Starting phenix.real_space_refine on Thu Mar 5 20:30:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_32360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_32360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_32360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_32360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w94_32360/03_2026/7w94_32360.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.23, per 1000 atoms: 0.25 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: 1.99 Conformation dependent library (CDL) restraints added in 967.7 milliseconds 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: 1.17 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: 5.67 Time building geometry restraints manager: 2.75 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: 4.320 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: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.100 Process input model: 24.710 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.000 ARG C 408 TYR 0.024 0.001 TYR C 451 PHE 0.015 0.001 PHE B 592 TRP 0.015 0.001 TRP B 152 HIS 0.003 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00290 (25662) covalent geometry : angle 0.66828 (34902) SS BOND : bond 0.00349 ( 39) SS BOND : angle 0.99940 ( 78) hydrogen bonds : bond 0.35024 ( 658) hydrogen bonds : angle 10.52896 ( 1848) *********************** 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 : 0.957 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 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: -0.4583 (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: 0.7598 (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: 0.7466 (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: 0.6551 (p90) REVERT: C 303 LEU cc_start: 0.8836 (tp) cc_final: 0.8451 (tt) REVERT: C 347 PHE cc_start: 0.4448 (m-10) cc_final: 0.2577 (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: 0.7556 (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: 0.7097 (t70) REVERT: A 55 PHE cc_start: 0.7187 (m-80) cc_final: 0.6799 (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: 0.5110 (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: 0.6648 (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: 0.6858 (p90) REVERT: A 528 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7746 (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: 0.6912 (t0) REVERT: A 606 ASN cc_start: 0.8486 (m-40) cc_final: 0.8269 (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: 0.7111 (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: 0.1850 time to fit residues: 185.1395 Evaluate side-chains 522 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 370 ASN B 394 ASN B 519 HIS B 655 HIS B 690 GLN B 709 ASN B 774 GLN B 969 ASN B1023 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 49 HIS C 99 ASN C 121 ASN C 137 ASN C 343 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 563 GLN C 655 HIS C 657 ASN C 764 ASN C 965 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 370 ASN A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1002 GLN A1074 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.152183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119335 restraints weight = 52405.315| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.65 r_work: 0.3522 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25701 Z= 0.293 Angle : 0.716 11.105 34980 Z= 0.375 Chirality : 0.050 0.336 3936 Planarity : 0.005 0.054 4529 Dihedral : 4.598 28.893 3441 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.54 % Allowed : 13.90 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.12), residues: 3164 helix: -3.00 (0.14), residues: 612 sheet: -1.03 (0.19), residues: 663 loop : -2.42 (0.12), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 102 TYR 0.027 0.002 TYR B 91 PHE 0.027 0.002 PHE C 55 TRP 0.032 0.002 TRP B 104 HIS 0.007 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00678 (25662) covalent geometry : angle 0.71312 (34902) SS BOND : bond 0.00441 ( 39) SS BOND : angle 1.54201 ( 78) hydrogen bonds : bond 0.07384 ( 658) hydrogen bonds : angle 6.29201 ( 1848) *********************** 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 615 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 544 time to evaluate : 0.919 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: 0.8669 (tm-30) cc_final: 0.8419 (tm-30) REVERT: B 138 ASP cc_start: 0.8435 (m-30) cc_final: 0.8233 (m-30) REVERT: B 177 MET cc_start: -0.4254 (mmp) cc_final: -0.4646 (mmp) REVERT: B 244 LEU cc_start: 0.2824 (OUTLIER) cc_final: 0.2262 (pt) REVERT: B 277 LEU cc_start: 0.8677 (mm) cc_final: 0.8458 (mp) REVERT: B 298 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6998 (tm-30) REVERT: B 353 TRP cc_start: 0.6576 (p90) cc_final: 0.6144 (p90) REVERT: B 432 CYS cc_start: 0.2560 (OUTLIER) cc_final: 0.1284 (m) REVERT: B 498 GLN cc_start: 0.6748 (mm110) cc_final: 0.6475 (mm-40) REVERT: B 773 GLU cc_start: 0.8223 (tt0) cc_final: 0.7918 (tt0) REVERT: B 820 ASP cc_start: 0.8687 (t0) cc_final: 0.8381 (t0) REVERT: B 855 PHE cc_start: 0.7695 (m-80) cc_final: 0.7270 (m-80) REVERT: B 902 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7710 (mmm) REVERT: B 1127 ASP cc_start: 0.7875 (t0) cc_final: 0.7470 (t0) REVERT: C 99 ASN cc_start: 0.8267 (m110) cc_final: 0.7832 (p0) REVERT: C 192 PHE cc_start: 0.7244 (m-80) cc_final: 0.6860 (m-80) REVERT: C 238 PHE cc_start: 0.6986 (p90) cc_final: 0.6648 (p90) REVERT: C 239 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6729 (mm-40) REVERT: C 277 LEU cc_start: 0.8367 (mm) cc_final: 0.7981 (mp) REVERT: C 324 GLU cc_start: 0.6812 (pp20) cc_final: 0.6552 (pp20) REVERT: C 353 TRP cc_start: 0.5608 (p-90) cc_final: 0.5206 (p-90) REVERT: C 355 ARG cc_start: 0.6430 (tpp-160) cc_final: 0.5750 (tpp-160) REVERT: C 441 LEU cc_start: 0.6920 (mt) cc_final: 0.6186 (tt) REVERT: C 515 PHE cc_start: 0.6947 (p90) cc_final: 0.6623 (p90) REVERT: C 559 PHE cc_start: 0.7556 (m-80) cc_final: 0.7129 (m-80) REVERT: C 646 ARG cc_start: 0.8804 (mpp80) cc_final: 0.8582 (ttp-110) REVERT: C 773 GLU cc_start: 0.7855 (tt0) cc_final: 0.7653 (tt0) REVERT: C 776 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8513 (ttmt) REVERT: C 804 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8506 (mm-40) REVERT: C 808 ASP cc_start: 0.8079 (m-30) cc_final: 0.7595 (p0) REVERT: C 896 ILE cc_start: 0.8472 (mt) cc_final: 0.8109 (tt) REVERT: C 1017 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8192 (tm-30) REVERT: C 1073 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8218 (mtpt) REVERT: C 1139 ASP cc_start: 0.8149 (t0) cc_final: 0.7876 (t0) REVERT: A 34 ARG cc_start: 0.6475 (mtp85) cc_final: 0.6127 (mmt90) REVERT: A 40 ASP cc_start: 0.8107 (t70) cc_final: 0.7735 (t0) REVERT: A 44 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7558 (mpp80) REVERT: A 86 PHE cc_start: 0.8012 (t80) cc_final: 0.7799 (t80) REVERT: A 104 TRP cc_start: 0.7708 (m-90) cc_final: 0.7487 (m-90) REVERT: A 133 PHE cc_start: 0.6350 (m-80) cc_final: 0.5551 (m-80) REVERT: A 177 MET cc_start: -0.2032 (mtp) cc_final: -0.2950 (mtt) REVERT: A 189 LEU cc_start: 0.8921 (tp) cc_final: 0.8668 (tp) REVERT: A 190 ARG cc_start: 0.6990 (mtt180) cc_final: 0.6392 (mtt180) REVERT: A 195 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7432 (mmmt) REVERT: A 201 PHE cc_start: 0.6923 (t80) cc_final: 0.6053 (t80) REVERT: A 390 LEU cc_start: 0.8381 (pp) cc_final: 