Starting phenix.real_space_refine on Sun Jun 7 06:57:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx2_47278/06_2026/9dx2_47278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx2_47278/06_2026/9dx2_47278.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/9dx2_47278/06_2026/9dx2_47278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx2_47278/06_2026/9dx2_47278.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dx2_47278/06_2026/9dx2_47278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx2_47278/06_2026/9dx2_47278.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= 0.015 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 224 5.16 5 C 21786 2.51 5 N 6013 2.21 5 O 6229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5894 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 24, 'TRANS': 761} Chain breaks: 5 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 21, 'PHE:plan': 1, 'ARG:plan': 6, 'ASP:plan': 15, 'ASN:plan1': 4, 'GLN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 199 Chain: "B" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5582 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 23, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 19, 'PHE:plan': 3, 'ASP:plan': 17, 'HIS:plan': 1, 'GLN:plan1': 5, 'ASN:plan1': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 254 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4367 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 5 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'ASP:plan': 2, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4010 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 23, 'TRANS': 521} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 7, 'HIS:plan': 3, 'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 13, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 179 Chain: "E" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2477 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 23, 'TRANS': 304} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2279 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 20, 'TRANS': 294} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 12, 'ASP:plan': 4, 'HIS:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 137 Chain: "G" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2084 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 18, 'TRANS': 265} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 97 Chain: "H" Number of atoms: 7559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7559 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 10 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 768 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 622 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 27, 'ASN:plan1': 12, 'ASP:plan': 27, 'GLN:plan1': 11, 'ARG:plan': 27, 'HIS:plan': 5, 'PHE:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 484 Time building chain proxies: 7.78, per 1000 atoms: 0.23 Number of scatterers: 34252 At special positions: 0 Unit cell: (225.252, 222.643, 231.34, 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 224 16.00 O 6229 8.00 N 6013 7.00 C 21786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 550 " distance=2.03 Simple disulfide: pdb=" SG CYS B1107 " - pdb=" SG CYS B1148 " distance=2.03 Simple disulfide: pdb=" SG CYS B1197 " - pdb=" SG CYS B1200 " distance=2.03 Simple disulfide: pdb=" SG CYS B1200 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS H 995 " - pdb=" SG CYS H 998 " distance=2.03 Simple disulfide: pdb=" SG CYS H1012 " - pdb=" SG CYS H1037 " 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 64 sheets defined 24.7% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.742A pdb=" N LEU A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.649A pdb=" N LEU A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 787 " --> pdb=" O HIS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 813 removed outlier: 4.296A pdb=" N SER A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 801 " --> pdb=" O TRP A 797 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 removed outlier: 3.577A pdb=" N ALA A 824 " --> pdb=" O LEU A 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 824' Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.683A pdb=" N ASN A 855 " --> pdb=" O ASP A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 867 removed outlier: 3.595A pdb=" N LEU A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 863 " --> pdb=" O GLU A 859 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 865 " --> pdb=" O ILE A 861 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 887 removed outlier: 3.874A pdb=" N GLN A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.529A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 916 Processing helix chain 'A' and resid 921 through 933 removed outlier: 4.454A pdb=" N ASN A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 933 " --> pdb=" O MET A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 950 removed outlier: 3.659A pdb=" N GLU A 944 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.524A pdb=" N PHE A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 removed outlier: 3.638A pdb=" N TYR A 977 " --> pdb=" O ASP A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.757A pdb=" N LYS A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1012 removed outlier: 3.659A pdb=" N ASN A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A1001 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 3.713A pdb=" N ASP A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1051 removed outlier: 4.111A pdb=" N ALA A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A1051 " --> pdb=" O TYR A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1060 through 1077 removed outlier: 3.562A pdb=" N TRP A1066 " --> pdb=" O ARG A1062 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A1067 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1094 removed outlier: 3.593A pdb=" N GLU A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1093 " --> pdb=" O HIS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1192 removed outlier: 3.621A pdb=" N ASN A1192 " --> pdb=" O GLN A1189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1189 through 1192' Processing helix chain 'A' and resid 1206 through 1214 removed outlier: 3.625A pdb=" N SER A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.767A pdb=" N GLY B 512 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 770 Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' Processing helix chain 'B' and resid 781 through 786 Processing helix chain 'B' and resid 790 through 813 removed outlier: 3.580A pdb=" N LYS B 794 " --> pdb=" O ASP B 790 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP B 797 " --> pdb=" O LEU B 793 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 798 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 813 " --> pdb=" O ASP B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 825 through 830 removed outlier: 3.554A pdb=" N ILE B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.737A pdb=" N LEU B 862 " --> pdb=" O GLU B 858 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.646A pdb=" N VAL B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN B 887 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 901 removed outlier: 3.777A pdb=" N ALA B 896 " --> pdb=" O GLU B 892 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 916 removed outlier: 4.057A pdb=" N SER B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.862A pdb=" N VAL B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 950 removed outlier: 3.970A pdb=" N GLU B 944 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 949 " --> pdb=" O MET B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 966 removed outlier: 3.511A pdb=" N CYS B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 961 " --> pdb=" O TYR B 957 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 963 " --> pdb=" O CYS B 959 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 977 removed outlier: 3.730A pdb=" N TYR B 977 " --> pdb=" O ASP B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 991 removed outlier: 3.624A pdb=" N ARG B 986 " --> pdb=" O ALA B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1011 removed outlier: 3.830A pdb=" N ASN B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B1002 " --> pdb=" O GLN B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1017 No H-bonds generated for 'chain 'B' and resid 1015 through 1017' Processing helix chain 'B' and resid 1018 through 1023 Processing helix chain 'B' and resid 1027 through 1040 removed outlier: 3.589A pdb=" N LEU B1031 " --> pdb=" O ASP B1027 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1050 removed outlier: 3.586A pdb=" N SER B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B1047 " --> pdb=" O GLN B1043 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1050 " --> pdb=" O SER B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.553A