.305: 3 Chirality restraints: 3936 Sorted by residual: chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE C 119 " pdb=" CA ILE C 119 " pdb=" CG1 ILE C 119 " pdb=" CG2 ILE C 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3933 not shown) Planarity restraints: 4529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO B 987 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.058 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO C 987 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 987 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.046 5.00e-02 4.00e+02 ... (remaining 4526 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7409 2.81 - 3.33: 18966 3.33 - 3.86: 39595 3.86 - 4.38: 42927 4.38 - 4.90: 75730 Nonbonded interactions: 184627 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 20 " pdb=" O LYS B 77 " model vdw 2.292 3.040 nonbonded pdb=" O GLN B 607 " pdb=" OH TYR B 674 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.313 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.320 3.040 ... (remaining 184622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 620 or resid 633 through 1147)) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 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: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 62.600 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 0.003 0.041 25701 Z= 0.146 Angle : 0.669 16.267 34980 Z= 0.361 Chirality : 0.049 0.305 3936 Planarity : 0.005 0.089 4529 Dihedral : 13.569 90.443 9186 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -4.24 (0.11), residues: 3164 helix: -4.98 (0.05), residues: 565 sheet: -1.34 (0.19), residues: 642 loop : -2.78 (0.11), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 152 HIS 0.003 0.000 HIS A 519 PHE 0.015 0.001 PHE B 592 TYR 0.024 0.001 TYR C 451 ARG 0.008 0.000 ARG C 408 Details of bonding type rmsd hydrogen bonds : bond 0.35024 ( 658) hydrogen bonds : angle 10.52896 ( 1848) SS BOND : bond 0.00349 ( 39) SS BOND : angle 0.99940 ( 78) covalent geometry : bond 0.00290 (25662) covalent geometry : angle 0.66828 (34902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 656 time to evaluate : 2.633 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: B 52 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 133 PHE cc_start: 0.7080 (m-80) cc_final: 0.6868 (m-80) REVERT: B 138 ASP cc_start: 0.8240 (m-30) cc_final: 0.7991 (m-30) REVERT: B 177 MET cc_start: -0.4190 (mmp) cc_final: -0.4582 (mmp) REVERT: B 353 TRP cc_start: 0.5899 (p90) cc_final: 0.5528 (p90) REVERT: B 641 ASN cc_start: 0.6793 (m110) cc_final: 0.5956 (p0) REVERT: B 726 ILE cc_start: 0.8755 (mp) cc_final: 0.8539 (mt) REVERT: B 773 GLU cc_start: 0.7609 (tt0) cc_final: 0.7148 (tt0) REVERT: B 804 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8053 (mm110) REVERT: B 820 ASP cc_start: 0.7970 (t0) cc_final: 0.7597 (t0) REVERT: B 1127 ASP cc_start: 0.7021 (t0) cc_final: 0.6608 (t0) REVERT: C 99 ASN cc_start: 0.8048 (m-40) cc_final: 0.7465 (p0) REVERT: C 140 PHE cc_start: 0.6860 (m-80) cc_final: 0.6535 (m-80) REVERT: C 190 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7551 (mtt180) REVERT: C 238 PHE cc_start: 0.6930 (p90) cc_final: 0.6552 (p90) REVERT: C 303 LEU cc_start: 0.8836 (tp) cc_final: 0.8450 (tt) REVERT: C 347 PHE cc_start: 0.4448 (m-10) cc_final: 0.2576 (m-10) REVERT: C 358 ILE cc_start: 0.5947 (mt) cc_final: 0.5715 (pt) REVERT: C 368 LEU cc_start: 0.8316 (pt) cc_final: 0.7937 (pt) REVERT: C 441 LEU cc_start: 0.6822 (mt) cc_final: 0.6165 (tt) REVERT: C 646 ARG cc_start: 0.7863 (mpp80) cc_final: 0.7660 (ttm-80) REVERT: C 748 GLU cc_start: 0.7761 (mp0) cc_final: 0.7558 (mp0) REVERT: C 758 SER cc_start: 0.8117 (p) cc_final: 0.7845 (p) REVERT: C 776 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8333 (ttmt) REVERT: C 960 ASN cc_start: 0.8315 (t0) cc_final: 0.7956 (t0) REVERT: A 40 ASP cc_start: 0.7358 (t70) cc_final: 0.7096 (t70) REVERT: A 55 PHE cc_start: 0.7187 (m-80) cc_final: 0.6800 (m-80) REVERT: A 86 PHE cc_start: 0.7882 (t80) cc_final: 0.7519 (t80) REVERT: A 133 PHE cc_start: 0.5969 (m-80) cc_final: 0.5109 (m-80) REVERT: A 189 LEU cc_start: 0.8657 (tp) cc_final: 0.8409 (tp) REVERT: A 196 ASN cc_start: 0.7476 (p0) cc_final: 0.6637 (p0) REVERT: A 239 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6647 (mm-40) REVERT: A 355 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6820 (ttp80) REVERT: A 400 PHE cc_start: 0.7204 (p90) cc_final: 0.6857 (p90) REVERT: A 528 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7747 (mptt) REVERT: A 556 ASN cc_start: 0.7561 (t0) cc_final: 0.7315 (t0) REVERT: A 578 ASP cc_start: 0.7322 (t0) cc_final: 0.6911 (t0) REVERT: A 606 ASN cc_start: 0.8486 (m-40) cc_final: 0.8270 (m-40) REVERT: A 607 GLN cc_start: 0.8003 (mp10) cc_final: 0.7409 (mp10) REVERT: A 675 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 790 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7112 (mtpt) REVERT: A 973 ILE cc_start: 0.9059 (tt) cc_final: 0.8779 (mt) REVERT: A 994 ASP cc_start: 0.7748 (t0) cc_final: 0.7472 (t0) outliers start: 4 outliers final: 1 residues processed: 659 average time/residue: 0.3951 time to fit residues: 393.6612 Evaluate side-chains 523 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 522 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 0.0470 chunk 241 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 49 HIS B 66 HIS B 99 ASN B 196 ASN B 239 GLN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 655 HIS B 690 GLN B 709 ASN B 774 GLN B 969 ASN B1023 ASN B1106 GLN B1135 ASN C 121 ASN C 137 ASN C 343 ASN C 544 ASN C 563 GLN C 655 HIS C 657 ASN C 965 GLN A 149 ASN A 370 ASN A 422 ASN A1002 GLN A1074 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123922 restraints weight = 52944.103| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.76 r_work: 0.3595 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25701 Z= 0.151 Angle : 0.609 11.463 34980 Z= 0.311 Chirality : 0.046 0.351 3936 Planarity : 0.005 0.067 4529 Dihedral : 4.140 24.945 3441 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.97 % Allowed : 12.01 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.10 (0.12), residues: 3164 helix: -2.82 (0.15), residues: 613 sheet: -0.88 (0.19), residues: 645 loop : -2.31 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.007 0.001 HIS B1083 PHE 0.027 0.002 PHE C 55 TYR 0.021 0.001 TYR B 91 ARG 0.012 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.06440 ( 658) hydrogen bonds : angle 6.10108 ( 1848) SS BOND : bond 0.00301 ( 39) SS BOND : angle 1.22299 ( 78) covalent geometry : bond 0.00336 (25662) covalent geometry : angle 0.60680 (34902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 