0.8040 (pp) REVERT: A 400 PHE cc_start: 0.7431 (p90) cc_final: 0.7110 (p90) REVERT: A 513 LEU cc_start: 0.8118 (mt) cc_final: 0.7811 (mp) REVERT: A 532 ASN cc_start: 0.8322 (t0) cc_final: 0.8103 (t0) REVERT: A 556 ASN cc_start: 0.7972 (t0) cc_final: 0.7718 (t0) REVERT: A 607 GLN cc_start: 0.8497 (mp10) cc_final: 0.7710 (mp10) REVERT: A 643 PHE cc_start: 0.8426 (t80) cc_final: 0.8200 (t80) REVERT: A 646 ARG cc_start: 0.8047 (mpp80) cc_final: 0.7472 (mpp80) REVERT: A 675 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 779 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 786 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7815 (mmmt) REVERT: A 787 GLN cc_start: 0.8371 (mp10) cc_final: 0.8031 (mm-40) REVERT: A 973 ILE cc_start: 0.9327 (tt) cc_final: 0.9022 (mt) REVERT: A 988 GLU cc_start: 0.8478 (tp30) cc_final: 0.8148 (tp30) REVERT: A 994 ASP cc_start: 0.8318 (t0) cc_final: 0.8079 (t0) REVERT: A 1030 SER cc_start: 0.9049 (m) cc_final: 0.8746 (t) outliers start: 71 outliers final: 40 residues processed: 583 average time/residue: 0.1853 time to fit residues: 164.7133 Evaluate side-chains 537 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 493 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1117 THR 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 56 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR 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 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN 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 395 VAL 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 779 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 67 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 240 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 99 ASN B 196 ASN B 544 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 969 ASN B1106 GLN C 657 ASN C 928 ASN C 955 ASN C1002 GLN A 99 ASN A 125 ASN A 448 ASN A 450 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121332 restraints weight = 52570.310| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.69 r_work: 0.3549 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25701 Z= 0.131 Angle : 0.575 12.780 34980 Z= 0.292 Chirality : 0.045 0.288 3936 Planarity : 0.004 0.056 4529 Dihedral : 4.246 20.003 3440 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.47 % Allowed : 16.23 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3164 helix: -1.32 (0.20), residues: 613 sheet: -0.81 (0.19), residues: 680 loop : -2.21 (0.12), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.022 0.001 TYR C1138 PHE 0.021 0.001 PHE B 374 TRP 0.018 0.001 TRP B 258 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00296 (25662) covalent geometry : angle 0.57237 (34902) SS BOND : bond 0.00304 ( 39) SS BOND : angle 1.20662 ( 78) hydrogen bonds : bond 0.05547 ( 658) hydrogen bonds : angle 5.63709 ( 1848) *********************** 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 578 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 509 time to evaluate : 0.939 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: 0.8703 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 140 PHE cc_start: 0.6268 (p90) cc_final: 0.6056 (p90) REVERT: B 177 MET cc_start: -0.4190 (mmp) cc_final: -0.4712 (mmp) REVERT: B 244 LEU cc_start: 0.3004 (OUTLIER) cc_final: 0.2521 (pt) REVERT: B 277 LEU cc_start: 0.8638 (mm) cc_final: 0.8373 (mp) REVERT: B 298 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6963 (tm-30) REVERT: B 353 TRP cc_start: 0.6440 (p90) cc_final: 0.6151 (p90) REVERT: B 432 CYS cc_start: 0.2130 (OUTLIER) cc_final: 0.0844 (m) REVERT: B 498 GLN cc_start: 0.7021 (mm110) cc_final: 0.6441 (tp-100) REVERT: B 560 LEU cc_start: 0.8425 (tp) cc_final: 0.8091 (tp) REVERT: B 820 ASP cc_start: 0.8679 (t0) cc_final: 0.8348 (t0) REVERT: B 902 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: B 994 ASP cc_start: 0.8267 (t0) cc_final: 0.8049 (t0) REVERT: B 1127 ASP cc_start: 0.7828 (t0) cc_final: 0.7386 (t0) REVERT: C 99 ASN cc_start: 0.8201 (m110) cc_final: 0.7814 (p0) REVERT: C 140 PHE cc_start: 0.7397 (m-80) cc_final: 0.7101 (m-80) REVERT: C 238 PHE cc_start: 0.7179 (p90) cc_final: 0.6876 (p90) REVERT: C 239 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6817 (mm-40) REVERT: C 277 LEU cc_start: 0.8278 (mm) cc_final: 0.7898 (mp) REVERT: C 328 ARG cc_start: 0.6187 (tpp-160) cc_final: 0.5922 (mmt90) REVERT: C 353 TRP cc_start: 0.5694 (p-90) cc_final: 0.5370 (p-90) REVERT: C 355 ARG cc_start: 0.6421 (tpp-160) cc_final: 0.5795 (tpp-160) REVERT: C 441 LEU cc_start: 0.6781 (mt) cc_final: 0.6032 (tt) REVERT: C 497 PHE cc_start: 0.3273 (m-80) cc_final: 0.2855 (m-80) REVERT: C 515 PHE cc_start: 0.6857 (p90) cc_final: 0.6511 (p90) REVERT: C 646 ARG cc_start: 0.8852 (mpp80) cc_final: 0.8567 (ttp-110) REVERT: C 745 ASP cc_start: 0.7654 (t0) cc_final: 0.7292 (t0) REVERT: C 776 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8459 (ttmt) REVERT: C 779 GLN cc_start: 0.8660 (tt0) cc_final: 0.8274 (tm-30) REVERT: C 804 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8407 (mm-40) REVERT: C 823 PHE cc_start: 0.8642 (t80) cc_final: 0.8428 (t80) REVERT: C 896 ILE cc_start: 0.8429 (mt) cc_final: 0.8067 (tt) REVERT: C 1005 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8011 (mt0) REVERT: C 1073 LYS cc_start: 0.8429 (tmtt) cc_final: 0.8208 (mtpt) REVERT: C 1139 ASP cc_start: 0.8171 (t0) cc_final: 0.7779 (t0) REVERT: A 34 ARG cc_start: 0.6425 (mtp85) cc_final: 0.6086 (mmt90) REVERT: A 40 ASP cc_start: 0.8030 (t70) cc_final: 0.7679 (t0) REVERT: A 53 ASP cc_start: 0.7741 (t0) cc_final: 0.7446 (t70) REVERT: A 55 PHE cc_start: 0.7648 (m-80) cc_final: 0.7212 (m-80) REVERT: A 86 PHE cc_start: 0.8063 (t80) cc_final: 0.7761 (t80) REVERT: A 177 MET cc_start: -0.2431 (mtp) cc_final: -0.3323 (mtt) REVERT: A 189 LEU cc_start: 0.8841 (tp) cc_final: 0.8587 (tp) REVERT: A 190 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6450 (mtt180) REVERT: A 390 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 400 PHE cc_start: 0.7337 (p90) cc_final: 0.6977 (p90) REVERT: A 513 LEU cc_start: 0.8026 (mt) cc_final: 0.7776 (mp) REVERT: A 556 ASN cc_start: 0.7974 (t0) cc_final: 0.7715 (t0) REVERT: A 607 GLN cc_start: 0.8368 (mp10) cc_final: 0.7615 (mp10) REVERT: A 646 ARG cc_start: 0.8064 (mpp80) cc_final: 0.7557 (mpp80) REVERT: A 661 GLU cc_start: 0.8023 (tp30) cc_final: 0.7736 (tp30) REVERT: A 759 PHE cc_start: 0.8024 (t80) cc_final: 0.7674 (t80) REVERT: A 779 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: A 790 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8445 (mtpt) REVERT: A 823 PHE cc_start: 0.8079 (t80) cc_final: 0.7685 (t80) REVERT: A 869 MET cc_start: 0.8489 (mtt) cc_final: 0.8210 (mtt) REVERT: A 918 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8480 (mp0) REVERT: A 973 ILE cc_start: 0.9234 (tt) cc_final: 0.8984 (pt) REVERT: A 988 GLU cc_start: 0.8382 (tp30) cc_final: 0.8061 (tp30) REVERT: A 994 ASP cc_start: 0.8176 (t0) cc_final: 0.7923 (t0) REVERT: A 1030 SER cc_start: 0.9010 (m) cc_final: 0.8789 (t) REVERT: A 1092 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 1111 GLU cc_start: 0.8252 (pm20) cc_final: 0.7483 (pm20) outliers start: 69 outliers final: 43 residues processed: 546 average time/residue: 0.1883 time to fit residues: 158.2276 Evaluate side-chains 536 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 488 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 196 