pdb=" N LEU B1058 " --> pdb=" O PRO B1054 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1054 through 1059' Processing helix chain 'B' and resid 1060 through 1077 removed outlier: 3.746A pdb=" N GLN B1064 " --> pdb=" O ASP B1060 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B1076 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1094 removed outlier: 3.641A pdb=" N PHE B1086 " --> pdb=" O LYS B1082 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B1093 " --> pdb=" O HIS B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1191 removed outlier: 3.740A pdb=" N PHE B1190 " --> pdb=" O LYS B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1216 removed outlier: 3.772A pdb=" N SER B1211 " --> pdb=" O GLY B1207 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B1212 " --> pdb=" O HIS B1208 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B1215 " --> pdb=" O SER B1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 780 through 790 Processing helix chain 'C' and resid 796 through 812 removed outlier: 3.705A pdb=" N ASP C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 811 " --> pdb=" O VAL C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 828 removed outlier: 3.553A pdb=" N THR C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 824 " --> pdb=" O TRP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.962A pdb=" N ARG C1009 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C1013 " --> pdb=" O ARG C1009 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1032 removed outlier: 3.755A pdb=" N ALA C1024 " --> pdb=" O ASP C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1039 removed outlier: 3.881A pdb=" N ARG C1036 " --> pdb=" O GLU C1033 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS C1037 " --> pdb=" O ARG C1034 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C1039 " --> pdb=" O ARG C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1058 removed outlier: 3.621A pdb=" N HIS C1046 " --> pdb=" O GLN C1042 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1070 Processing helix chain 'C' and resid 1136 through 1147 removed outlier: 3.800A pdb=" N GLU C1145 " --> pdb=" O MET C1141 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY C1146 " --> pdb=" O LYS C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 699 through 702 Processing helix chain 'D' and resid 723 through 727 Processing helix chain 'D' and resid 826 through 830 Processing helix chain 'D' and resid 1002 through 1007 removed outlier: 3.631A pdb=" N GLY D1006 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D1007 " --> pdb=" O LYS D1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1002 through 1007' Processing helix chain 'D' and resid 1015 through 1031 removed outlier: 3.547A pdb=" N GLN D1021 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D1028 " --> pdb=" O ALA D1024 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D1029 " --> pdb=" O ALA D1025 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D1030 " --> pdb=" O SER D1026 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D1031 " --> pdb=" O ALA D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1046 removed outlier: 3.800A pdb=" N VAL D1036 " --> pdb=" O ARG D1032 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D1037 " --> pdb=" O LYS D1033 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D1043 " --> pdb=" O TRP D1039 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL D1044 " --> pdb=" O SER D1040 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D1046 " --> pdb=" O ALA D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1065 Processing helix chain 'D' and resid 1068 through 1083 removed outlier: 4.085A pdb=" N ARG D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D1082 " --> pdb=" O HIS D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 3.543A pdb=" N SER D1093 " --> pdb=" O ALA D1089 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D1099 " --> pdb=" O PHE D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1179 through 1191 removed outlier: 3.521A pdb=" N ARG D1184 " --> pdb=" O ARG D1180 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN D1186 " --> pdb=" O ARG D1182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D1188 " --> pdb=" O ARG D1184 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS D1189 " --> pdb=" O ASP D1185 " (cutoff:3.500A) Processing helix chain 'D' and resid 1195 through 1197 No H-bonds generated for 'chain 'D' and resid 1195 through 1197' Processing helix chain 'D' and resid 1198 through 1216 removed outlier: 3.536A pdb=" N PHE D1202 " --> pdb=" O ASN D1198 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D1206 " --> pdb=" O PHE D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1226 removed outlier: 3.684A pdb=" N GLU D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1227 through 1229 No H-bonds generated for 'chain 'D' and resid 1227 through 1229' Processing helix chain 'E' and resid 19 through 22 removed outlier: 3.641A pdb=" N LEU E 22 " --> pdb=" O GLY E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 23 through 30 removed outlier: 3.730A pdb=" N LYS E 29 " --> pdb=" O HIS E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.522A pdb=" N ARG E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 37 " --> pdb=" O PRO E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 58 through 63 removed outlier: 3.654A pdb=" N LEU E 63 " --> pdb=" O PHE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 removed outlier: 3.977A pdb=" N ARG E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 108 removed outlier: 3.582A pdb=" N GLU E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 138 removed outlier: 3.673A pdb=" N ILE E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 196 Proline residue: E 195 - end of helix Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.609A pdb=" N LYS E 248 " --> pdb=" O THR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.610A pdb=" N ALA E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 291' Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.686A pdb=" N VAL E 316 " --> pdb=" O GLY E 312 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 318 " --> pdb=" O GLY E 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 22 removed outlier: 3.554A pdb=" N LEU F 22 " --> pdb=" O GLY F 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 22' Processing helix chain 'F' and resid 23 through 32 removed outlier: 3.730A pdb=" N LYS F 29 " --> pdb=" O HIS F 25 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.944A pdb=" N LYS F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 63 " --> pdb=" O PHE F 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 63' Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.612A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) Proline residue: F 104 - end of helix removed outlier: 3.678A pdb=" N GLU F 107 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS F 108 " --> pdb=" O PRO F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 138 removed outlier: 3.526A pdb=" N ILE F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 137 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 196 removed outlier: 3.570A pdb=" N LEU F 194 " --> pdb=" O PRO F 191 " (cutoff:3.500A) Proline residue: F 195 - end of helix Processing helix chain 'F' and resid 197 through 206 removed outlier: 3.526A pdb=" N VAL F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 Processing helix chain 'F' and resid 281 through 291 Proline residue: F 287 - end of helix removed outlier: 3.682A pdb=" N ALA F 291 " --> pdb=" O PRO F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.505A pdb=" N VAL F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 317 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 320 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.507A pdb=" N LEU G 27 " --> pdb=" O TYR G 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS G 29 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.513A pdb=" N ARG G 36 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER G 37 " --> pdb=" O PRO G 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 33 through 37' Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.528A pdb=" N LYS G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.706A pdb=" N HIS G 108 " --> pdb=" O PRO G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 removed outlier: 3.862A pdb=" N VAL G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 196 Proline residue: G 195 - end of helix Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'G' and resid 243 through 247 removed outlier: 4.171A pdb=" N LYS G 247 " --> pdb=" O ALA G 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 243 through 247' Processing helix chain 'G' and resid 279 through 292 removed outlier: 4.179A pdb=" N GLN G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) Proline residue: G 287 - end of helix Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.504A pdb=" N VAL G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 