538 time to evaluate : 2.504 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: B 52 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 177 MET cc_start: -0.4681 (mmp) cc_final: -0.4958 (mmp) REVERT: B 227 VAL cc_start: 0.7557 (m) cc_final: 0.7351 (p) REVERT: B 277 LEU cc_start: 0.8579 (mm) cc_final: 0.8328 (mp) REVERT: B 298 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6906 (tm-30) REVERT: B 353 TRP cc_start: 0.6348 (p90) cc_final: 0.5946 (p90) REVERT: B 355 ARG cc_start: 0.7612 (mpp-170) cc_final: 0.7194 (ttp80) REVERT: B 432 CYS cc_start: 0.2391 (OUTLIER) cc_final: 0.1197 (m) REVERT: B 498 GLN cc_start: 0.6844 (mm110) cc_final: 0.6242 (tp40) REVERT: B 773 GLU cc_start: 0.8118 (tt0) cc_final: 0.7425 (tt0) REVERT: B 820 ASP cc_start: 0.8655 (t0) cc_final: 0.8286 (t0) REVERT: B 855 PHE cc_start: 0.7631 (m-80) cc_final: 0.7277 (m-80) REVERT: B 902 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: B 1127 ASP cc_start: 0.7752 (t0) cc_final: 0.7308 (t0) REVERT: C 99 ASN cc_start: 0.8224 (m-40) cc_final: 0.7722 (p0) REVERT: C 140 PHE cc_start: 0.7317 (m-80) cc_final: 0.6987 (m-80) REVERT: C 190 ARG cc_start: 0.8396 (mtt180) cc_final: 0.8106 (mmm160) REVERT: C 238 PHE cc_start: 0.6970 (p90) cc_final: 0.6653 (p90) REVERT: C 239 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6660 (mm-40) REVERT: C 301 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7632 (m) REVERT: C 324 GLU cc_start: 0.6519 (pp20) cc_final: 0.6220 (pp20) REVERT: C 353 TRP cc_start: 0.5253 (p-90) cc_final: 0.4916 (p-90) REVERT: C 355 ARG cc_start: 0.6261 (tpp-160) cc_final: 0.5664 (tpp-160) REVERT: C 441 LEU cc_start: 0.6785 (mt) cc_final: 0.6100 (tt) REVERT: C 515 PHE cc_start: 0.6878 (p90) cc_final: 0.6362 (p90) REVERT: C 559 PHE cc_start: 0.7554 (m-80) cc_final: 0.7094 (m-80) REVERT: C 646 ARG cc_start: 0.8790 (mpp80) cc_final: 0.8471 (ttm-80) REVERT: C 745 ASP cc_start: 0.7271 (t0) cc_final: 0.6881 (t0) REVERT: C 773 GLU cc_start: 0.7782 (tt0) cc_final: 0.7581 (tt0) REVERT: C 776 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8509 (ttmt) REVERT: C 804 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8426 (mm110) REVERT: C 825 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8451 (mttm) REVERT: C 960 ASN cc_start: 0.8401 (t0) cc_final: 0.8179 (t0) REVERT: C 1017 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 1073 LYS cc_start: 0.8414 (tmtt) cc_final: 0.8198 (mtpt) REVERT: C 1139 ASP cc_start: 0.8176 (t0) cc_final: 0.7922 (t0) REVERT: A 34 ARG cc_start: 0.6293 (mtp85) cc_final: 0.5913 (mmt90) REVERT: A 40 ASP cc_start: 0.7843 (t70) cc_final: 0.7466 (t0) REVERT: A 53 ASP cc_start: 0.7680 (t0) cc_final: 0.7098 (t0) REVERT: A 55 PHE cc_start: 0.7563 (m-80) cc_final: 0.7163 (m-80) REVERT: A 86 PHE cc_start: 0.7852 (t80) cc_final: 0.7547 (t80) REVERT: A 133 PHE cc_start: 0.6232 (m-80) cc_final: 0.5367 (m-80) REVERT: A 177 MET cc_start: -0.2360 (mtp) cc_final: -0.3197 (mtt) REVERT: A 189 LEU cc_start: 0.8890 (tp) cc_final: 0.8624 (tp) REVERT: A 190 ARG cc_start: 0.6945 (mtt180) cc_final: 0.6369 (mtt180) REVERT: A 201 PHE cc_start: 0.6928 (t80) cc_final: 0.6210 (t80) REVERT: A 356 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8412 (tttm) REVERT: A 390 LEU cc_start: 0.8317 (pp) cc_final: 0.7953 (pp) REVERT: A 400 PHE cc_start: 0.7285 (p90) cc_final: 0.6917 (p90) REVERT: A 528 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8313 (mptt) REVERT: A 556 ASN cc_start: 0.7975 (t0) cc_final: 0.7691 (t0) REVERT: A 606 ASN cc_start: 0.8804 (m-40) cc_final: 0.8576 (m-40) REVERT: A 607 GLN cc_start: 0.8379 (mp10) cc_final: 0.7615 (mp10) REVERT: A 643 PHE cc_start: 0.8403 (t80) cc_final: 0.8161 (t80) REVERT: A 646 ARG cc_start: 0.8023 (mpp80) cc_final: 0.7515 (mpp80) REVERT: A 651 ILE cc_start: 0.8868 (tt) cc_final: 0.8625 (pt) REVERT: A 675 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 779 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: A 786 LYS cc_start: 0.8228 (mmmt) cc_final: 0.8007 (mmmt) REVERT: A 820 ASP cc_start: 0.8223 (m-30) cc_final: 0.8015 (m-30) REVERT: A 869 MET cc_start: 0.8414 (mtt) cc_final: 0.8151 (mtt) REVERT: A 900 MET cc_start: 0.8672 (mtm) cc_final: 0.8446 (mtm) REVERT: A 918 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: A 973 ILE cc_start: 0.9269 (tt) cc_final: 0.8972 (pt) REVERT: A 988 GLU cc_start: 0.8426 (tp30) cc_final: 0.8160 (tp30) REVERT: A 1030 SER cc_start: 0.8991 (m) cc_final: 0.8676 (t) REVERT: A 1111 GLU cc_start: 0.8225 (pm20) cc_final: 0.7495 (pm20) outliers start: 55 outliers final: 24 residues processed: 563 average time/residue: 0.3961 time to fit residues: 335.1592 Evaluate side-chains 518 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 488 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 918 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 11 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 563 GLN B 969 ASN B1023 ASN C 239 GLN C 657 ASN C 901 GLN C 928 ASN C1002 GLN A 99 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A1083 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122436 restraints weight = 52532.459| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.63 r_work: 0.3557 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25701 Z= 0.158 Angle : 0.572 12.439 34980 Z= 0.293 Chirality : 0.045 0.289 3936 Planarity : 0.004 0.051 4529 Dihedral : 4.095 20.815 3440 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.64 % Allowed : 14.65 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.42 (0.13), residues: 3164 helix: -1.21 (0.20), residues: 615 sheet: -0.78 (0.19), residues: 673 loop : -2.14 (0.12), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 258 HIS 0.006 0.001 HIS B1083 PHE 0.021 0.001 PHE B 374 TYR 0.028 0.001 TYR A 421 ARG 0.008 0.001 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.05626 ( 658) hydrogen bonds : angle 5.55043 ( 1848) SS BOND : bond 0.00290 ( 39) SS BOND : angle 1.10576 ( 78) covalent geometry : bond 0.00359 (25662) covalent geometry : angle 0.57073 (34902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 508 time to evaluate : 2.548 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: B 52 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 140 PHE cc_start: 0.6324 (p90) cc_final: 0.6110 (p90) REVERT: B 177 MET cc_start: -0.4371 (mmp) cc_final: -0.4884 (mmp) REVERT: B 244 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2320 (pt) REVERT: B 277 LEU cc_start: 0.8618 (mm) cc_final: 0.8351 (mp) REVERT: B 298 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6944 (tm-30) REVERT: B 353 TRP cc_start: 0.6613 (p90) cc_final: 0.6068 (p90) REVERT: B 355 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7127 (ttp80) REVERT: B 432 CYS cc_start: 0.2214 (OUTLIER) cc_final: 0.0985 (m) REVERT: B 498 GLN cc_start: 0.6848 (mm110) cc_final: 0.6333 (tp-100) REVERT: B 560 LEU cc_start: 0.8393 (tp) cc_final: 0.8027 (tp) REVERT: B 820 ASP cc_start: 0.8668 (t0) cc_final: 0.8333 (t0) REVERT: B 825 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8977 (mttp) REVERT: B 902 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7670 (mmm) REVERT: B 1127 ASP cc_start: 0.7804 (t0) cc_final: 0.7365 (t0) REVERT: C 99 ASN cc_start: 0.8192 (m-40) cc_final: 0.7788 (p0) REVERT: C 140 PHE cc_start: 0.7360 (m-80) cc_final: 0.7058 (m-80) REVERT: C 238 PHE cc_start: 0.6910 (p90) cc_final: 0.6613 (p90) REVERT: C 239 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6534 (mm-40) REVERT: C 441 LEU cc_start: 0.6758 (mt) cc_final: 0.6119 (tt) REVERT: C 497 PHE cc_start: 0.3263 (m-80) cc_final: 0.2813 (m-80) REVERT: C 646 ARG cc_start: 0.8758 (mpp80) cc_final: 0.8455 (ttm-80) REVERT: C 745 ASP cc_start: 0.7469 (t0) cc_final: 0.7073 (t0) REVERT: C 776 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8430 (ttpp) REVERT: C 779 GLN cc_start: 0.8624 (tt0) cc_final: 0.8249 (tm-30) REVERT: C 804 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8374 (mm110) REVERT: C 896 ILE cc_start: 0.8403 (mt) cc_final: 0.8069 (tt) REVERT: C 960 ASN cc_start: 0.8447 (t0) cc_final: 0.8230 (t0) REVERT: C 1005 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8007 (mt0) REVERT: C 1073 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8185 (mtpt) REVERT: C 1139 ASP cc_start: 0.8220 (t0) cc_final: 0.7824 (t0) REVERT: A 34 ARG cc_start: 0.6345 (mtp85) cc_final: 0.5982 (mmt90) REVERT: A 40 ASP cc_start: 0.7942 (t70) cc_final: 0.7536 (t0) REVERT: A 86 PHE cc_start: 0.8021 (t80) cc_final: 0.7713 (t80) REVERT: A 133 PHE cc_start: 0.6341 (m-80) cc_final: 0.5463 (m-80) REVERT: A 177 MET cc_start: -0.2571 (mtp) cc_final: -0.3442 (mtt) REVERT: A 189 LEU cc_start: 0.8901 (tp) cc_final: 0.8647 (tp) REVERT: A 190 ARG cc_start: 0.6978 (mtt180) cc_final: 0.6415 (mtt180) REVERT: A 195 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7234 (mmmt) REVERT: A 196 ASN cc_start: 0.8053 (p0) cc_final: 0.7744 (p0) REVERT: A 201 PHE cc_start: 0.6811 (t80) cc_final: 0.6072 (t80) REVERT: A 390 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (pp) REVERT: A 400 PHE cc_start: 0.7323 (p90) cc_final: 0.6925 (p90) REVERT: A 495 TYR cc_start: 0.7650 (m-80) cc_final: 0.7359 (t80) REVERT: A 513 LEU cc_start: 0.8029 (mt) cc_final: 0.7713 (mp) REVERT: A 556 ASN cc_start: 0.8010 (t0) cc_final: 0.7742 (t0) REVERT: A 606 ASN cc_start: 0.8771 (m-40) cc_final: 0.8559 (m-40) REVERT: A 607 GLN cc_start: 0.8406 (mp10) cc_final: 0.7696 (mp10) REVERT: A 643 PHE cc_start: 0.8335 (t80) cc_final: 0.8129 (t80) REVERT: A 790 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8449 (mtpt) REVERT: A 820 ASP cc_start: 0.8234 (m-30) cc_final: 0.8030 (m-30) REVERT: A 900 MET cc_start: 0.8765 (mtm) cc_final: 0.8488 (mtm) REVERT: A 918 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: A 973 ILE cc_start: 0.9199 (tt) cc_final: 0.8960 (pt) REVERT: A 994 ASP cc_start: 0.8246 (t0) cc_final: 0.7977 (t0) REVERT: A 1030 SER cc_start: 0.9000 (m) cc_final: 0.8783 (t) REVERT: A 1092 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7882 (mm-30) outliers start: 74 outliers final: 43 residues processed: 546 average time/residue: 0.3839 time to fit residues: 319.3632 Evaluate side-chains 538 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 489 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 213 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 242 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 151 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 240 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 544 ASN B 787 GLN B 969 ASN C 655 HIS C 928 ASN C 955 ASN A 125 ASN A 969 ASN A1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123336 restraints weight = 53147.851| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.72 r_work: 0.3582 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25701 Z= 0.104 Angle : 0.535 9.347 34980 Z= 0.271 Chirality : 0.044 0.272 3936 Planarity : 0.004 0.048 4529 Dihedral : 3.976 20.040 3440 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.22 % Allowed : 16.51 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.00 (0.14), residues: 3164 helix: -0.46 (0.21), residues: 617 sheet: -0.59 (0.19), residues: 673 loop : -1.99 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.011 0.001 HIS A1083 PHE 0.016 0.001 PHE B 374 TYR 0.027 0.001 TYR C1138 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 658) hydrogen bonds : angle 5.20559 ( 1848) SS BOND : bond 0.00354 ( 39) SS BOND : angle 0.87794 ( 78) covalent geometry : bond 0.00229 (25662) covalent geometry : angle 0.53419 (34902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 504 time to evaluate : 2.814 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: B 52 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 177 MET cc_start: -0.4524 (mmp) cc_final: -0.4963 (mmp) REVERT: B 244 LEU cc_start: 0.2956 (OUTLIER) cc_final: 0.2474 (pt) REVERT: B 277 LEU cc_start: 0.8613 (mm) cc_final: 0.8339 (mp) REVERT: B 298 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6873 (tm-30) REVERT: B 324 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 353 TRP cc_start: 0.6371 (p90) cc_final: 0.5892 (p90) REVERT: B 355 ARG cc_start: 0.7812 (mpp-170) cc_final: 0.7258 (ttp80) REVERT: B 432 CYS cc_start: 0.1943 (OUTLIER) cc_final: 0.0775 (m) REVERT: B 498 GLN cc_start: 0.6895 (mm110) cc_final: 0.6271 (tp-100) REVERT: B 820 ASP cc_start: 0.8669 (t0) cc_final: 0.8358 (t0) REVERT: B 1010 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7889 (mm-40) REVERT: B 1127 ASP cc_start: 0.7778 (t0) cc_final: 0.7290 (t0) REVERT: C 99 ASN cc_start: 0.8230 (m-40) cc_final: 0.7822 (p0) REVERT: C 120 VAL cc_start: 0.8723 (m) cc_final: 0.8480 (p) REVERT: C 140 PHE cc_start: 0.7388 (m-80) cc_final: 0.7076 (m-80) REVERT: C 238 PHE cc_start: 0.7027 (p90) cc_final: 0.6696 (p90) REVERT: C 353 TRP cc_start: 0.5363 (p-90) cc_final: 0.4822 (p-90) REVERT: C 355 ARG cc_start: 0.6399 (tpp-160) cc_final: 0.5593 (tpp80) REVERT: C 441 LEU cc_start: 0.6613 (mt) cc_final: 0.6024 (tt) REVERT: C 497 PHE cc_start: 0.3278 (m-80) cc_final: 0.2956 (m-80) REVERT: C 646 ARG cc_start: 0.8787 (mpp80) cc_final: 0.8461 (ttm-80) REVERT: C 745 ASP cc_start: 0.7578 (t0) cc_final: 0.7175 (t0) REVERT: C 776 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8410 (ttpp) REVERT: C 779 GLN cc_start: 0.8694 (tt0) cc_final: 0.8289 (tm-30) REVERT: C 787 GLN cc_start: 0.8347 (mp10) cc_final: 0.8140 (mp10) REVERT: C 804 