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1050 MET 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 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 451 TYR 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 816 SER 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 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 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 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 896 ILE 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 85 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 563 GLN B 709 ASN B 787 GLN B 935 GLN B 969 ASN B1010 GLN B1023 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN A 450 ASN A 969 ASN A1106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.150694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117507 restraints weight = 52579.226| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.67 r_work: 0.3502 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25701 Z= 0.212 Angle : 0.609 9.399 34980 Z= 0.314 Chirality : 0.047 0.257 3936 Planarity : 0.004 0.064 4529 Dihedral : 4.426 19.642 3440 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.22 % Allowed : 17.73 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.14), residues: 3164 helix: -0.76 (0.21), residues: 615 sheet: -0.83 (0.19), residues: 678 loop : -2.14 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 328 TYR 0.030 0.002 TYR C1138 PHE 0.021 0.002 PHE A 643 TRP 0.019 0.002 TRP B 258 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00492 (25662) covalent geometry : angle 0.60511 (34902) SS BOND : bond 0.00358 ( 39) SS BOND : angle 1.53639 ( 78) hydrogen bonds : bond 0.05569 ( 658) hydrogen bonds : angle 5.50137 ( 1848) *********************** 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 597 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 507 time to evaluate : 0.688 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: 0.8724 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 99 ASN cc_start: 0.8265 (t0) cc_final: 0.8041 (t0) REVERT: B 177 MET cc_start: -0.3961 (mmp) cc_final: -0.4699 (mmt) REVERT: B 244 LEU cc_start: 0.3170 (OUTLIER) cc_final: 0.2670 (pt) REVERT: B 277 LEU cc_start: 0.8668 (mm) cc_final: 0.8408 (mp) REVERT: B 298 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6973 (tm-30) REVERT: B 324 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 353 TRP cc_start: 0.6663 (p90) cc_final: 0.6156 (p90) REVERT: B 355 ARG cc_start: 0.8076 (mpp-170) cc_final: 0.7845 (mpp-170) REVERT: B 432 CYS cc_start: 0.2103 (OUTLIER) cc_final: 0.0711 (m) REVERT: B 498 GLN cc_start: 0.6957 (mm110) cc_final: 0.6704 (mm-40) REVERT: B 567 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8398 (ttm170) REVERT: B 773 GLU cc_start: 0.8140 (tp30) cc_final: 0.7638 (tp30) REVERT: B 776 LYS cc_start: 0.8499 (ttpp) cc_final: 0.7839 (ttpp) REVERT: B 820 ASP cc_start: 0.8692 (t0) cc_final: 0.8440 (t0) REVERT: B 854 LYS cc_start: 0.8615 (tptt) cc_final: 0.8148 (tptt) REVERT: B 855 PHE cc_start: 0.7585 (m-80) cc_final: 0.7381 (m-80) REVERT: B 902 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7780 (mmm) REVERT: B 979 ASP cc_start: 0.8368 (t0) cc_final: 0.8165 (t0) REVERT: B 994 ASP cc_start: 0.8318 (t0) cc_final: 0.8095 (t0) REVERT: B 1127 ASP cc_start: 0.7865 (t0) cc_final: 0.7413 (t0) REVERT: C 99 ASN cc_start: 0.8243 (m110) cc_final: 0.7901 (p0) REVERT: C 120 VAL cc_start: 0.8727 (m) cc_final: 0.8497 (p) REVERT: C 238 PHE cc_start: 0.7243 (p90) cc_final: 0.6952 (p90) REVERT: C 239 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6673 (mm-40) REVERT: C 277 LEU cc_start: 0.8344 (mm) cc_final: 0.7963 (mp) REVERT: C 324 GLU cc_start: 0.6802 (pp20) cc_final: 0.6554 (pp20) REVERT: C 328 ARG cc_start: 0.6084 (tpp-160) cc_final: 0.5817 (mmt90) REVERT: C 441 LEU cc_start: 0.6728 (mt) cc_final: 0.5973 (tt) REVERT: C 497 PHE cc_start: 0.3118 (m-80) cc_final: 0.2910 (m-80) REVERT: C 646 ARG cc_start: 0.8827 (mpp80) cc_final: 0.8583 (ttp-110) REVERT: C 776 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8443 (ttpp) REVERT: C 779 GLN cc_start: 0.8739 (tt0) cc_final: 0.8309 (tm-30) REVERT: C 804 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8411 (mm-40) REVERT: C 823 PHE cc_start: 0.8760 (t80) cc_final: 0.8558 (t80) REVERT: C 896 ILE cc_start: 0.8540 (mt) cc_final: 0.8164 (tt) REVERT: C 1005 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8059 (mt0) REVERT: C 1017 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 1073 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8211 (mtpt) REVERT: C 1092 GLU cc_start: 0.7980 (pm20) cc_final: 0.7717 (pm20) REVERT: C 1139 ASP cc_start: 0.8148 (t0) cc_final: 0.7790 (t0) REVERT: A 34 ARG cc_start: 0.6477 (mtp85) cc_final: 0.6056 (mmt90) REVERT: A 40 ASP cc_start: 0.8232 (t70) cc_final: 0.7857 (t0) REVERT: A 53 ASP cc_start: 0.7790 (t0) cc_final: 0.7464 (t70) REVERT: A 55 PHE cc_start: 0.7641 (m-80) cc_final: 0.7102 (m-80) REVERT: A 104 TRP cc_start: 0.7773 (m-90) cc_final: 0.7450 (m-90) REVERT: A 133 PHE cc_start: 0.6487 (m-80) cc_final: 0.5300 (m-80) REVERT: A 177 MET cc_start: -0.2148 (mtp) cc_final: -0.3189 (mtt) REVERT: A 189 LEU cc_start: 0.8831 (tp) cc_final: 0.8581 (tp) REVERT: A 400 PHE cc_start: 0.7388 (p90) cc_final: 0.7040 (p90) REVERT: A 513 LEU cc_start: 0.8072 (mt) cc_final: 0.7791 (mp) REVERT: A 532 ASN cc_start: 0.8375 (t0) cc_final: 0.8124 (t0) REVERT: A 556 ASN cc_start: 0.8074 (t0) cc_final: 0.7811 (t0) REVERT: A 607 GLN cc_start: 0.8461 (mp10) cc_final: 0.7686 (mp10) REVERT: A 661 GLU cc_start: 0.8113 (tp30) cc_final: 0.7840 (tp30) REVERT: A 779 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 814 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8157 (mmmt) REVERT: A 823 PHE cc_start: 0.8190 (t80) cc_final: 0.7799 (t80) REVERT: A 988 GLU cc_start: 0.8445 (tp30) cc_final: 0.8130 (tp30) REVERT: A 994 ASP cc_start: 0.8146 (t0) cc_final: 0.7934 (t0) REVERT: A 1092 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 1111 GLU cc_start: 0.8294 (pm20) cc_final: 0.8082 (pm20) outliers start: 90 outliers final: 61 residues processed: 559 average time/residue: 0.1761 time to fit residues: 151.4334 Evaluate side-chains 552 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 487 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 244 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 358 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1117 THR 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 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL 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 753 LEU 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 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 64 TRP 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 281 GLU 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 395 VAL 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 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 33 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 241 optimal weight: 0.4980 chunk 185 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 196 ASN B 370 ASN B 935 GLN B 969 ASN C 239 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN A 969 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119793 restraints weight = 52410.073| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.71 r_work: 0.3544 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3476 