426 removed outlier: 3.604A pdb=" N ILE H 426 " --> pdb=" O LYS H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 698 through 701 removed outlier: 3.520A pdb=" N LEU H 701 " --> pdb=" O SER H 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 698 through 701' Processing helix chain 'H' and resid 955 through 957 No H-bonds generated for 'chain 'H' and resid 955 through 957' Processing helix chain 'H' and resid 1018 through 1028 removed outlier: 3.696A pdb=" N GLU H1023 " --> pdb=" O SER H1019 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR H1027 " --> pdb=" O GLU H1023 " (cutoff:3.500A) Processing helix chain 'H' and resid 1038 through 1044 removed outlier: 3.500A pdb=" N THR H1044 " --> pdb=" O LEU H1040 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.803A pdb=" N GLU A 376 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 405 removed outlier: 6.738A pdb=" N CYS A 415 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 403 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 413 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE A 405 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG A 411 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 421 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 437 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 423 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 450 removed outlier: 6.743A pdb=" N CYS A 462 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 448 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 460 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 459 " --> pdb=" O TRP A 471 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 471 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 461 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A 492 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 472 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS A 490 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE A 474 " --> pdb=" O TRP A 488 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TRP A 488 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 501 through 506 removed outlier: 7.217A pdb=" N CYS A 518 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 504 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 516 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE A 506 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N MET A 514 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 524 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A 543 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 526 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.252A pdb=" N CYS A 552 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 582 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR A 599 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 584 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 588 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 593 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 612 removed outlier: 3.854A pdb=" N ASP A 609 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 631 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 630 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 658 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 632 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 671 removed outlier: 6.888A pdb=" N SER A 681 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 669 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 679 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 682 " --> pdb=" O CYS A 686 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 689 " --> pdb=" O GLY A 702 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYS A 691 " --> pdb=" O CYS A 700 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N CYS A 700 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1104 through 1105 Processing sheet with id=AA9, first strand: chain 'A' and resid 1203 through 1205 removed outlier: 4.042A pdb=" N PHE A1194 " --> pdb=" O TRP C1127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 361 removed outlier: 3.575A pdb=" N SER B 357 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 366 " --> pdb=" O CYS B 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 405 removed outlier: 6.728A pdb=" N CYS B 415 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 403 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 413 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE B 405 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 411 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 436 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 425 " --> pdb=" O CYS B 434 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N CYS B 434 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 450 removed outlier: 4.044A pdb=" N ARG B 447 " --> pdb=" O CYS B 462 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 463 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 501 through 506 removed outlier: 7.148A pdb=" N CYS B 518 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 504 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 516 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 506 " --> pdb=" O MET B 514 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET B 514 " --> pdb=" O PHE B 506 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS B 542 " --> pdb=" O ILE B 526 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 552 through 555 removed outlier: 3.923A pdb=" N CYS B 552 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 582 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR B 599 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 584 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 593 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 609 through 612 removed outlier: 3.927A pdb=" N ASP B 609 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 631 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 657 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR B 634 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE B 655 " --> pdb=" O THR B 634 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 668 through 671 removed outlier: 3.887A pdb=" N ARG B 668 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 678 " --> pdb=" O TRP B 690 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 691 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1103 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 1196 through 1197 removed outlier: 3.688A pdb=" N GLY H1016 " --> pdb=" O ASN H1007 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 355 through 356 removed outlier: 4.453A pdb=" N LEU C 397 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 412 " --> pdb=" O GLU C 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 355 through 356 removed outlier: 3.684A pdb=" N SER C 398 " --> pdb=" O PHE H 979 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 424 through 429 removed outlier: 3.929A pdb=" N ASP C 426 " --> pdb=" O CYS C 439 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 440 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 444 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 445 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C 461 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 447 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 469 through 474 removed outlier: 4.002A pdb=" N ARG C 471 " --> pdb=" O CYS C 486 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 492 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR C 517 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 494 " --> pdb=" O ARG C 515 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 530 removed outlier: 4.122A pdb=" N ASP C 527 " --> pdb=" O CYS C 542 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS C 566 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU C 552 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 564 " --> pdb=" O GLU C 552 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 577 through 579 removed outlier: 7.767A pdb=" N VAL C 606 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR C 623 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 617 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.524A pdb=" N ASP C 633 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 654 " --> pdb=" O GLN C 682 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 682 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 656 " --> pdb=" O VAL C 680 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 690 through 695 removed outlier: 3.820A pdb=" N ARG C 692 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 706 " --> pdb=" O CYS C 710 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 726 " --> pdb=" O LEU C 713 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS C 715 " --> pdb=" O CYS C 724 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS C 724 " --> pdb=" O LYS C 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.891A