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8382 (mm-40) REVERT: C 808 ASP cc_start: 0.8091 (m-30) cc_final: 0.7581 (p0) REVERT: C 896 ILE cc_start: 0.8388 (mt) cc_final: 0.8059 (tt) REVERT: C 983 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7480 (mtm180) REVERT: C 1005 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7980 (mt0) REVERT: C 1017 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 1073 LYS cc_start: 0.8412 (tmtt) cc_final: 0.8171 (mtpt) REVERT: C 1139 ASP cc_start: 0.8213 (t0) cc_final: 0.7800 (t0) REVERT: A 34 ARG cc_start: 0.6363 (mtp85) cc_final: 0.6023 (mmt90) REVERT: A 40 ASP cc_start: 0.7884 (t70) cc_final: 0.7519 (t0) REVERT: A 53 ASP cc_start: 0.7798 (t0) cc_final: 0.7513 (t70) REVERT: A 55 PHE cc_start: 0.7662 (m-80) cc_final: 0.7189 (m-80) REVERT: A 86 PHE cc_start: 0.7845 (t80) cc_final: 0.7573 (t80) REVERT: A 177 MET cc_start: -0.2486 (mtp) cc_final: -0.3237 (mtt) REVERT: A 189 LEU cc_start: 0.8813 (tp) cc_final: 0.8560 (tp) REVERT: A 190 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6430 (mtt180) REVERT: A 195 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7447 (mmmt) REVERT: A 196 ASN cc_start: 0.7983 (p0) cc_final: 0.7622 (p0) REVERT: A 201 PHE cc_start: 0.6751 (t80) cc_final: 0.6091 (t80) REVERT: A 281 GLU cc_start: 0.7634 (pm20) cc_final: 0.7209 (pp20) REVERT: A 390 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7953 (pp) REVERT: A 400 PHE cc_start: 0.7165 (p90) cc_final: 0.6829 (p90) REVERT: A 513 LEU cc_start: 0.7989 (mt) cc_final: 0.7689 (mp) REVERT: A 556 ASN cc_start: 0.7989 (t0) cc_final: 0.7717 (t0) REVERT: A 606 ASN cc_start: 0.8769 (m-40) cc_final: 0.8552 (m-40) REVERT: A 607 GLN cc_start: 0.8370 (mp10) cc_final: 0.7625 (mp10) REVERT: A 643 PHE cc_start: 0.8256 (t80) cc_final: 0.8052 (t80) REVERT: A 651 ILE cc_start: 0.9099 (tt) cc_final: 0.8871 (pt) REVERT: A 661 GLU cc_start: 0.8013 (tp30) cc_final: 0.7711 (tp30) REVERT: A 759 PHE cc_start: 0.7963 (t80) cc_final: 0.7754 (t80) REVERT: A 869 MET cc_start: 0.8401 (mtt) cc_final: 0.8079 (mtt) REVERT: A 900 MET cc_start: 0.8760 (mtm) cc_final: 0.8499 (mtm) REVERT: A 918 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 994 ASP cc_start: 0.8149 (t0) cc_final: 0.7911 (t0) REVERT: A 1092 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7883 (mm-30) outliers start: 62 outliers final: 41 residues processed: 540 average time/residue: 0.3796 time to fit residues: 313.3328 Evaluate side-chains 520 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 475 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 918 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 251 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 101 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN B 969 ASN B1106 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN A 969 ASN A1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.155435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.122411 restraints weight = 52984.559| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.71 r_work: 0.3567 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25701 Z= 0.116 Angle : 0.541 13.927 34980 Z= 0.273 Chirality : 0.044 0.239 3936 Planarity : 0.004 0.050 4529 Dihedral : 3.966 21.780 3440 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.86 % Allowed : 17.12 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.72 (0.14), residues: 3164 helix: 0.02 (0.22), residues: 611 sheet: -0.49 (0.19), residues: 653 loop : -1.86 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.004 0.001 HIS B1083 PHE 0.023 0.001 PHE A 374 TYR 0.027 0.001 TYR C1138 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 658) hydrogen bonds : angle 5.03746 ( 1848) SS BOND : bond 0.00247 ( 39) SS BOND : angle 1.06038 ( 78) covalent geometry : bond 0.00263 (25662) covalent geometry : angle 0.53965 (34902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 483 time to evaluate : 2.703 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: B 52 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8473 (tm-30) REVERT: B 177 MET cc_start: -0.4377 (mmp) cc_final: -0.4902 (mmt) REVERT: B 277 LEU cc_start: 0.8635 (mm) cc_final: 0.8360 (mp) REVERT: B 298 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 324 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 353 TRP cc_start: 0.6408 (p90) cc_final: 0.5881 (p90) REVERT: B 355 ARG cc_start: 0.7893 (mpp-170) cc_final: 0.7305 (ttp80) REVERT: B 432 CYS cc_start: 0.1929 (OUTLIER) cc_final: 0.0601 (m) REVERT: B 498 GLN cc_start: 0.6809 (mm110) cc_final: 0.6105 (tp40) REVERT: B 690 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: B 760 CYS cc_start: 0.7282 (m) cc_final: 0.6837 (m) REVERT: B 773 GLU cc_start: 0.8169 (tp30) cc_final: 0.7553 (tp30) REVERT: B 776 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7648 (ttpp) REVERT: B 820 ASP cc_start: 0.8683 (t0) cc_final: 0.8389 (t0) REVERT: B 994 ASP cc_start: 0.8188 (t0) cc_final: 0.7987 (t0) REVERT: B 1127 ASP cc_start: 0.7787 (t0) cc_final: 0.7284 (t0) REVERT: C 99 ASN cc_start: 0.8231 (m-40) cc_final: 0.7831 (p0) REVERT: C 120 VAL cc_start: 0.8785 (m) cc_final: 0.8452 (p) REVERT: C 238 PHE cc_start: 0.6901 (p90) cc_final: 0.6552 (p90) REVERT: C 353 TRP cc_start: 0.5465 (p-90) cc_final: 0.4924 (p-90) REVERT: C 441 LEU cc_start: 0.6563 (mt) cc_final: 0.5934 (tt) REVERT: C 497 PHE cc_start: 0.3387 (m-80) cc_final: 0.3138 (m-80) REVERT: C 525 CYS cc_start: 0.2949 (OUTLIER) cc_final: 0.2245 (m) REVERT: C 646 ARG cc_start: 0.8780 (mpp80) cc_final: 0.8454 (ttm-80) REVERT: C 745 ASP cc_start: 0.7700 (t0) cc_final: 0.7305 (t0) REVERT: C 776 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8498 (tttp) REVERT: C 779 GLN cc_start: 0.8730 (tt0) cc_final: 0.8316 (tm-30) REVERT: C 787 GLN cc_start: 0.8366 (mp10) cc_final: 0.8105 (mp10) REVERT: C 804 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8363 (mm-40) REVERT: C 896 ILE cc_start: 0.8403 (mt) cc_final: 0.8069 (tt) REVERT: C 983 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7505 (mtm180) REVERT: C 1005 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8013 (mt0) REVERT: C 1017 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 1073 LYS cc_start: 0.8428 (tmtt) cc_final: 0.8195 (mtpt) REVERT: C 1139 ASP cc_start: 0.8224 (t0) cc_final: 0.7808 (t0) REVERT: A 34 ARG cc_start: 0.6322 (mtp85) cc_final: 0.5994 (mmt90) REVERT: A 40 ASP cc_start: 0.7991 (t70) cc_final: 0.7619 (t0) REVERT: A 53 ASP cc_start: 0.7819 (t0) cc_final: 0.7558 (t0) REVERT: A 55 PHE cc_start: 0.7589 (m-80) cc_final: 0.7103 (m-80) REVERT: A 86 PHE cc_start: 0.7926 (t80) cc_final: 0.7556 (t80) REVERT: A 104 TRP cc_start: 0.7629 (m-90) cc_final: 0.7338 (m-90) REVERT: A 133 PHE