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= 0.113 Angle : 0.563 12.230 34980 Z= 0.284 Chirality : 0.045 0.260 3936 Planarity : 0.004 0.062 4529 Dihedral : 4.190 21.074 3440 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.97 % Allowed : 19.19 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3164 helix: -0.29 (0.21), residues: 621 sheet: -0.69 (0.19), residues: 669 loop : -2.01 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.023 0.001 TYR C1138 PHE 0.026 0.001 PHE A 374 TRP 0.016 0.001 TRP B 258 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00255 (25662) covalent geometry : angle 0.55975 (34902) SS BOND : bond 0.00284 ( 39) SS BOND : angle 1.30541 ( 78) hydrogen bonds : bond 0.04525 ( 658) hydrogen bonds : angle 5.18454 ( 1848) *********************** 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 588 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 505 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 159 VAL cc_start: 0.8020 (p) cc_final: 0.7781 (m) REVERT: B 177 MET cc_start: -0.3980 (mmp) cc_final: -0.4627 (mmt) REVERT: B 277 LEU cc_start: 0.8636 (mm) cc_final: 0.8365 (mp) REVERT: B 298 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 324 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 353 TRP cc_start: 0.6463 (p90) cc_final: 0.6167 (p90) REVERT: B 355 ARG cc_start: 0.8020 (mpp-170) cc_final: 0.7791 (mpp-170) REVERT: B 400 PHE cc_start: 0.8281 (p90) cc_final: 0.7873 (p90) REVERT: B 432 CYS cc_start: 0.2026 (OUTLIER) cc_final: 0.0580 (m) REVERT: B 498 GLN cc_start: 0.6999 (mm110) cc_final: 0.6418 (tp-100) REVERT: B 567 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8377 (ttm170) REVERT: B 760 CYS cc_start: 0.7441 (m) cc_final: 0.7036 (m) REVERT: B 773 GLU cc_start: 0.8156 (tp30) cc_final: 0.7701 (tp30) REVERT: B 776 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7781 (ttpp) REVERT: B 819 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7390 (mt-10) REVERT: B 820 ASP cc_start: 0.8689 (t0) cc_final: 0.8462 (t0) REVERT: B 854 LYS cc_start: 0.8593 (tptt) cc_final: 0.8364 (tppt) REVERT: B 979 ASP cc_start: 0.8391 (t0) cc_final: 0.8185 (t0) REVERT: B 994 ASP cc_start: 0.8215 (t0) cc_final: 0.7999 (t0) REVERT: B 1127 ASP cc_start: 0.7851 (t0) cc_final: 0.7371 (t0) REVERT: C 99 ASN cc_start: 0.8163 (m110) cc_final: 0.7826 (p0) REVERT: C 120 VAL cc_start: 0.8762 (m) cc_final: 0.8418 (p) REVERT: C 238 PHE cc_start: 0.7217 (p90) cc_final: 0.6984 (p90) REVERT: C 239 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: C 277 LEU cc_start: 0.8268 (mm) cc_final: 0.7870 (mp) REVERT: C 294 ASP cc_start: 0.7531 (p0) cc_final: 0.7245 (p0) REVERT: C 353 TRP cc_start: 0.5722 (p-90) cc_final: 0.5103 (p-90) REVERT: C 441 LEU cc_start: 0.6642 (mt) cc_final: 0.5892 (tt) REVERT: C 497 PHE cc_start: 0.3228 (m-80) cc_final: 0.2993 (m-80) REVERT: C 515 PHE cc_start: 0.6934 (p90) cc_final: 0.6509 (p90) REVERT: C 646 ARG cc_start: 0.8859 (mpp80) cc_final: 0.8608 (ttp-110) REVERT: C 776 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8438 (ttpp) REVERT: C 779 GLN cc_start: 0.8753 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 896 ILE cc_start: 0.8513 (mt) cc_final: 0.8137 (tt) REVERT: C 1005 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8027 (mt0) REVERT: C 1017 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 1073 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8194 (mtpt) REVERT: C 1092 GLU cc_start: 0.7950 (pm20) cc_final: 0.7622 (pm20) REVERT: C 1139 ASP cc_start: 0.8175 (t0) cc_final: 0.7833 (t0) REVERT: A 34 ARG cc_start: 0.6430 (mtp85) cc_final: 0.6023 (mmt90) REVERT: A 40 ASP cc_start: 0.8179 (t70) cc_final: 0.7817 (t0) REVERT: A 53 ASP cc_start: 0.7825 (t0) cc_final: 0.7456 (t70) REVERT: A 55 PHE cc_start: 0.7612 (m-80) cc_final: 0.6973 (m-80) REVERT: A 104 TRP cc_start: 0.7683 (m-90) cc_final: 0.7388 (m-90) REVERT: A 133 PHE cc_start: 0.6559 (m-80) cc_final: 0.5389 (m-80) REVERT: A 189 LEU cc_start: 0.8777 (tp) cc_final: 0.8555 (tp) REVERT: A 195 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7058 (mmmt) REVERT: A 400 PHE cc_start: 0.7279 (p90) cc_final: 0.6892 (p90) REVERT: A 607 GLN cc_start: 0.8350 (mp10) cc_final: 0.7627 (mp10) REVERT: A 661 GLU cc_start: 0.8075 (tp30) cc_final: 0.7799 (tp30) REVERT: A 814 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8110 (mmmt) REVERT: A 823 PHE cc_start: 0.8197 (t80) cc_final: 0.7822 (t80) REVERT: A 988 GLU cc_start: 0.8388 (tp30) cc_final: 0.8075 (tp30) REVERT: A 994 ASP cc_start: 0.8085 (t0) cc_final: 0.7874 (t0) REVERT: A 1092 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 1111 GLU cc_start: 0.8470 (pm20) cc_final: 0.8228 (pm20) outliers start: 83 outliers final: 59 residues processed: 555 average time/residue: 0.1832 time to fit residues: 157.0106 Evaluate side-chains 554 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 270 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 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1050 MET 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 98 SER 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 341 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 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 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1002 GLN 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 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE 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 515 PHE 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 615 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 803 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 215 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 969 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119504 restraints weight = 52511.179| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.63 r_work: 0.3527 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25701 Z= 0.140 Angle : 0.570 13.225 34980 Z= 0.288 Chirality : 0.045 0.243 3936 Planarity : 0.004 0.067 4529 Dihedral : 4.164 20.888 3440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.04 % Allowed : 19.91 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3164 helix: -0.06 (0.21), residues: 622 sheet: -0.65 (0.19), residues: 662 loop : -1.97 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.021 0.001 TYR C1138 PHE 0.032 0.001 PHE C 306 TRP 0.014 0.001 TRP B 258 HIS 0.009 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00325 (25662) covalent geometry : angle 0.56738 (34902) SS BOND : bond 0.00286 ( 39) SS BOND : angle 1.33663 ( 78) hydrogen bonds : bond 0.04599 ( 658) hydrogen bonds : angle 5.08708 ( 1848) *********************** 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 573 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 488 time to evaluate : 1.045 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: 0.8696 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 177 MET cc_start: -0.3876 (mmp) cc_final: -0.4449 (mmt) REVERT: B 277 LEU cc_start: 0.8641 (mm) cc_final: 0.8380 (mp) REVERT: B 298 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7050 (tm-30) REVERT: B 324 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 353 TRP cc_start: 0.6537 (p90) cc_final: 0.5907 (p90) REVERT: B 400 PHE cc_start: 0.8310 (p90) cc_final: 0.7933 (p90) REVERT: B 432 CYS cc_start: 0.2068 (OUTLIER) cc_final: 0.0559 (m) REVERT: B 498 GLN cc_start: 0.6956 (mm110) cc_final: 0.6744 (mm-40) REVERT: B 567 