pdb=" N GLY D 541 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 553 " --> pdb=" O GLY D 541 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 647 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 672 through 677 removed outlier: 6.770A pdb=" N CYS D 687 " --> pdb=" O HIS D 673 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA D 675 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 685 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D 677 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG D 683 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 694 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 695 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 707 " --> pdb=" O ILE D 695 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP D 697 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 705 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 716 through 721 removed outlier: 6.934A pdb=" N CYS D 733 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL D 719 " --> pdb=" O ALA D 731 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA D 731 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP D 721 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE D 729 " --> pdb=" O TRP D 721 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 740 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 739 " --> pdb=" O GLU D 754 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU D 754 " --> pdb=" O VAL D 739 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE D 741 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 762 through 767 removed outlier: 6.728A pdb=" N GLY D 779 " --> pdb=" O ASN D 763 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL D 765 " --> pdb=" O ALA D 777 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 777 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP D 767 " --> pdb=" O ILE D 775 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE D 775 " --> pdb=" O TRP D 767 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 786 " --> pdb=" O CYS D 778 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 791 " --> pdb=" O GLN D 795 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN D 795 " --> pdb=" O THR D 791 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 809 through 814 removed outlier: 3.552A pdb=" N ALA D 811 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN D 862 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS D 851 " --> pdb=" O GLU D 860 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU D 860 " --> pdb=" O LYS D 851 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 871 through 876 removed outlier: 4.046A pdb=" N ASP D 873 " --> pdb=" O CYS D 890 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 885 " --> pdb=" O CYS D 901 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS D 901 " --> pdb=" O SER D 885 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 897 " --> pdb=" O SER D 889 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D 891 " --> pdb=" O ARG D 895 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG D 895 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 896 " --> pdb=" O LEU D 914 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 900 " --> pdb=" O SER D 910 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 921 through 925 removed outlier: 3.504A pdb=" N HIS D 923 " --> pdb=" O SER D 936 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.294A pdb=" N LEU E 3 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU E 146 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 5 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.852A pdb=" N TRP E 76 " --> pdb=" O HIS E 8 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS E 8 " --> pdb=" O TRP E 76 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL E 78 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE E 41 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 42 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 228 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 240 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 263 through 268 removed outlier: 3.641A pdb=" N ILE E 268 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 304 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 112 through 116 removed outlier: 3.816A pdb=" N GLU F 146 " --> pdb=" O ILE F 5 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 69 through 71 removed outlier: 3.526A pdb=" N VAL F 55 " --> pdb=" O ARG F 11 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 53 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE F 41 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 228 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 263 through 268 Processing sheet with id=AE4, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.122A pdb=" N LEU G 3 " --> pdb=" O TYR G 144 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU G 146 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG G 145 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 69 through 71 removed outlier: 4.007A pdb=" N GLN G 70 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER G 14 " --> pdb=" O GLN G 70 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 54 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE G 228 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL G 240 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G 241 " --> pdb=" O CYS G 185 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 76 through 79 Processing sheet with id=AE7, first strand: chain 'G' and resid 177 through 178 removed outlier: 3.528A pdb=" N ALA G 306 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 268 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP G 304 " --> pdb=" O ILE G 268 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 7 through 10 removed outlier: 6.923A pdb=" N LEU H 25 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE H 56 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU H 27 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 51 " --> pdb=" O LEU H 43 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 43 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 63 through 68 removed outlier: 6.672A pdb=" N GLY H 81 " --> pdb=" O LYS H 64 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL H 66 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA H 79 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP H 68 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU H 77 " --> pdb=" O TRP H 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 116 through 121 removed outlier: 4.074A pdb=" N THR H 118 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY H 132 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER H 141 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE H 140 " --> pdb=" O GLN H 159 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN H 159 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 155 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.975A pdb=" N SER H 165 " --> pdb=" O GLY H 179 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 188 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.892A pdb=" N GLN H 204 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL H 206 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA H 217 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL H 208 " --> pdb=" O ARG H 215 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG H 215 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 216 " --> pdb=" O TRP H 227 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 237 " --> pdb=" O ILE H 226 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 246 through 251 removed outlier: 7.051A pdb=" N LEU H 262 " --> pdb=" O THR H 247 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL H 249 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA H 260 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP H 251 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU H 258 " --> pdb=" O TRP H 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE H 286 " --> pdb=" O ASP H 273 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 299 through 302 removed outlier: 3.824A pdb=" N SER H 299 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 313 " --> pdb=" O SER H 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 311 " --> pdb=" O ALA H 301 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 330 through 332 removed outlier: 3.512A pdb=" N PHE H 340 " --> pdb=" O TYR H 350 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 348 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU H 347 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE H 378 " --> pdb=" O LEU H 347 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU H 349 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER H 371 " --> pdb=" O LEU H 367 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 385 through 390 removed outlier: 6.596A pdb=" N GLY H 403 " --> pdb=" O