cc_start: 0.6386 (m-80) cc_final: 0.5261 (m-80) REVERT: A 177 MET cc_start: -0.2419 (mtp) cc_final: -0.3110 (mtt) REVERT: A 189 LEU cc_start: 0.8825 (tp) cc_final: 0.8578 (tp) REVERT: A 195 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7477 (mmmt) REVERT: A 201 PHE cc_start: 0.6736 (t80) cc_final: 0.6164 (t80) REVERT: A 281 GLU cc_start: 0.7793 (pm20) cc_final: 0.7274 (pp20) REVERT: A 400 PHE cc_start: 0.7115 (p90) cc_final: 0.6765 (p90) REVERT: A 495 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6300 (t80) REVERT: A 556 ASN cc_start: 0.8077 (t0) cc_final: 0.7800 (t0) REVERT: A 580 GLN cc_start: 0.6553 (tp40) cc_final: 0.5968 (tp40) REVERT: A 607 GLN cc_start: 0.8377 (mp10) cc_final: 0.7581 (mp10) REVERT: A 661 GLU cc_start: 0.7992 (tp30) cc_final: 0.7707 (tp30) REVERT: A 790 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8473 (mtpt) REVERT: A 900 MET cc_start: 0.8780 (mtm) cc_final: 0.8490 (mtm) REVERT: A 994 ASP cc_start: 0.8144 (t0) cc_final: 0.7905 (t0) REVERT: A 1092 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7863 (mm-30) outliers start: 80 outliers final: 54 residues processed: 535 average time/residue: 0.3834 time to fit residues: 315.0316 Evaluate side-chains 535 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 477 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN B 787 GLN B 969 ASN C 49 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 764 ASN C 928 ASN C1088 HIS A 450 ASN A 655 HIS A 969 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.149610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116408 restraints weight = 52357.003| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.68 r_work: 0.3498 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25701 Z= 0.231 Angle : 0.639 13.315 34980 Z= 0.330 Chirality : 0.048 0.234 3936 Planarity : 0.004 0.051 4529 Dihedral : 4.468 22.566 3440 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.40 % Allowed : 18.01 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.89 (0.14), residues: 3164 helix: -0.09 (0.21), residues: 621 sheet: -0.61 (0.19), residues: 651 loop : -1.98 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 886 HIS 0.006 0.001 HIS C1064 PHE 0.034 0.002 PHE C 306 TYR 0.030 0.002 TYR C1138 ARG 0.008 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.05552 ( 658) hydrogen bonds : angle 5.27799 ( 1848) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.40111 ( 78) covalent geometry : bond 0.00535 (25662) covalent geometry : angle 0.63667 (34902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 506 time to evaluate : 2.539 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: B 52 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 159 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7837 (m) REVERT: B 177 MET cc_start: -0.4022 (mmp) cc_final: -0.4730 (mmt) REVERT: B 202 LYS cc_start: 0.7942 (pttp) cc_final: 0.7560 (ptpp) REVERT: B 277 LEU cc_start: 0.8686 (mm) cc_final: 0.8445 (mp) REVERT: B 298 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 324 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 353 TRP cc_start: 0.6675 (p90) cc_final: 0.6141 (p90) REVERT: B 400 PHE cc_start: 0.8378 (p90) cc_final: 0.7968 (p90) REVERT: B 432 CYS cc_start: 0.2149 (OUTLIER) cc_final: 0.0628 (m) REVERT: B 498 GLN cc_start: 0.6693 (mm110) cc_final: 0.6466 (mm-40) REVERT: B 661 GLU cc_start: 0.8293 (tp30) cc_final: 0.7708 (tm-30) REVERT: B 690 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7565 (mm-40) REVERT: B 714 ILE cc_start: 0.9026 (mm) cc_final: 0.8822 (mm) REVERT: B 773 GLU cc_start: 0.8236 (tp30) cc_final: 0.7742 (tp30) REVERT: B 776 LYS cc_start: 0.8488 (ttpp) cc_final: 0.7808 (ttpp) REVERT: B 820 ASP cc_start: 0.8692 (t0) cc_final: 0.8473 (t0) REVERT: B 994 ASP cc_start: 0.8310 (t0) cc_final: 0.8098 (t0) REVERT: B 1127 ASP cc_start: 0.7873 (t0) cc_final: 0.7457 (t0) REVERT: C 99 ASN cc_start: 0.8349 (m-40) cc_final: 0.7966 (p0) REVERT: C 120 VAL cc_start: 0.8832 (m) cc_final: 0.8500 (p) REVERT: C 238 PHE cc_start: 0.6784 (p90) cc_final: 0.6500 (p90) REVERT: C 269 TYR cc_start: 0.7632 (m-80) cc_final: 0.7410 (m-80) REVERT: C 403 ARG cc_start: 0.5462 (ttm170) cc_final: 0.5215 (ttm170) REVERT: C 441 LEU cc_start: 0.6806 (mt) cc_final: 0.6034 (tt) REVERT: C 525 CYS cc_start: 0.3029 (OUTLIER) cc_final: 0.2685 (m) REVERT: C 646 ARG cc_start: 0.8803 (mpp80) cc_final: 0.8531 (ttp-110) REVERT: C 776 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8473 (ttpp) REVERT: C 779 GLN cc_start: 0.8748 (tt0) cc_final: 0.8298 (tm-30) REVERT: C 787 GLN cc_start: 0.8541 (mp10) cc_final: 0.8228 (mp10) REVERT: C 804 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8444 (mm-40) REVERT: C 808 ASP cc_start: 0.8200 (m-30) cc_final: 0.7665 (p0) REVERT: C 896 ILE cc_start: 0.8601 (mt) cc_final: 0.8195 (tt) REVERT: C 1005 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8069 (mt0) REVERT: C 1073 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8206 (mtpt) REVERT: C 1092 GLU cc_start: 0.7992 (pm20) cc_final: 0.7671 (pm20) REVERT: C 1139 ASP cc_start: 0.8209 (t0) cc_final: 0.7864 (t0) REVERT: A 34 ARG cc_start: 0.6545 (mtp85) cc_final: 0.6083 (mmt90) REVERT: A 40 ASP cc_start: 0.8261 (t70) cc_final: 0.7929 (t0) REVERT: A 55 PHE cc_start: 0.7612 (m-80) cc_final: 0.7204 (m-80) REVERT: A 104 TRP cc_start: 0.7609 (m-90) cc_final: 0.7389 (m-90) REVERT: A 133 PHE cc_start: 0.6608 (m-80) cc_final: 0.5503 (m-80) REVERT: A 189 LEU cc_start: 0.8837 (tp) cc_final: 0.8631 (tp) REVERT: A 195 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7270 (mmmt) REVERT: A 196 ASN cc_start: 0.7900 (p0) cc_final: 0.7439 (p0) REVERT: A 201 PHE cc_start: 0.6682 (t80) cc_final: 0.6029 (t80) REVERT: A 400 PHE cc_start: 0.7418 (p90) cc_final: 0.7042 (p90) REVERT: A 495 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6128 (t80) REVERT: A 513 LEU cc_start: 0.8073 (mt) cc_final: 0.7850 (mp) REVERT: A 580 GLN cc_start: 0.6711 (tp40) cc_final: 0.6131 (tp40) REVERT: A 607 GLN cc_start: 0.8509 (mp10) cc_final: 0.7775 (mp10) REVERT: A 661 GLU cc_start: 0.8117 (tp30) cc_final: 0.7860 (tp30) REVERT: A 896 ILE cc_start: 0.8309 (mt) cc_final: 0.8052 (tt) REVERT: A 994 ASP cc_start: 0.8234 (t0) cc_final: 0.8012 (t0) REVERT: A 1002 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: A 1092 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7894 (mm-30) outliers start: 95 outliers final: 73 residues processed: 562 average time/residue: 0.4576 time to fit residues: 399.0842 Evaluate side-chains 570 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 491 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 237 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 787 GLN B 969 ASN B1142 