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8442 (ttm170) REVERT: B 773 GLU cc_start: 0.8188 (tp30) cc_final: 0.7817 (tp30) REVERT: B 776 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7849 (ttpp) REVERT: B 820 ASP cc_start: 0.8681 (t0) cc_final: 0.8474 (t0) REVERT: B 979 ASP cc_start: 0.8420 (t0) cc_final: 0.8169 (t0) REVERT: B 994 ASP cc_start: 0.8193 (t0) cc_final: 0.7983 (t0) REVERT: B 1127 ASP cc_start: 0.7874 (t0) cc_final: 0.7397 (t0) REVERT: C 99 ASN cc_start: 0.8217 (m110) cc_final: 0.7917 (p0) REVERT: C 120 VAL cc_start: 0.8797 (m) cc_final: 0.8453 (p) REVERT: C 238 PHE cc_start: 0.7241 (p90) cc_final: 0.6816 (p90) REVERT: C 277 LEU cc_start: 0.8282 (mm) cc_final: 0.7890 (mp) REVERT: C 353 TRP cc_start: 0.5836 (p-90) cc_final: 0.5283 (p-90) REVERT: C 441 LEU cc_start: 0.6654 (mt) cc_final: 0.5905 (tt) REVERT: C 525 CYS cc_start: 0.2673 (OUTLIER) cc_final: 0.2394 (m) REVERT: C 646 ARG cc_start: 0.8824 (mpp80) cc_final: 0.8582 (ttp-110) REVERT: C 776 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8462 (ttpp) REVERT: C 779 GLN cc_start: 0.8771 (tt0) cc_final: 0.8307 (tm-30) REVERT: C 896 ILE cc_start: 0.8533 (mt) cc_final: 0.8154 (tt) REVERT: C 1005 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8031 (mt0) REVERT: C 1017 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 1073 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8192 (mtpt) REVERT: C 1092 GLU cc_start: 0.7945 (pm20) cc_final: 0.7648 (pm20) REVERT: C 1139 ASP cc_start: 0.8150 (t0) cc_final: 0.7846 (t0) REVERT: A 34 ARG cc_start: 0.6516 (mtp85) cc_final: 0.6104 (mmt90) REVERT: A 40 ASP cc_start: 0.8228 (t70) cc_final: 0.7883 (t0) REVERT: A 53 ASP cc_start: 0.7829 (t0) cc_final: 0.7452 (t70) REVERT: A 55 PHE cc_start: 0.7581 (m-80) cc_final: 0.6922 (m-80) REVERT: A 129 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7721 (mmmt) REVERT: A 133 PHE cc_start: 0.6602 (m-80) cc_final: 0.5458 (m-80) REVERT: A 190 ARG cc_start: 0.8506 (mtt180) cc_final: 0.8090 (mtt180) REVERT: A 195 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7070 (mmmt) REVERT: A 400 PHE cc_start: 0.7279 (p90) cc_final: 0.6906 (p90) REVERT: A 532 ASN cc_start: 0.8297 (t0) cc_final: 0.8055 (t0) REVERT: A 580 GLN cc_start: 0.6672 (tp40) cc_final: 0.6101 (tp40) REVERT: A 607 GLN cc_start: 0.8362 (mp10) cc_final: 0.7595 (mp10) REVERT: A 661 GLU cc_start: 0.8093 (tp30) cc_final: 0.7821 (tp30) REVERT: A 779 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 790 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8518 (mtpt) REVERT: A 823 PHE cc_start: 0.8231 (t80) cc_final: 0.7868 (t80) REVERT: A 869 MET cc_start: 0.8528 (mtt) cc_final: 0.8235 (mtt) REVERT: A 935 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7897 (tp-100) REVERT: A 988 GLU cc_start: 0.8381 (tp30) cc_final: 0.8057 (tp30) REVERT: A 1092 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 1111 GLU cc_start: 0.8448 (pm20) cc_final: 0.8221 (pm20) outliers start: 85 outliers final: 72 residues processed: 531 average time/residue: 0.1848 time to fit residues: 151.7556 Evaluate side-chains 557 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 482 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1050 MET 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 98 SER 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 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 712 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE 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 991 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 TRP 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 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE 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 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU 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 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 99 ASN B 969 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 969 ASN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.152661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119972 restraints weight = 52101.899| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.61 r_work: 0.3539 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25701 Z= 0.123 Angle : 0.559 11.894 34980 Z= 0.283 Chirality : 0.044 0.230 3936 Planarity : 0.004 0.064 4529 Dihedral : 4.102 20.284 3440 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.11 % Allowed : 20.48 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3164 helix: 0.21 (0.22), residues: 621 sheet: -0.60 (0.19), residues: 658 loop : -1.92 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.021 0.001 TYR C 495 PHE 0.039 0.001 PHE C 306 TRP 0.024 0.001 TRP A 104 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00284 (25662) covalent geometry : angle 0.55684 (34902) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.23673 ( 78) hydrogen bonds : bond 0.04333 ( 658) hydrogen bonds : angle 4.96143 ( 1848) *********************** 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 574 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 487 time to evaluate : 1.050 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 177 MET cc_start: -0.3690 (mmp) cc_final: -0.4390 (mmt) REVERT: B 277 LEU cc_start: 0.8641 (mm) cc_final: 0.8381 (mp) REVERT: B 298 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 324 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 353 TRP cc_start: 0.6387 (p90) cc_final: 0.6015 (p90) REVERT: B 400 PHE cc_start: 0.8288 (p90) cc_final: 0.7932 (p90) REVERT: B 432 CYS cc_start: 0.2273 (OUTLIER) cc_final: 0.0683 (m) REVERT: B 567 ARG cc_start: 0.8676 (mtt180) cc_final: 0.8428 (ttm170) REVERT: B 773 GLU cc_start: 0.8160 (tp30) cc_final: 0.7794 (tp30) REVERT: B 776 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7838 (ttpp) REVERT: B 820 ASP cc_start: 0.8657 (t0) cc_final: 0.8455 (t0) REVERT: B 955 ASN cc_start: 0.8593 (t0) cc_final: 0.8339 (t0) REVERT: B 979 ASP cc_start: 0.8462 (t0) cc_final: 0.8179 (t0) REVERT: B 994 ASP cc_start: 0.8137 (t0) cc_final: 0.7894 (t0) REVERT: B 1127 ASP cc_start: 0.7810 (t0) cc_final: 0.7321 (t0) REVERT: C 99 ASN cc_start: 0.8203 (m110) cc_final: 0.7873 (p0) REVERT: C 120 VAL cc_start: 0.8817 (m) cc_final: 0.8484 (p) REVERT: C 238 PHE cc_start: 0.7128 (p90) cc_final: 0.6861 (p90) REVERT: C 277 LEU cc_start: 0.8261 (mm) cc_final: 0.7873 (mp) REVERT: C 324 GLU cc_start: 0.6641 (tp30) cc_final: 0.6352 (tp30) REVERT: C 441 LEU cc_start: 0.6767 (mt) cc_final: 0.6028 (tt) REVERT: C 515 PHE cc_start: 0.6878 (p90) cc_final: 0.6507 (p90) REVERT: C 525 CYS cc_start: 0.2748 (OUTLIER) cc_final: 0.2397 (m) REVERT: C 646 ARG cc_start: 0.8828 (mpp80) cc_final: 0.8582 (ttp-110) REVERT: C 657 ASN cc_start: 0.8613 (t0) cc_final: 0.8405 (t0) REVERT: C 776 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8507 (tttm) REVERT: C 779 GLN cc_start: 0.8773 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 896 ILE cc_start: 0.8526 (mt) cc_final: 0.8155 (tt) REVERT: C 1005 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8028 (mt0) REVERT: C 1017 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 1073 LYS cc_start: 0.8425 (tmtt) cc_final: 0.8188 (mtpt) REVERT: C 1092 GLU cc_start: 0.7904 (pm20) cc_final: 0.7625 (pm20) REVERT: C 1139 ASP cc_start: 0.8158 (t0) cc_final: 0.7862 (t0) REVERT: A 34 ARG cc_start: 0.6542 (mtp85) cc_final: 0.6133 (mmt90) REVERT: A 40 ASP cc_start: 0.8235 (t70) cc_final: 0.7911 (t0) REVERT: A 53 ASP