LYS H 386 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL H 388 " --> pdb=" O ALA H 401 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA H 401 " --> pdb=" O VAL H 388 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP H 390 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU H 399 " --> pdb=" O TRP H 390 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 409 " --> pdb=" O PHE H 430 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 438 through 443 removed outlier: 6.643A pdb=" N GLY H 454 " --> pdb=" O ASN H 439 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU H 441 " --> pdb=" O ALA H 452 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA H 452 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP H 443 " --> pdb=" O TRP H 450 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP H 450 " --> pdb=" O TRP H 443 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER H 463 " --> pdb=" O LEU H 455 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE H 462 " --> pdb=" O GLN H 481 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN H 481 " --> pdb=" O PHE H 462 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.514A pdb=" N VAL H 520 " --> pdb=" O LEU H 506 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 508 " --> pdb=" O MET H 518 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET H 518 " --> pdb=" O ILE H 508 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP H 510 " --> pdb=" O GLN H 516 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLN H 516 " --> pdb=" O ASP H 510 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 526 through 530 removed outlier: 3.672A pdb=" N GLN H 526 " --> pdb=" O PHE H 541 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL H 528 " --> pdb=" O ALA H 539 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA H 539 " --> pdb=" O VAL H 528 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL H 530 " --> pdb=" O ARG H 537 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG H 537 " --> pdb=" O VAL H 530 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL H 538 " --> pdb=" O TRP H 549 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 559 " --> pdb=" O ILE H 548 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 568 through 573 removed outlier: 6.893A pdb=" N LEU H 584 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL H 571 " --> pdb=" O ALA H 582 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA H 582 " --> pdb=" O VAL H 571 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP H 573 " --> pdb=" O LEU H 580 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU H 580 " --> pdb=" O TRP H 573 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H 592 " --> pdb=" O THR H 583 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 603 " --> pdb=" O LEU H 593 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 614 through 617 removed outlier: 3.908A pdb=" N SER H 614 " --> pdb=" O VAL H 628 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 647 through 650 removed outlier: 3.655A pdb=" N MET H 647 " --> pdb=" O GLN H 951 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER H 948 " --> pdb=" O SER H 944 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 944 " --> pdb=" O SER H 948 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 655 through 660 removed outlier: 8.009A pdb=" N PHE H 675 " --> pdb=" O ASN H 690 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN H 690 " --> pdb=" O PHE H 675 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE H 677 " --> pdb=" O LYS H 688 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 703 through 708 removed outlier: 3.608A pdb=" N ALA H 717 " --> pdb=" O VAL H 707 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU H 716 " --> pdb=" O TRP H 728 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 749 through 754 removed outlier: 3.844A pdb=" N LYS H 751 " --> pdb=" O GLY H 765 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER H 766 " --> pdb=" O PHE H 770 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE H 770 " --> pdb=" O SER H 766 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS H 773 " --> pdb=" O SER H 783 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER H 783 " --> pdb=" O CYS H 773 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 792 through 797 removed outlier: 4.398A pdb=" N ASP H 794 " --> pdb=" O THR H 808 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER H 807 " --> pdb=" O GLN H 815 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN H 815 " --> pdb=" O SER H 807 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN H 813 " --> pdb=" O PHE H 809 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP H 818 " --> pdb=" O CYS H 825 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS H 825 " --> pdb=" O ASP H 818 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 836 through 841 removed outlier: 7.099A pdb=" N GLY H 852 " --> pdb=" O PHE H 837 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS H 839 " --> pdb=" O ALA H 850 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA H 850 " --> pdb=" O CYS H 839 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP H 841 " --> pdb=" O TRP H 848 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N TRP H 848 " --> pdb=" O TRP H 841 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY H 853 " --> pdb=" O MET H 857 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET H 857 " --> pdb=" O GLY H 853 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS H 872 " --> pdb=" O VAL H 860 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP H 862 " --> pdb=" O GLU H 870 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU H 870 " --> pdb=" O ASP H 862 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 880 through 885 removed outlier: 6.884A pdb=" N CYS H 896 " --> pdb=" O ALA H 881 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL H 883 " --> pdb=" O ALA H 894 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA H 894 " --> pdb=" O VAL H 883 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TRP H 885 " --> pdb=" O HIS H 892 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N HIS H 892 " --> pdb=" O TRP H 885 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 917 " --> pdb=" O VAL H 906 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 2976 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: 8.48 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11244 1.34 - 1.46: 8578 1.46 - 1.58: 14956 1.58 - 1.70: 0 1.70 - 1.82: 309 Bond restraints: 35087 Sorted by residual: bond pdb=" C THR H 279 " pdb=" N PRO H 280 " ideal model delta sigma weight residual 1.330 1.344 -0.014 1.19e-02 7.06e+03 1.30e+00 bond pdb=" N VAL E 281 " pdb=" CA VAL E 281 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" C GLN F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 bond pdb=" C THR D 569 " pdb=" N PRO D 570 " ideal model delta sigma weight residual 1.334 1.357 -0.024 2.34e-02 1.83e+03 1.01e+00 bond pdb=" N GLY A 646 " pdb=" CA GLY A 646 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.00e+00 ... (remaining 35082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 47372 1.55 - 3.10: 459 3.10 - 4.65: 80 4.65 - 6.20: 13 6.20 - 7.75: 2 Bond angle restraints: 47926 Sorted by residual: angle pdb=" N ILE F 284 " pdb=" CA ILE F 284 " pdb=" C ILE F 284 " ideal model delta sigma weight residual 113.53 109.86 3.67 9.80e-01 1.04e+00 1.40e+01 angle pdb=" N VAL B 532 " pdb=" CA VAL B 532 " pdb=" C VAL B 532 " ideal model delta sigma weight residual 111.81 108.94 2.87 8.60e-01 1.35e+00 1.11e+01 angle pdb=" C ILE E 280 " pdb=" N VAL E 281 " pdb=" CA VAL E 281 " ideal model delta sigma weight residual 121.65 118.61 3.04 9.40e-01 1.13e+00 1.05e+01 angle pdb=" N GLY C 726 " pdb=" CA GLY C 726 " pdb=" C GLY C 726 " ideal model delta sigma weight residual 111.37 115.13 -3.76 1.29e+00 6.01e-01 8.48e+00 angle pdb=" N ASP H 395 " pdb=" CA ASP H 395 " pdb=" C ASP H 395 " ideal model delta sigma weight residual 109.81 116.08 -6.27 2.21e+00 2.05e-01 8.05e+00 ... (remaining 47921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 19526 16.40 - 32.81: 759 32.81 - 49.21: 161 49.21 - 65.61: 30 65.61 - 82.02: 2 Dihedral angle restraints: 20478 sinusoidal: 7041 harmonic: 13437 Sorted by residual: dihedral pdb=" CA ASP H 395 " pdb=" C ASP H 395 " pdb=" N PRO H 396 " pdb=" CA PRO H 396 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA PRO H 396 " pdb=" C PRO H 396 " pdb=" N GLU H 397 " pdb=" CA GLU H 397 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS B1200 " pdb=" SG CYS B1200 " pdb=" SG CYS B1228 " pdb=" CB CYS B1228 " ideal model delta sinusoidal sigma weight residual -86.00 -121.05 35.05 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 20475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3141 0.027 - 0.053: 1450 0.053 - 0.079: 495 0.079 - 0.106: 313 0.106 - 0.132: 137 Chirality restraints: 5536 Sorted by residual: chirality pdb=" CA VAL A 669 " pdb=" N VAL A 669 " pdb=" C VAL A 669 " pdb=" CB