GLN C 99 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 969 ASN A 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117766 restraints weight = 52260.078| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.65 r_work: 0.3518 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25701 Z= 0.208 Angle : 0.621 11.248 34980 Z= 0.321 Chirality : 0.047 0.209 3936 Planarity : 0.004 0.071 4529 Dihedral : 4.480 21.967 3440 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.18 % Allowed : 19.44 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.83 (0.14), residues: 3164 helix: 0.21 (0.22), residues: 612 sheet: -0.69 (0.19), residues: 648 loop : -1.98 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 258 HIS 0.004 0.001 HIS C1064 PHE 0.038 0.002 PHE C 497 TYR 0.028 0.002 TYR C1138 ARG 0.009 0.001 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 658) hydrogen bonds : angle 5.15615 ( 1848) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.34076 ( 78) covalent geometry : bond 0.00482 (25662) covalent geometry : angle 0.61865 (34902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 499 time to evaluate : 3.107 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: B 52 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 159 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 177 MET cc_start: -0.4012 (mmp) cc_final: -0.4735 (mmt) REVERT: B 202 LYS cc_start: 0.7947 (pttp) cc_final: 0.7580 (ptpp) REVERT: B 277 LEU cc_start: 0.8690 (mm) cc_final: 0.8397 (mp) REVERT: B 298 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7165 (tm-30) REVERT: B 324 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 353 TRP cc_start: 0.6397 (p90) cc_final: 0.5866 (p90) REVERT: B 400 PHE cc_start: 0.8334 (p90) cc_final: 0.7943 (p90) REVERT: B 432 CYS cc_start: 0.2204 (OUTLIER) cc_final: 0.0564 (m) REVERT: B 537 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8123 (mmtm) REVERT: B 661 GLU cc_start: 0.8302 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 690 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7610 (mm-40) REVERT: B 714 ILE cc_start: 0.9056 (mm) cc_final: 0.8843 (mm) REVERT: B 773 GLU cc_start: 0.8168 (tp30) cc_final: 0.7587 (tp30) REVERT: B 776 LYS cc_start: 0.8432 (ttpp) cc_final: 0.7548 (ttpp) REVERT: B 994 ASP cc_start: 0.8271 (t0) cc_final: 0.8068 (t0) REVERT: B 1127 ASP cc_start: 0.7953 (t0) cc_final: 0.7537 (t0) REVERT: B 1137 VAL cc_start: 0.9246 (t) cc_final: 0.9010 (m) REVERT: C 99 ASN cc_start: 0.8314 (m110) cc_final: 0.7952 (p0) REVERT: C 120 VAL cc_start: 0.8853 (m) cc_final: 0.8530 (p) REVERT: C 269 TYR cc_start: 0.7614 (m-80) cc_final: 0.7251 (m-80) REVERT: C 441 LEU cc_start: 0.6867 (mt) cc_final: 0.6056 (tt) REVERT: C 497 PHE cc_start: 0.2854 (m-80) cc_final: 0.2596 (m-80) REVERT: C 646 ARG cc_start: 0.8784 (mpp80) cc_final: 0.8545 (ttp-110) REVERT: C 776 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8441 (ttpp) REVERT: C 779 GLN cc_start: 0.8736 (tt0) cc_final: 0.8288 (tm-30) REVERT: C 787 GLN cc_start: 0.8546 (mp10) cc_final: 0.8197 (mp10) REVERT: C 896 ILE cc_start: 0.8592 (mt) cc_final: 0.8189 (tt) REVERT: C 1005 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8055 (mt0) REVERT: C 1073 LYS cc_start: 0.8439 (tmtt) cc_final: 0.8208 (mtpt) REVERT: C 1092 GLU cc_start: 0.7987 (pm20) cc_final: 0.7751 (pm20) REVERT: C 1139 ASP cc_start: 0.8194 (t0) cc_final: 0.7907 (t0) REVERT: A 40 ASP cc_start: 0.8316 (t70) cc_final: 0.8039 (t0) REVERT: A 55 PHE cc_start: 0.7543 (m-80) cc_final: 0.7234 (m-80) REVERT: A 104 TRP cc_start: 0.7544 (m-90) cc_final: 0.7321 (m-90) REVERT: A 133 PHE cc_start: 0.6771 (m-80) cc_final: 0.5562 (m-80) REVERT: A 195 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7283 (mmmt) REVERT: A 201 PHE cc_start: 0.6789 (t80) cc_final: 0.6264 (t80) REVERT: A 400 PHE cc_start: 0.7332 (p90) cc_final: 0.6994 (p90) REVERT: A 495 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6474 (t80) REVERT: A 580 GLN cc_start: 0.6878 (tp40) cc_final: 0.6292 (tp40) REVERT: A 607 GLN cc_start: 0.8500 (mp10) cc_final: 0.7751 (mp10) REVERT: A 661 GLU cc_start: 0.8175 (tp30) cc_final: 0.7919 (tp30) REVERT: A 779 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: A 896 ILE cc_start: 0.8340 (mt) cc_final: 0.8063 (tt) REVERT: A 988 GLU cc_start: 0.8289 (tp30) cc_final: 0.7994 (tp30) REVERT: A 1092 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7920 (mm-30) outliers start: 89 outliers final: 66 residues processed: 553 average time/residue: 0.4689 time to fit residues: 401.7483 Evaluate side-chains 558 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 487 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 177 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 153 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 657 ASN A 99 ASN A 196 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 969 ASN A1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118687 restraints weight = 52456.858| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.81 r_work: 0.3514 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25701 Z= 0.118 Angle : 0.591 11.467 34980 Z= 0.300 Chirality : 0.045 0.200 3936 Planarity : 0.004 0.063 4529 Dihedral : 4.226 22.222 3440 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.32 % Allowed : 20.84 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.58 (0.14), residues: 3164 helix: 0.54 (0.22), residues: 617 sheet: -0.48 (0.19), residues: 633 loop : -1.88 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 353 HIS 0.006 0.001 HIS A 655 PHE 0.036 0.001 PHE C 306 TYR 0.026 0.001 TYR A1138 ARG 0.012 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 658) hydrogen bonds : angle 4.93257 ( 1848) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.85172 ( 78) covalent geometry : bond 0.00269 (25662) covalent geometry : angle 0.58491 (34902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 485 time to evaluate : 3.730 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: B 41 LYS cc_start: 0.7397 (mmtp) cc_final: 0.7170 (mmtp) REVERT: B 52 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 159 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7736 (m) REVERT: B 177 MET cc_start: -0.4220 (mmp) cc_final: -0.4877 (mmt) REVERT: B 202 LYS cc_start: 0.8040 (pttp) cc_final: 0.7617 (ptpp) REVERT: B 277 LEU cc_start: 0.8627 (mm) cc_final: 0.8330 (mp) REVERT: B 298 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 324 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 353 TRP cc_start: 0.6413 (p90) cc_final: 0.5992 (p90) REVERT: B 355 ARG cc_start: 0.8075 (mpp-170) cc_final: 0.7328 (ttp80) REVERT: B 400 PHE cc_start: 0.8286 (p90) cc_final: 0.7911 (p90) REVERT: B 432 CYS cc_start: 