cc_start: 0.7834 (t0) cc_final: 0.7449 (t70) REVERT: A 55 PHE cc_start: 0.7558 (m-80) cc_final: 0.6867 (m-80) REVERT: A 104 TRP cc_start: 0.7625 (m-90) cc_final: 0.7275 (m-90) REVERT: A 129 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7763 (mmmt) REVERT: A 133 PHE cc_start: 0.6623 (m-80) cc_final: 0.5452 (m-80) REVERT: A 190 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8054 (mtt180) REVERT: A 195 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7209 (mmmt) REVERT: A 400 PHE cc_start: 0.7246 (p90) cc_final: 0.6890 (p90) REVERT: A 532 ASN cc_start: 0.8293 (t0) cc_final: 0.8051 (t0) REVERT: A 580 GLN cc_start: 0.6809 (tp40) cc_final: 0.6249 (tp40) REVERT: A 607 GLN cc_start: 0.8340 (mp10) cc_final: 0.7626 (mp10) REVERT: A 661 GLU cc_start: 0.8103 (tp30) cc_final: 0.7830 (tp30) REVERT: A 775 ASP cc_start: 0.8410 (m-30) cc_final: 0.8105 (t0) REVERT: A 779 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: A 790 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8505 (mtpt) REVERT: A 823 PHE cc_start: 0.8250 (t80) cc_final: 0.7896 (t80) REVERT: A 935 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7904 (tp-100) REVERT: A 988 GLU cc_start: 0.8361 (tp30) cc_final: 0.8050 (tp30) REVERT: A 995 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: A 1092 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 1111 GLU cc_start: 0.8441 (pm20) cc_final: 0.8219 (pm20) outliers start: 87 outliers final: 67 residues processed: 535 average time/residue: 0.1809 time to fit residues: 149.7926 Evaluate side-chains 553 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 483 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL 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 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1082 CYS 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 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 495 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 712 ILE Chi-restraints excluded: chain C residue 791 THR 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 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 281 GLU 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 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 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU 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 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 66 HIS B 969 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C 965 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 655 HIS A 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116010 restraints weight = 52501.549| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.67 r_work: 0.3487 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3996 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= 0.212 Angle : 0.622 11.459 34980 Z= 0.318 Chirality : 0.047 0.218 3936 Planarity : 0.004 0.056 4529 Dihedral : 4.400 22.055 3440 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.18 % Allowed : 20.87 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3164 helix: 0.27 (0.22), residues: 614 sheet: -0.67 (0.19), residues: 640 loop : -2.00 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 995 TYR 0.020 0.002 TYR C1138 PHE 0.040 0.002 PHE C 306 TRP 0.027 0.002 TRP A 353 HIS 0.015 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00494 (25662) covalent geometry : angle 0.61756 (34902) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.62454 ( 78) hydrogen bonds : bond 0.05064 ( 658) hydrogen bonds : angle 5.12237 ( 1848) *********************** 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 586 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 497 time to evaluate : 0.881 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: 0.7368 (mmtp) cc_final: 0.7129 (mmtp) REVERT: B 159 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 177 MET cc_start: -0.3781 (mmp) cc_final: -0.4500 (mmt) REVERT: B 202 LYS cc_start: 0.7937 (pttp) cc_final: 0.7497 (ptpp) REVERT: B 277 LEU cc_start: 0.8675 (mm) cc_final: 0.8430 (mp) REVERT: B 298 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 324 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8144 (mm-30) REVERT: B 353 TRP cc_start: 0.6598 (p90) cc_final: 0.6005 (p90) REVERT: B 400 PHE cc_start: 0.8330 (p90) cc_final: 0.7963 (p90) REVERT: B 432 CYS cc_start: 0.2325 (OUTLIER) cc_final: 0.0638 (m) REVERT: B 567 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8479 (ttm170) REVERT: B 661 GLU cc_start: 0.8344 (tp30) cc_final: 0.7800 (tm-30) REVERT: B 773 GLU cc_start: 0.8198 (tp30) cc_final: 0.7827 (tp30) REVERT: B 776 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7833 (ttpp) REVERT: B 955 ASN cc_start: 0.8719 (t0) cc_final: 0.8500 (t0) REVERT: B 979 ASP cc_start: 0.8545 (t0) cc_final: 0.8280 (t0) REVERT: B 994 ASP cc_start: 0.8258 (t0) cc_final: 0.7990 (t0) REVERT: B 1127 ASP cc_start: 0.7910 (t0) cc_final: 0.7456 (t0) REVERT: B 1137 VAL cc_start: 0.9226 (t) cc_final: 0.9010 (m) REVERT: C 99 ASN cc_start: 0.8293 (m110) cc_final: 0.7976 (p0) REVERT: C 120 VAL cc_start: 0.8861 (m) cc_final: 0.8527 (p) REVERT: C 238 PHE cc_start: 0.7109 (p90) cc_final: 0.6762 (p90) REVERT: C 277 LEU cc_start: 0.8356 (mm) cc_final: 0.7972 (mp) REVERT: C 294 ASP cc_start: 0.7282 (p0) cc_final: 0.6874 (p0) REVERT: C 441 LEU cc_start: 0.6885 (mt) cc_final: 0.6478 (tp) REVERT: C 497 PHE cc_start: 0.2620 (m-80) cc_final: 0.2202 (m-80) REVERT: C 525 CYS cc_start: 0.2878 (OUTLIER) cc_final: 0.2678 (m) REVERT: C 646 ARG cc_start: 0.8819 (mpp80) cc_final: 0.8598 (ttp-110) REVERT: C 776 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8494 (tttm) REVERT: C 779 GLN cc_start: 0.8815 (tt0) cc_final: 0.8325 (tm-30) REVERT: C 896 ILE cc_start: 0.8603 (mt) cc_final: 0.8197 (tt) REVERT: C 1005 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8087 (mt0) REVERT: C 1017 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 1073 LYS cc_start: 0.8420 (tmtt) cc_final: 0.8184 (mtpt) REVERT: C 1092 GLU cc_start: 0.7965 (pm20) cc_final: 0.7721 (pm20) REVERT: C 1139 ASP cc_start: 0.8175 (t0) cc_final: 0.7876 (t0) REVERT: A 34 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6135 (mmt90) REVERT: A 40 ASP cc_start: 0.8327 (t70) cc_final: 0.8017 (t0) REVERT: A 53 ASP cc_start: 0.7834 (t0) cc_final: 0.7469 (t0) REVERT: A 55 PHE cc_start: 0.7568 (m-80) cc_final: 0.6943 (m-80) REVERT: A 133 PHE cc_start: 0.6815 (m-80) cc_final: 0.5607 (m-80) REVERT: A 190 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8168 (mtt180) REVERT: A 195 LYS cc_start: 0.7444 (mmmt) cc_final: 0.6737 (mmmt) REVERT: A 400 PHE cc_start: 0.7389 (p90) cc_final: 0.6999 (p90) REVERT: A 495 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7007 (t80) REVERT: A 532 ASN cc_start: 0.8359 (t0) cc_final: 0.8142 (t0) REVERT: A 580 GLN cc_start: 0.6910 (tp40) cc_final: 0.6347 (tp40) REVERT: A 607 GLN cc_start: 0.8440 (mp10) cc_final: 0.7693 (mp10) REVERT: A 661 GLU cc_start: 0.8162 (tp30) cc_final: 0.7895 (tp30) REVERT: A 711 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 790 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8630 (mtpt) REVERT: A 823 PHE cc_start: 0.8342 (t80) cc_final: 0.8011 (t80) REVERT: A 988 GLU cc_start: 0.8427 (tp30) cc_final: 0.7962 (tp30) REVERT: A 995 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: A 1002 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8019 (mp-120) REVERT: A 1092 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7875 (mm-30) outliers start: 89 outliers final: 68 residues processed: 547 average time/residue: 0.1834 time to fit residues: 155.1191 Evaluate side-chains 560 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 486 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 127 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 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS 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 1082 CYS 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 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 495 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 712 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 878 LEU 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 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 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE 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 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 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 770 ILE 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 896 ILE 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 Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 295 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 214 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN B 969 ASN B1106 GLN C 657 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.151178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118309 restraints weight = 52098.806| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.78 r_work: 0.3497 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4073 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= 0.128 Angle : 0.587 11.294 34980 Z= 0.299 Chirality : 0.045 0.210 3936 Planarity : 0.004 0.053 4529 Dihedral : 4.240 20.735 3440 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.97 % Allowed : 21.66 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3164 helix: 0.55 (0.22), residues: 614 sheet: -0.58 (0.19), residues: 667 loop : -1.93 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.020 0.001 TYR C 495 PHE 0.038 0.001 PHE C 306 TRP 0.025 0.001 TRP A 353 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00299 (25662) covalent geometry : angle 0.58417 (34902) SS BOND : bond 0.00266 ( 39) SS BOND : angle 1.40493 ( 78) hydrogen bonds : bond 0.04368 ( 658) hydrogen bonds : angle 4.95719 ( 1848) *********************** 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 571 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 488 time to evaluate : 0.944 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 41 LYS cc_start: 0.7395 (mmtp) cc_final: 0.7151 (mmtp) REVERT: B 177 MET cc_start: -0.3924 (mmp) cc_final: -0.4598 (mmt) REVERT: B 202 LYS cc_start: 0.7875 (pttp) cc_final: 0.7438 (ptpp) REVERT: B 277 LEU cc_start: 0.8603 (mm) cc_final: 0.8357 (mp) REVERT: B 298 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7100 (tm-30) REVERT: B 309 GLU cc_start: 0.8174 (tp30) cc_final: 0.7962 (tp30) REVERT: B 324 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 353 TRP cc_start: 0.6467 (p90) cc_final: 0.6096 (p90) REVERT: B 400 PHE cc_start: 0.8306 (p90) cc_final: 0.7919 (p90) REVERT: B 432 CYS cc_start: 0.2302 (OUTLIER) cc_final: 0.0591 (m) REVERT: B 551 VAL cc_start: 0.7752 (p) cc_final: 0.7524 (m) REVERT: B 567 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8384 (ttm170) REVERT: B 661 GLU cc_start: 0.8363 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 773 GLU cc_start: 0.8153 (tp30) cc_final: 0.7784 (tp30) REVERT: B 776 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7752 (ttpp) REVERT: B 825 LYS cc_start: 0.9288 (mttm) cc_final: 0.8978 (mmmt) REVERT: B 955 ASN cc_start: 0.8681 (t0) cc_final: 0.8462 (t0) REVERT: B 979 ASP cc_start: 0.8517 (t0) cc_final: 0.8210 (t0) REVERT: B 994 ASP cc_start: 0.8213 (t0) cc_final: 0.7960 (t0) REVERT: B 1127 ASP cc_start: 0.7949 (t0) cc_final: 0.7479 (t0) REVERT: C 99 ASN cc_start: 0.8239 (m110) cc_final: 0.7904 (p0) REVERT: C 120 VAL cc_start: 0.8853 (m) cc_final: 0.8516 (p) REVERT: C 131 CYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5845 (m) REVERT: C 238 PHE cc_start: 0.7130 (p90) cc_final: 0.6750 (p90) REVERT: C 277 LEU cc_start: 0.8263 (mm) cc_final: 0.7960 (mp) REVERT: C 441 LEU cc_start: 0.6758 (mt) cc_final: 0.5992 (tt) REVERT: C 497 PHE cc_start: 0.2579 (m-80) cc_final: 0.2199 (m-80) REVERT: C 525 CYS cc_start: 0.2822 (OUTLIER) cc_final: 0.2532 (m) REVERT: C 646 ARG cc_start: 0.8906 (mpp80) cc_final: 0.8664 (ttp-110) REVERT: C 776 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8389 (tttm) REVERT: C 779 GLN cc_start: 0.8827 (tt0) cc_final: 0.8290 (tm-30) REVERT: C 896 ILE cc_start: 0.8554 (mt) cc_final: 0.8154 (tt) REVERT: C 1005 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8026 (mt0) REVERT: C 1017 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 1073 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8218 (mtpt) REVERT: C 1092 GLU cc_start: 0.8079 (pm20) cc_final: 0.7764 (pm20) REVERT: C 1139 ASP cc_start: 0.8225 (t0) cc_final: 0.7917 (t0) REVERT: A 34 ARG cc_start: 0.6510 (mtp85) cc_final: 0.6067 (mmt90) REVERT: A 40 ASP cc_start: 0.8288 (t70) cc_final: 0.7982 (t0) REVERT: A 53 ASP cc_start: 0.7868 (t0) cc_final: 0.7486 (t0) REVERT: A 55 PHE cc_start: 0.7623 (m-80) cc_final: 0.6973 (m-80) REVERT: A 129 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7680 (mmtt) REVERT: A 133 PHE cc_start: 0.6737 (m-80) cc_final: 0.5521 (m-80) REVERT: A 190 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8182 (mtt180) REVERT: A 195 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6726 (mmmt) REVERT: A 353 TRP cc_start: 0.7035 (p90) cc_final: 0.6397 (p90) REVERT: A 400 PHE cc_start: 0.7336 (p90) cc_final: 0.6882 (p90) REVERT: A 495 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6923 (t80) REVERT: A 532 ASN cc_start: 0.8377 (t0) cc_final: 0.8141 (t0) REVERT: A 580 GLN cc_start: 0.6909 (tp40) cc_final: 0.6323 (tp40) REVERT: A 607 GLN cc_start: 0.8419 (mp10) cc_final: 0.7662 (mp10) REVERT: A 661 GLU cc_start: 0.8199 (tp30) cc_final: 0.7913 (tp30) REVERT: A 790 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8641 (mtpt) REVERT: A 823 PHE cc_start: 0.8340 (t80) cc_final: 0.7981 (t80) REVERT: A 869 MET cc_start: 0.8499 (mtt) cc_final: 0.8196 (mtt) REVERT: A 988 GLU cc_start: 0.8504 (tp30) cc_final: 0.7969 (tp30) REVERT: A 995 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: A 1002 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (mp-120) REVERT: A 1092 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7878 (mm-30) outliers start: 83 outliers final: 67 residues processed: 535 average time/residue: 0.1860 time to fit residues: 153.2481 Evaluate side-chains 554 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 482 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU 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 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 703 ASN 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 131 CYS 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 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 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 712 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 878 LEU 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 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 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 395 VAL 