VAL A 669 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE H 378 " pdb=" N ILE H 378 " pdb=" C ILE H 378 " pdb=" CB ILE H 378 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE E 123 " pdb=" N ILE E 123 " pdb=" C ILE E 123 " pdb=" CB ILE E 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 5533 not shown) Planarity restraints: 6100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 647 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 648 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 648 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 648 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 395 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO H 396 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 221 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO E 222 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " 0.026 5.00e-02 4.00e+02 ... (remaining 6097 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5552 2.77 - 3.30: 29617 3.30 - 3.83: 49439 3.83 - 4.37: 54784 4.37 - 4.90: 100648 Nonbonded interactions: 240040 Sorted by model distance: nonbonded pdb=" OG1 THR D 929 " pdb=" OD1 ASN D 931 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 416 " pdb=" OD1 ASP A 418 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR G 47 " pdb=" O ASP G 50 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR F 75 " pdb=" OE1 GLU F 127 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP H 447 " pdb=" ND2 ASN H 449 " model vdw 2.273 3.120 ... (remaining 240035 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 354 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB )) or resid 373 through 379 or resid 387 through 396 o \ r (resid 397 through 399 and (name N or name CA or name C or name O or name CB ) \ ) or resid 400 through 417 or (resid 418 and (name N or name CA or name C or nam \ e O or name CB )) or resid 419 through 424 or (resid 425 through 429 and (name N \ or name CA or name C or name O or name CB )) or resid 430 through 438 or (resid \ 439 through 440 and (name N or name CA or name C or name O or name CB )) or res \ id 441 through 463 or (resid 464 through 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 through 473 or (resid 474 and (name N or name \ CA or name C or name O or name CB )) or (resid 486 through 487 and (name N or n \ ame CA or name C or name O or name CB )) or resid 488 through 489 or (resid 490 \ and (name N or name CA or name C or name O or name CB )) or resid 491 through 49 \ 3 or (resid 494 through 496 and (name N or name CA or name C or name O or name C \ B )) or resid 497 through 520 or (resid 521 and (name N or name CA or name C or \ name O or name CB )) or resid 522 through 524 or (resid 525 and (name N or name \ CA or name C or name O or name CB )) or resid 526 through 534 or (resid 535 and \ (name N or name CA or name C or name O or name CB )) or resid 536 through 560 or \ (resid 561 through 562 and (name N or name CA or name C or name O or name CB )) \ or resid 563 through 576 or (resid 577 through 581 and (name N or name CA or na \ me C or name O or name CB )) or resid 582 through 585 or (resid 586 and (name N \ or name CA or name C or name O or name CB )) or resid 587 through 589 or (resid \ 590 and (name N or name CA or name C or name O or name CB )) or resid 591 or (re \ sid 592 through 593 and (name N or name CA or name C or name O or name CB )) or \ resid 594 through 595 or (resid 596 through 597 and (name N or name CA or name C \ or name O or name CB )) or resid 598 through 659 or (resid 660 and (name N or n \ ame CA or name C or name O or name CB )) or resid 661 through 685 or (resid 686 \ and (name N or name CA or name C or name O or name CB )) or resid 687 through 69 \ 0 or (resid 691 through 695 and (name N or name CA or name C or name O or name C \ B )) or resid 696 through 698 or (resid 699 and (name N or name CA or name C or \ name O or name CB )) or resid 700 through 706 or (resid 707 and (name N or name \ CA or name C or name O or name CB )) or resid 708 through 709 or resid 757 throu \ gh 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) or \ resid 795 through 809 or (resid 810 through 813 and (name N or name CA or name \ C or name O or name CB )) or resid 814 through 830 or (resid 831 and (name N or \ name CA or name C or name O or name CB )) or resid 832 through 845 or (resid 853 \ through 854 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 55 through 864 or (resid 865 and (name N or name CA or name C or name O or name \ CB )) or resid 866 through 884 or (resid 885 and (name N or name CA or name C or \ name O or name CB )) or resid 886 through 944 or (resid 945 and (name N or name \ CA or name C or name O or name CB )) or resid 946 through 947 or (resid 948 and \ (name N or name CA or name C or name O or name CB )) or resid 949 through 952 o \ r (resid 953 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 54 or (resid 955 and (name N or name CA or name C or name O or name CB )) or res \ id 956 through 966 or (resid 967 through 969 and (name N or name CA or name C or \ name O or name CB )) or resid 970 through 1025 or (resid 1026 through 1027 and \ (name N or name CA or name C or name O or name CB )) or resid 1028 through 1054 \ or (resid 1055 through 1056 and (name N or name CA or name C or name O or name C \ B )) or resid 1057 through 1060 or (resid 1061 and (name N or name CA or name C \ or name O or name CB )) or resid 1062 through 1098 or (resid 1099 through 1102 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1103 through 11 \ 07 or (resid 1108 through 1109 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1110 through 1111 or (resid 1112 and (name N or name CA or name \ C or name O or name CB )) or resid 1113 or (resid 1114 and (name N or name CA o \ r name C or name O or name CB )) or resid 1115 or (resid 1144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1145 through 1148 or (resid 1149 \ through 1150 and (name N or name CA or name C or name O or name CB )) or resid \ 1151 through 1165 or resid 1185 through 1233)) selection = (chain 'B' and (resid 354 through 387 or (resid 388 through 390 and (name N or n \ ame CA or name C or name O or name CB )) or resid 391 through 471 or (resid 472 \ and (name N or name CA or name C or name O or name CB )) or resid 473 through 54 \ 7 or (resid 548 and (name N or name CA or name C or name O or name CB )) or resi \ d 549 through 604 or (resid 605 and (name N or name CA or name C or name O or na \ me CB )) or resid 606 through 635 or (resid 636 and (name N or name CA or name C \ or name O or name CB )) or resid 637 through 833 or (resid 834 and (name N or n \ ame CA or name C or name O or name CB )) or resid 835 or (resid 836 through 841 \ and (name N or name CA or name C or name O or name CB )) or resid 842 through 87 \ 3 or (resid 874 through 877 and (name N or name CA or name C or name O or name C \ B )) or resid 878 through 905 or (resid 906 through 907 and (name N or name CA o \ r name C or name O or name CB )) or resid 908 through 912 or (resid 913 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 914 through 919 and ( \ name N or name CA or name C or name O or name CB )) or resid 920 or (resid 921 t \ hrough 922 and (name N or name CA or name C or name O or name CB )) or resid 923 \ through 928 or (resid 929 through 930 and (name N or name CA or name C or name \ O or name CB )) or resid 931 through 935 or (resid 936 through 939 and (name N o \ r name CA or name C or name O or name CB )) or resid 940 through 1008 or (resid \ 1009 and (name N or name CA or name C or name O or name CB )) or resid 1010 thro \ ugh 1011 or (resid 1012 through 1013 and (name N or name CA or name C or name O \ or name CB )) or resid 1014 through 1233)) } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 44 or (resid 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 48 or (res \ id 49 through 50 and (name N or name CA or name C or name O or name CB )) or res \ id 51 through 61 or (resid 62 and (name N or name CA or name C or name O or name \ CB )) or resid 63 through 72 or (resid 73 through 74 and (name N or name CA or \ name C or name O or name CB )) or resid 75 through 81 or resid 94 through 126 or \ (resid 127 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 8 through 138 or (resid 139 through 140 and (name N or name CA or name C or name \ O or name CB )) or resid 141 or (resid 142 through 143 and (name N or name CA o \ r name C or name O or name CB )) or resid 144 through 146 or (resid 147 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 148 through 154 and ( \ name N or name CA or name C or name O or name CB )) or (resid 171 through 174 an \ d (name N or name CA or name C or name O or name CB )) or resid 175 through 176 \ or (resid 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 191 or (resid 192 and (name N or name CA or name C or name O or name \ CB )) or resid 193 through 208 or (resid 209 and (name N or name CA or name C o \ r name O or name CB )) or (resid 225 and (name N or name CA or name C or name O \ or name CB )) or resid 226 through 233 or (resid 234 and (name N or name CA or n \ ame C or name O or name CB )) or resid 235 through 243 or (resid 244 and (name N \ or name CA or name C or name O or name CB )) or resid 245 through 246 or (resid \ 247 and (name N or name CA or name C or name O or name CB )) or resid 248 throu \ gh 257 or (resid 258 through 259 and (name N or name CA or name C or name O or n \ ame CB )) or resid 260 or (resid 261 through 262 and (name N or name CA or name \ C or name O or name CB )) or resid 263 through 266 or (resid 267 through 268 and \ (name N or name CA or name C or name O or name CB )) or resid 269 through 275 o \ r (resid 276 through 278 and (name N or name CA or name C or name O or name CB ) \ ) or resid 279 through 280 or (resid 281 through 282 and (name N or name CA or n \ ame C or name O or name CB )) or resid 283 or (resid 284 through 285 and (name N \ or name CA or name C or name O or name CB )) or resid 286 through 287 or (resid \ 288 through 292 and (name N or name CA or name C or name O or name CB )) or res \ id 293 through 299 or (resid 300 and (name N or name CA or name C or name O or n \ ame CB )) or resid 301 or (resid 302 and (name N or name CA or name C or name O \ or name CB )) or resid 303 through 310 or (resid 311 and (name N or name CA or n \ ame C or name O or name CB )) or resid 312 or (resid 313 and (name N or name CA \ or name C or name O or name CB )) or resid 314 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 or (resid 320 thr \ ough 325 and (name N or name CA or name C or name O or name CB )) or resid 326 t \ hrough 328)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 61 or (resid 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 81 or resid 94 through \ 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) or re \ sid 128 through 141 or (resid 142 through 143 and (name N or name CA or name C o \ r name O or name CB )) or resid 144 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 through 154 or (resid 171 th \ rough 174 and (name N or name CA or name C or name O or name CB )) or resid 175 \ through 176 or (resid 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 209 or (resid 225 and (name N or name CA or name C or na \ me O or name CB )) or resid 226 through 257 or (resid 258 through 259 and (name \ N or name CA or name C or name O or name CB )) or (resid 260 through 262 and (na \ me N or name CA or name C or name O or name CB )) or resid 263 through 266 or (r \ esid 267 through 268 and (name N or name CA or name C or name O or name CB )) or \ resid 269 through 275 or (resid 276 through 278 and (name N or name CA or name \ C or name O or name CB )) or resid 279 through 280 or (resid 281 through 282 and \ (name N or name CA or name C or name O or name CB )) or resid 283 or (resid 284 \ through 285 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 86 through 287 or (resid 288 through 292 and (name N or name CA or name C or nam \ e O or name CB )) or resid 293 through 299 or (resid 300 and (name N or name CA \ or name C or name O or name CB )) or resid 301 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB )) or resid 312 or (resid 313 and \ (name N or name CA or name C or name O or name CB )) or resid 314 through 319 o \ r (resid 320 through 325 and (name N or name CA or name C or name O or name CB ) \ ) or resid 326 through 328)) selection = (chain 'G' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 48 or (resid 49 throug \ h 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throug \ h 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 233 or (resid 234 and (name N or name \ CA or name C or name O or name CB )) or resid 235 through 246 or (resid 247 and \ (name N or name CA or name C or name O or name CB )) or resid 248 through 291 or \ (resid 292 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 3 through 317 or (resid 318 and (name N or name CA or name C or name O or name C \ B )) or resid 319 through 328)) } 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: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.510 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 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 : 0.002 0.031 35093 Z= 0.080 Angle : 0.440 7.753 47938 Z= 0.236 Chirality : 0.041 0.132 5536 Planarity : 0.003 0.053 6100 Dihedral : 9.441 82.016 11718 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 7.14 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.55 (0.12), residues: 4548 helix: -0.56 (0.18), residues: 753 sheet: -0.01 (0.15), residues: 1222 loop : -1.74 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1083 TYR 0.010 0.001 TYR F 118 PHE 0.007 0.001 PHE B 651 TRP 0.010 0.001 TRP B 471 HIS 0.002 0.000 HIS H 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00155 / 0.08 (35087) covalent geometry : angle 0.43954 / 0.24 (47926) SS BOND : bond 0.00267 / 0.14 ( 6) SS BOND : angle 0.49982 / 0.24 ( 12) hydrogen bonds : bond 0.33008 / 22.30 ( 1067) hydrogen bonds : angle 8.38381 / 5.84 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 279 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 836 MET cc_start: 0.4428 (tpt) cc_final: 0.2898 (ppp) REVERT: D 668 HIS cc_start: 0.5468 (OUTLIER) cc_final: 0.5262 (m170) REVERT: E 54 MET cc_start: -0.0519 (mtm) cc_final: -0.4252 (tpp) REVERT: G 54 MET cc_start: 0.0029 (mpp) cc_final: -0.1371 (tpp) REVERT: G 115 LEU cc_start: -0.3126 (OUTLIER) cc_final: -0.4129 (mt) REVERT: G 242 ASP cc_start: -0.0117 (m-30) cc_final: -0.1624 (m-30) REVERT: H 355 THR cc_start: -0.0923 (OUTLIER) cc_final: -0.1483 (p) REVERT: H 998 CYS cc_start: 0.6525 (OUTLIER) cc_final: 0.0480 (t) outliers start: 125 outliers final: 20 residues processed: 391 average time/residue: 0.2178 time to fit residues: 137.6039 Evaluate side-chains 193 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1197 CYS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 668 HIS Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 845 ASN Chi-restraints excluded: chain D residue 889 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain H residue 355 THR Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 998 CYS Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 50.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 HIS A 419 GLN A 457 GLN A 485 GLN A 556 ASN A 583 GLN A 615 ASN A 658 GLN A 783 HIS A 887 GLN A 952 GLN A 955 ASN A 998 GLN A1043 GLN A1051 GLN A1102 GLN A1208 HIS A1230 GLN B 457 GLN B 541 GLN B 542 HIS B 658 GLN ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B1000 ASN B1015 ASN B1051 GLN B1064 GLN B1189 GLN B1208 HIS B1230 GLN C 432 HIS C 457 HIS C 481 GLN C 511 HIS C 686 HIS C 818 GLN C1013 HIS C1022 GLN C1044 GLN C1129 GLN C1138 GLN D 805 HIS ** D 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 940 ASN F 4 HIS F 246 GLN F 283 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN H 434 HIS H 760 HIS H 832 HIS H 999 HIS H1028 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.091499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.069115 restraints weight = 250302.982| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 8.33 r_work: 0.3259 rms_B_bonded: 7.57 restraints_weight: 2.0000 r_work: 0.3330 rms_B_bonded: 5.40 restraints_weight: 4.0000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35093 Z= 0.155 Angle : 0.586 11.299 47938 Z= 0.308 Chirality : 0.045 0.177 5536 Planarity : 0.005 0.128 6100 Dihedral : 4.686 54.297 4923 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.13 % Allowed : 10.61 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.27 (0.12), residues: 4548 helix: -0.09 (0.17), residues: 855 sheet: 0.23 (0.15), residues: 1226 loop : -1.73 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 17 TYR 0.014 0.001 TYR D1209 PHE 0.020 0.002 PHE G 68 TRP 0.026 0.001 TRP F 263 HIS 0.008 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (35087) covalent geometry : angle 0.58606 / 0.31 (47926) SS BOND : bond 0.00278 / 0.16 ( 6) SS BOND : angle 1.42846 / 0.78 ( 12) hydrogen bonds : bond 0.04778 / 3.30 ( 1067) hydrogen bonds : angle 5.56372 / 3.85 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8152 (tm-30) REVERT: A 955 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.7748 (t0) REVERT: B 764 MET cc_start: 0.8145 (mmm) cc_final: 0.7570 (mmt) REVERT: B 836 MET cc_start: 0.5169 (tpt) cc_final: 0.3315 (ppp) REVERT: B 837 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7445 (p) REVERT: B 929 MET cc_start: 0.7679 (mtp) cc_final: 0.7399 (mtp) REVERT: B 1209 MET cc_start: 0.7815 (mtt) cc_final: 0.7529 (mtt) REVERT: D 668 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6985 (m170) REVERT: F 107 GLU cc_start: 0.7366 (mp0) cc_final: 0.6829 (mp0) REVERT: F 175 HIS cc_start: 0.5775 (m-70) cc_final: 0.5420 (p-80) REVERT: F 178 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7441 (tm-30) REVERT: F 283 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: G 54 MET cc_start: 0.1618 (mpp) cc_final: -0.0237 (tpp) REVERT: G 57 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7431 (mm-30) REVERT: G 73 GLU cc_start: 0.7763 (pm20) cc_final: 0.7299 (pm20) REVERT: H 1022 MET cc_start: 0.8124 (tmm) cc_final: 0.7895 (tmm) outliers start: 72 outliers final: 35 residues processed: 242 average time/residue: 0.2220 time to fit residues: 88.1188 Evaluate side-chains 206 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 668 HIS Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 355 THR Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 280 optimal weight: 30.0000 chunk 396 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 67 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 295 optimal weight: 50.