0.2214 (OUTLIER) cc_final: 0.0561 (m) REVERT: B 537 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8068 (mmtm) REVERT: B 551 VAL cc_start: 0.7715 (p) cc_final: 0.7494 (m) REVERT: B 563 GLN cc_start: 0.5222 (tp40) cc_final: 0.4952 (tp40) REVERT: B 646 ARG cc_start: 0.8042 (mmp-170) cc_final: 0.7717 (mmp-170) REVERT: B 661 GLU cc_start: 0.8349 (tp30) cc_final: 0.7768 (tm-30) REVERT: B 690 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7494 (mm-40) REVERT: B 773 GLU cc_start: 0.8102 (tp30) cc_final: 0.7662 (tp30) REVERT: B 776 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7619 (ttpp) REVERT: B 1127 ASP cc_start: 0.7954 (t0) cc_final: 0.7515 (t0) REVERT: B 1137 VAL cc_start: 0.9230 (t) cc_final: 0.9010 (m) REVERT: C 99 ASN cc_start: 0.8270 (m110) cc_final: 0.7875 (p0) REVERT: C 120 VAL cc_start: 0.8785 (m) cc_final: 0.8470 (p) REVERT: C 269 TYR cc_start: 0.7560 (m-80) cc_final: 0.7104 (m-80) REVERT: C 441 LEU cc_start: 0.6700 (mt) cc_final: 0.5928 (tt) REVERT: C 646 ARG cc_start: 0.8894 (mpp80) cc_final: 0.8634 (ttp-110) REVERT: C 702 GLU cc_start: 0.7825 (tp30) cc_final: 0.7594 (tp30) REVERT: C 776 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8302 (tttm) REVERT: C 779 GLN cc_start: 0.8780 (tt0) cc_final: 0.8287 (tm-30) REVERT: C 787 GLN cc_start: 0.8487 (mp10) cc_final: 0.8118 (mp10) REVERT: C 896 ILE cc_start: 0.8522 (mt) cc_final: 0.8143 (tt) REVERT: C 1005 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8020 (mt0) REVERT: C 1073 LYS cc_start: 0.8437 (tmtt) cc_final: 0.8214 (mtpt) REVERT: C 1092 GLU cc_start: 0.8128 (pm20) cc_final: 0.7777 (pm20) REVERT: C 1139 ASP cc_start: 0.8224 (t0) cc_final: 0.7911 (t0) REVERT: A 34 ARG cc_start: 0.6464 (mtp85) cc_final: 0.6024 (mmt90) REVERT: A 40 ASP cc_start: 0.8288 (t70) cc_final: 0.7920 (t0) REVERT: A 55 PHE cc_start: 0.7620 (m-80) cc_final: 0.7250 (m-80) REVERT: A 104 TRP cc_start: 0.7655 (m-90) cc_final: 0.7374 (m-90) REVERT: A 129 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7870 (mmmt) REVERT: A 201 PHE cc_start: 0.6917 (t80) cc_final: 0.6381 (t80) REVERT: A 353 TRP cc_start: 0.6918 (p90) cc_final: 0.6308 (p90) REVERT: A 400 PHE cc_start: 0.7473 (p90) cc_final: 0.6996 (p90) REVERT: A 495 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 580 GLN cc_start: 0.6879 (tp40) cc_final: 0.6464 (tp40) REVERT: A 607 GLN cc_start: 0.8435 (mp10) cc_final: 0.7651 (mp10) REVERT: A 661 GLU cc_start: 0.8194 (tp30) cc_final: 0.7884 (tp30) REVERT: A 896 ILE cc_start: 0.8257 (mt) cc_final: 0.7978 (tt) REVERT: A 988 GLU cc_start: 0.8420 (tp30) cc_final: 0.8098 (tp30) REVERT: A 1092 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7934 (mm-30) outliers start: 65 outliers final: 52 residues processed: 524 average time/residue: 0.4091 time to fit residues: 332.8029 Evaluate side-chains 527 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 471 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 4 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 245 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 969 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 969 ASN A1002 GLN A1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.147135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114134 restraints weight = 52090.393| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.71 r_work: 0.3458 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 25701 Z= 0.263 Angle : 0.691 11.417 34980 Z= 0.359 Chirality : 0.049 0.199 3936 Planarity : 0.005 0.067 4529 Dihedral : 4.717 23.264 3440 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.97 % Allowed : 20.69 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.78 (0.14), residues: 3164 helix: 0.36 (0.22), residues: 603 sheet: -0.57 (0.19), residues: 633 loop : -2.01 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.007 0.001 HIS A1083 PHE 0.050 0.002 PHE B 374 TYR 0.028 0.002 TYR C1138 ARG 0.010 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 658) hydrogen bonds : angle 5.24149 ( 1848) SS BOND : bond 0.00433 ( 39) SS BOND : angle 2.07221 ( 78) covalent geometry : bond 0.00613 (25662) covalent geometry : angle 0.68521 (34902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 495 time to evaluate : 3.956 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: B 41 LYS cc_start: 0.7379 (mmtp) cc_final: 0.7122 (mmtp) REVERT: B 52 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 177 MET cc_start: -0.3811 (mmp) cc_final: -0.4658 (mmt) REVERT: B 202 LYS cc_start: 0.8135 (pttp) cc_final: 0.7814 (ptpp) REVERT: B 277 LEU cc_start: 0.8690 (mm) cc_final: 0.8456 (mp) REVERT: B 298 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 353 TRP cc_start: 0.6604 (p90) cc_final: 0.5979 (p90) REVERT: B 400 PHE cc_start: 0.8340 (p90) cc_final: 0.7983 (p90) REVERT: B 432 CYS cc_start: 0.2424 (OUTLIER) cc_final: 0.0497 (m) REVERT: B 537 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8163 (mmtm) REVERT: B 551 VAL cc_start: 0.8096 (p) cc_final: 0.7853 (m) REVERT: B 646 ARG cc_start: 0.7976 (mmp-170) cc_final: 0.7647 (mmp-170) REVERT: B 661 GLU cc_start: 0.8326 (tp30) cc_final: 0.7765 (tm-30) REVERT: B 690 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: B 773 GLU cc_start: 0.8234 (tp30) cc_final: 0.7675 (tp30) REVERT: B 776 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7561 (ttpp) REVERT: B 819 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 1127 ASP cc_start: 0.8024 (t0) cc_final: 0.7624 (t0) REVERT: C 99 ASN cc_start: 0.8345 (m110) cc_final: 0.7990 (p0) REVERT: C 120 VAL cc_start: 0.8835 (m) cc_final: 0.8506 (p) REVERT: C 441 LEU cc_start: 0.6685 (mt) cc_final: 0.6202 (tp) REVERT: C 646 ARG cc_start: 0.8862 (mpp80) cc_final: 0.8618 (ttp-110) REVERT: C 776 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8447 (tttm) REVERT: C 779 GLN cc_start: 0.8783 (tt0) cc_final: 0.8302 (tm-30) REVERT: C 787 GLN cc_start: 0.8595 (mp10) cc_final: 0.8258 (mp10) REVERT: C 796 ASP cc_start: 0.8489 (t0) cc_final: 0.8032 (t70) REVERT: C 896 ILE cc_start: 0.8627 (mt) cc_final: 0.8225 (tt) REVERT: C 1005 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8092 (mt0) REVERT: C 1073 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8202 (mtpt) REVERT: C 1139 ASP cc_start: 0.8165 (t0) cc_final: 0.7912 (t0) REVERT: A 34 ARG cc_start: 0.6548 (mtp85) cc_final: 0.6047 (mmt90) REVERT: A 40 ASP cc_start: 0.8375 (t70) cc_final: 0.8064 (p0) REVERT: A 55 PHE cc_start: 0.7576 (m-80) cc_final: 0.7318 (m-80) REVERT: A 104 TRP cc_start: 0.7660 (m-90) cc_final: 0.7389 (m-90) REVERT: A 133 PHE cc_start: 0.6790 (m-80) cc_final: 0.5591 (m-80) REVERT: A 201 PHE cc_start: 0.6754 (t80) cc_final: 0.6255 (t80) REVERT: A 353 TRP cc_start: 0.7248 (p90) cc_final: 0.6742 (p90) REVERT: A 400 PHE cc_start: 0.7474 (p90) cc_final: 0.7087 (p90) REVERT: A 495 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6541 (t80) REVERT: A 580 GLN cc_start: 0.7031 (tp40) cc_final: 0.6350 (tp40) REVERT: A 607 GLN cc_start: 0.8561 (mp10) cc_final: 0.7888 (mp10) REVERT: A 661 GLU cc_start: 0.8172 (tp30) cc_final: 0.7924 (tp30) REVERT: A 796 ASP cc_start: 0.8180 (t0) cc_final: 0.7795 (t0) REVERT: A 896 ILE cc_start: 0.8382 (mt) cc_final: 0.8101 (tt) REVERT: A 988 GLU cc_start: 0.8316 (tp30) cc_final: 0.8007 (tp30) REVERT: A 995 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8192 (mmm-85) outliers start: 83 outliers final: 68 residues processed: 539 average time/residue: 0.5479 time to fit residues: 454.6897 Evaluate side-chains 553 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 482 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 52 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 302 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN C 784 GLN A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 779 GLN A 969 ASN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117910 restraints weight = 51887.299| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.68 r_work: 0.3500 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25701 Z= 0.149 Angle : 0.637 11.335 34980 Z= 0.325 Chirality : 0.046 0.190 3936 Planarity : 0.004 0.059 4529 Dihedral : 4.509 22.464 3440 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.54 % Allowed : 21.66 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.14), residues: 3164 helix: 0.54 (0.22), residues: 613 sheet: -0.44 (0.19), residues: 633 loop : -1.96 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 353 HIS 0.007 0.001 HIS A1083 PHE 0.053 0.002 PHE B 374 TYR 0.027 0.001 TYR A1138 ARG 0.010 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 658) hydrogen bonds : angle 5.01963 ( 1848) SS BOND : bond 0.00301 ( 39) SS BOND : angle 1.72153 ( 78) covalent geometry : bond 0.00348 (25662) covalent geometry : angle 0.63215 (34902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 483 time to evaluate : 2.627 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: B 41 LYS cc_start: 0.7381 (mmtp) cc_final: 0.7170 (mmtp) REVERT: B 177 MET cc_start: -0.3948 (mmp) cc_final: -0.4786 (mmt) REVERT: B 202 LYS cc_start: 0.8030 (pttp) cc_final: 0.7690 (ptpp) REVERT: B 277 LEU cc_start: 0.8652 (mm) cc_final: 0.8346 (mp) REVERT: B 298 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 353 TRP cc_start: 0.6365 (p90) cc_final: 0.5806 (p90) REVERT: B 355 ARG cc_start: 0.8049 (mpp-170) cc_final: 0.7191 (ttp80) REVERT: B 400 PHE cc_start: 0.8271 (p90) cc_final: 0.7930 (p90) REVERT: B 432 CYS cc_start: 0.2206 (OUTLIER) cc_final: 0.0256 (m) REVERT: B 551 VAL cc_start: 0.7945 (p) cc_final: 0.7721 (m) REVERT: B 563 GLN cc_start: 0.5372 (tp40) cc_final: 0.5126 (tp40) REVERT: B 646 ARG cc_start: 0.7958 (mmp-170) cc_final: 0.7649 (mmp-170) REVERT: B 661 GLU cc_start: 0.8331 (tp30) cc_final: 0.7728 (tm-30) REVERT: B 690 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7621 (mm-40) REVERT: B 773 GLU cc_start: 0.8198 (tp30) cc_final: 0.7751 (tp30) REVERT: B 776 LYS cc_start: 0.8464 (ttpp) cc_final: 0.7744 (ttpp) REVERT: B 819 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 1127 ASP cc_start: 0.7917 (t0) cc_final: 0.7538 (t0) REVERT: C 99 ASN cc_start: 0.8315 (m110) cc_final: 0.7952 (p0) REVERT: C 102 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7213 (mmm160) REVERT: C 120 VAL cc_start: 0.8827 (m) cc_final: 0.8496 (p) REVERT: C 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7495 (m-80) REVERT: C 277 LEU cc_start: 0.8410 (mm) cc_final: 0.8106 (mp) REVERT: C 441 LEU cc_start: 0.6641 (mt) cc_final: 0.6139 (tp) REVERT: C 646 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8602 (ttp-110) REVERT: C 776 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8437 (ttpp) REVERT: C 779 GLN cc_start: 0.8743 (tt0) cc_final: 0.8312 (tm-30) REVERT: C 787 GLN cc_start: 0.8560 (mp10) cc_final: 0.8215 (mp10) REVERT: C 896 ILE cc_start: 0.8585 (mt) cc_final: 0.8198 (tt) REVERT: C 1005 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8022 (mt0) REVERT: C 1073 LYS cc_start: 0.8406 (tmtt) cc_final: 0.8176 (mtpt) REVERT: C 1139 ASP cc_start: 0.8164 (t0) cc_final: 0.7912 (t0) REVERT: A 34 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6059 (mmt90) REVERT: A 40 ASP cc_start: 0.8288 (t70) cc_final: 0.7891 (t0) REVERT: A 55 PHE cc_start: 0.7592 (m-80) cc_final: 0.7280 (m-80) REVERT: A 104 TRP cc_start: 0.7579 (m-90) cc_final: 0.7286 (m-90) REVERT: A 129 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7487 (mmmt) REVERT: A 201 PHE cc_start: 0.6776 (t80) cc_final: 0.6245 (t80) REVERT: A 353 TRP cc_start: 0.6961 (p90) cc_final: 0.6374 (p90) REVERT: A 400 PHE cc_start: 0.7373 (p90) cc_final: 0.6986 (p90) REVERT: A 495 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 607 GLN cc_start: 0.8441 (mp10) cc_final: 0.7767 (mp10) REVERT: A 661 GLU cc_start: 0.8152 (tp30) cc_final: 0.7893 (tp30) REVERT: A 896 ILE cc_start: 0.8309 (mt) cc_final: 0.8039 (tt) REVERT: A 988 GLU cc_start: 0.8279 (tp30) cc_final: 0.7970 (tp30) REVERT: A 995 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8145 (mmm-85) outliers start: 71 outliers final: 60 residues processed: 522 average time/residue: 0.3896 time to fit residues: 312.9513 Evaluate side-chains 543 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 480 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 163 optimal weight: 0.7980 chunk 207 optimal weight: 0.0070 chunk 291 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117273 restraints weight = 51744.771| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.65 r_work: 0.3500 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25701 Z= 0.164 Angle : 0.639 11.349 34980 Z= 0.325 Chirality : 0.046 0.191 3936 Planarity : 0.004 0.053 4529 Dihedral : 4.468 23.164 3440 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.61 % Allowed : 21.55 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.62 (0.14), residues: 3164 helix: 0.60 (0.22), residues: 613 sheet: -0.45 (0.20), residues: 627 loop : -1.95 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 353 HIS 0.007 0.001 HIS A1083 PHE 0.036 0.002 PHE B 374 TYR 0.027 0.001 TYR A1138 ARG 0.010 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 658) hydrogen bonds : angle 4.97416 ( 1848) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.59801 ( 78) covalent geometry : bond 0.00387 (25662) covalent geometry : angle 0.63546 (34902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14526.33 seconds wall clock time: 254 minutes 21.97 seconds (15261.97 seconds total)