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 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 896 ILE 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 Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 230 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 856 ASN B 969 ASN A 99 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119177 restraints weight = 52259.630| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.63 r_work: 0.3533 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4143 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= 0.121 Angle : 0.586 11.285 34980 Z= 0.297 Chirality : 0.044 0.212 3936 Planarity : 0.004 0.097 4529 Dihedral : 4.162 24.845 3440 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.89 % Allowed : 21.62 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3164 helix: 0.75 (0.22), residues: 614 sheet: -0.50 (0.19), residues: 646 loop : -1.90 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.020 0.001 TYR C 495 PHE 0.038 0.001 PHE C 306 TRP 0.022 0.001 TRP A 353 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00283 (25662) covalent geometry : angle 0.58352 (34902) SS BOND : bond 0.00249 ( 39) SS BOND : angle 1.33237 ( 78) hydrogen bonds : bond 0.04140 ( 658) hydrogen bonds : angle 4.87516 ( 1848) ********************** 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 562 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 481 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3741 (mmp) cc_final: -0.4493 (mmt) REVERT: B 202 LYS cc_start: 0.7827 (pttp) cc_final: 0.7406 (ptpp) REVERT: B 277 LEU cc_start: 0.8668 (mm) cc_final: 0.8411 (mp) REVERT: B 298 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7048 (tm-30) REVERT: B 355 ARG cc_start: 0.7987 (mpp-170) cc_final: 0.7633 (mtm-85) REVERT: B 400 PHE cc_start: 0.8302 (p90) cc_final: 0.7930 (p90) REVERT: B 432 CYS cc_start: 0.2356 (OUTLIER) cc_final: 0.0533 (m) REVERT: B 567 ARG cc_start: 0.8738 (mtt180) cc_final: 0.8516 (ttm170) REVERT: B 661 GLU cc_start: 0.8299 (tp30) cc_final: 0.7790 (tm-30) REVERT: B 773 GLU cc_start: 0.8121 (tp30) cc_final: 0.7788 (tp30) REVERT: B 776 LYS cc_start: 0.8439 (ttpp) cc_final: 0.7718 (ttpp) REVERT: B 825 LYS cc_start: 0.9250 (mttm) cc_final: 0.8980 (mmmt) REVERT: B 955 ASN cc_start: 0.8632 (t0) cc_final: 0.8393 (t0) REVERT: B 979 ASP cc_start: 0.8446 (t0) cc_final: 0.8197 (t0) REVERT: B 994 ASP cc_start: 0.8140 (t0) cc_final: 0.7929 (t0) REVERT: B 1127 ASP cc_start: 0.7778 (t0) cc_final: 0.7350 (t0) REVERT: C 99 ASN cc_start: 0.8227 (m110) cc_final: 0.7906 (p0) REVERT: C 120 VAL cc_start: 0.8817 (m) cc_final: 0.8456 (p) REVERT: C 131 CYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5823 (m) REVERT: C 238 PHE cc_start: 0.6988 (p90) cc_final: 0.6754 (p90) REVERT: C 277 LEU cc_start: 0.8303 (mm) cc_final: 0.8051 (mt) REVERT: C 355 ARG cc_start: 0.6714 (tpp-160) cc_final: 0.6428 (tpp-160) REVERT: C 441 LEU cc_start: 0.6748 (mt) cc_final: 0.5985 (tt) REVERT: C 497 PHE cc_start: 0.2434 (m-80) cc_final: 0.2096 (m-80) REVERT: C 646 ARG cc_start: 0.8803 (mpp80) cc_final: 0.8579 (ttp-110) REVERT: C 776 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8478 (tttm) REVERT: C 779 GLN cc_start: 0.8762 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 896 ILE cc_start: 0.8538 (mt) cc_final: 0.8164 (tt) REVERT: C 1005 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8006 (mt0) REVERT: C 1017 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 1092 GLU cc_start: 0.7926 (pm20) cc_final: 0.7655 (pm20) REVERT: C 1139 ASP cc_start: 0.8144 (t0) cc_final: 0.7881 (t0) REVERT: A 34 ARG cc_start: 0.6538 (mtp85) cc_final: 0.6169 (mmt90) REVERT: A 40 ASP cc_start: 0.8094 (t70) cc_final: 0.7719 (t0) REVERT: A 53 ASP cc_start: 0.7828 (t0) cc_final: 0.7451 (t0) REVERT: A 55 PHE cc_start: 0.7517 (m-80) cc_final: 0.6947 (m-80) REVERT: A 104 TRP cc_start: 0.7441 (m-90) cc_final: 0.7069 (m-90) REVERT: A 129 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7652 (mmtt) REVERT: A 133 PHE cc_start: 0.6630 (m-80) cc_final: 0.5472 (m-80) REVERT: A 190 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8119 (mtt180) REVERT: A 353 TRP cc_start: 0.6857 (p90) cc_final: 0.6320 (p90) REVERT: A 400 PHE cc_start: 0.7206 (p90) cc_final: 0.6856 (p90) REVERT: A 495 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6735 (t80) REVERT: A 532 ASN cc_start: 0.8299 (t0) cc_final: 0.8090 (t0) REVERT: A 580 GLN cc_start: 0.6854 (tp40) cc_final: 0.6296 (tp40) REVERT: A 607 GLN cc_start: 0.8381 (mp10) cc_final: 0.7654 (mp10) REVERT: A 661 GLU cc_start: 0.8147 (tp30) cc_final: 0.7887 (tp30) REVERT: A 790 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8562 (mtpt) REVERT: A 823 PHE cc_start: 0.8290 (t80) cc_final: 0.7959 (t80) REVERT: A 869 MET cc_start: 0.8507 (mtt) cc_final: 0.8224 (mtt) REVERT: A 988 GLU cc_start: 0.8342 (tp30) cc_final: 0.7873 (tp30) REVERT: A 995 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: A 1002 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: A 1092 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7918 (mm-30) outliers start: 81 outliers final: 70 residues processed: 529 average time/residue: 0.1806 time to fit residues: 147.9977 Evaluate side-chains 552 residues out of total 2798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 478 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU 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 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 805 ILE 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 131 CYS 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 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 712 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 878 LEU 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 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 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 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 395 VAL 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 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 770 ILE 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 896 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 117 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 236 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN B 969 ASN B1142 GLN C 657 ASN C 764 ASN C1088 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN A 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116628 restraints weight = 51785.948| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.65 r_work: 0.3474 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25701 Z= 0.205 Angle : 0.652 11.560 34980 Z= 0.334 Chirality : 0.047 0.208 3936 Planarity : 0.004 0.051 4529 Dihedral : 4.483 24.477 3440 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.97 % Allowed : 21.80 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3164 helix: 0.62 (0.22), residues: 611 sheet: -0.55 (0.19), residues: 644 loop : -1.98 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.023 0.002 TYR C 707 PHE 0.057 0.002 PHE B 374 TRP 0.018 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00478 (25662) covalent geometry : angle 0.64467 (34902) SS BOND : bond 0.00340 ( 39) SS BOND : angle 2.21078 ( 78) hydrogen bonds : bond 0.04966 ( 658) hydrogen bonds : angle 5.07154 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6682.42 seconds wall clock time: 115 minutes 8.17 seconds (6908.17 seconds total)