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS A 621 HIS A 661 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 ASN B 510 HIS B 534 ASN B 608 HIS ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN B 883 ASN B1043 GLN B1205 HIS B1208 HIS C 614 ASN C 632 HIS C1046 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 GLN D 915 HIS F 135 HIS F 246 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN H 13 HIS ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 HIS H 650 HIS H 891 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.088065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.060322 restraints weight = 191907.850| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 8.13 r_work: 0.3037 rms_B_bonded: 6.51 restraints_weight: 2.0000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.007 0.112 35093 Z= 0.309 Angle : 0.702 9.256 47938 Z= 0.370 Chirality : 0.048 0.244 5536 Planarity : 0.005 0.076 6100 Dihedral : 4.997 58.747 4909 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.05 % Allowed : 10.73 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.32 (0.12), residues: 4548 helix: -0.12 (0.17), residues: 858 sheet: 0.04 (0.15), residues: 1285 loop : -1.71 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 586 TYR 0.029 0.002 TYR B 823 PHE 0.030 0.002 PHE A 405 TRP 0.055 0.003 TRP F 263 HIS 0.017 0.002 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.31 (35087) covalent geometry : angle 0.70189 / 0.37 (47926) SS BOND : bond 0.02529 / 1.31 ( 6) SS BOND : angle 1.86909 / 0.84 ( 12) hydrogen bonds : bond 0.06150 / 4.17 ( 1067) hydrogen bonds : angle 5.53371 / 3.86 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 177 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8320 (tt0) REVERT: B 836 MET cc_start: 0.5282 (tpt) cc_final: 0.3475 (ppp) REVERT: B 1209 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7845 (mtt) REVERT: C 712 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7227 (mmm-85) REVERT: C 1023 MET cc_start: 0.9300 (tpt) cc_final: 0.9066 (tpt) REVERT: D 668 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7108 (m170) REVERT: E 69 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7189 (pp) REVERT: E 114 MET cc_start: 0.2790 (mmp) cc_final: 0.2031 (mmm) REVERT: F 1 MET cc_start: 0.4319 (tpp) cc_final: 0.3930 (tpp) REVERT: F 128 GLN cc_start: 0.6709 (pm20) cc_final: 0.6411 (pm20) REVERT: F 147 VAL cc_start: 0.3606 (OUTLIER) cc_final: 0.3263 (t) REVERT: F 175 HIS cc_start: 0.5454 (m-70) cc_final: 0.4884 (p-80) REVERT: F 178 GLN cc_start: 0.7787 (tm-30) cc_final: 0.6782 (pp30) REVERT: F 267 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7791 (mtt90) REVERT: G 54 MET cc_start: 0.1543 (mpp) cc_final: -0.0278 (tpp) REVERT: G 56 ASP cc_start: 0.7219 (p0) cc_final: 0.7002 (p0) REVERT: G 57 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7084 (mp0) REVERT: G 190 ASP cc_start: 0.8324 (m-30) cc_final: 0.8098 (t70) REVERT: H 518 MET cc_start: 0.7723 (pmm) cc_final: 0.7424 (pmm) REVERT: H 625 MET cc_start: 0.8584 (mmm) cc_final: 0.8297 (mmm) outliers start: 103 outliers final: 53 residues processed: 266 average time/residue: 0.2251 time to fit residues: 97.1802 Evaluate side-chains 219 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 1064 SER Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 668 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 612 ILE Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 157 optimal weight: 0.4980 chunk 150 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 386 optimal weight: 0.1980 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 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN C1081 GLN E 182 ASN F 246 GLN F 321 GLN G 178 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.089987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.066405 restraints weight = 243744.175| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 7.39 r_work: 0.3133 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work: 0.3207 rms_B_bonded: 5.61 restraints_weight: 4.0000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35093 Z= 0.090 Angle : 0.503 7.597 47938 Z= 0.260 Chirality : 0.042 0.175 5536 Planarity : 0.004 0.099 6100 Dihedral : 4.465 59.421 4908 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.66 % Allowed : 11.71 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4548 helix: 0.47 (0.18), residues: 868 sheet: 0.22 (0.15), residues: 1278 loop : -1.56 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 183 TYR 0.018 0.001 TYR F 296 PHE 0.018 0.001 PHE A1194 TRP 0.044 0.001 TRP F 263 HIS 0.005 0.001 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (35087) covalent geometry : angle 0.50255 / 0.26 (47926) SS BOND : bond 0.01026 / 0.68 ( 6) SS BOND : angle 0.97863 / 0.48 ( 12) hydrogen bonds : bond 0.03514 / 2.39 ( 1067) hydrogen bonds : angle 4.81553 / 3.35 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 1.289 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 1209 MET cc_start: 0.7870 (mtt) cc_final: 0.7576 (mtt) REVERT: D 668 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.6959 (m170) REVERT: E 69 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7483 (pp) REVERT: E 114 MET cc_start: 0.3071 (mmp) cc_final: 0.2379 (mmm) REVERT: F 1 MET cc_start: 0.4668 (tpp) cc_final: 0.4289 (tpp) REVERT: F 36 ARG cc_start: 0.6455 (ttp-110) cc_final: 0.6172 (ttt-90) REVERT: F 175 HIS cc_start: 0.4675 (m-70) cc_final: 0.4442 (p-80) REVERT: F 178 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7408 (tm-30) REVERT: F 264 ARG cc_start: 0.8279 (ptm160) cc_final: 0.8016 (tmm-80) REVERT: G 54 MET cc_start: 0.1487 (mpp) cc_final: -0.0323 (tpp) REVERT: G 129 ASP cc_start: 0.3479 (p0) cc_final: 0.3161 (p0) REVERT: G 190 ASP cc_start: 0.8261 (m-30) cc_final: 0.7987 (t70) REVERT: H 518 MET cc_start: 0.7476 (pmm) cc_final: 0.7150 (pmm) REVERT: H 625 MET cc_start: 0.8625 (mmm) cc_final: 0.8368 (mmm) outliers start: 56 outliers final: 40 residues processed: 225 average time/residue: 0.2227 time to fit residues: 80.7188 Evaluate side-chains 209 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 CYS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 668 HIS Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 612 ILE Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 250 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 423 optimal weight: 9.9990 chunk 297 optimal weight: 50.0000 chunk 239 optimal weight: 20.0000 chunk 319 optimal weight: 4.9990 chunk 367 optimal weight: 0.3980 chunk 166 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 458 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 HIS ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 178 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.088560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062026 restraints weight = 195048.835| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 7.05 r_work: 0.3079 rms_B_bonded: 6.93 restraints_weight: 2.0000 r_work: 0.3149 rms_B_bonded: 6.08 restraints_weight: 4.0000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35093 Z= 0.198 Angle : 0.569 7.406 47938 Z= 0.295 Chirality : 0.044 0.150 5536 Planarity : 0.004 0.062 6100 Dihedral : 4.593 57.442 4906 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.58 % Allowed : 11.44 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4548 helix: 0.52 (0.18), residues: 859 sheet: 0.13 (0.15), residues: 1286 loop : -1.53 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1001 TYR 0.019 0.001 TYR B 823 PHE 0.021 0.001 PHE A 405 TRP 0.049 0.002 TRP F 263 HIS 0.012 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (35087) covalent geometry : angle 0.56849 / 0.29 (47926) SS BOND : bond 0.00926 / 0.46 ( 6) SS BOND : angle 1.14703 / 0.59 ( 12) hydrogen bonds : bond 0.04514 / 3.07 ( 1067) hydrogen bonds : angle 4.87643 / 3.39 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 843 ASN cc_start: 0.9513 (OUTLIER) cc_final: 0.9264 (p0) REVERT: B 377 CYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8848 (p) REVERT: B 1209 MET cc_start: 0.7980 (mtt) cc_final: 0.7606 (mtt) REVERT: C 623 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8144 (p) REVERT: D 668 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7315 (m170) REVERT: E 69 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7156 (pp) REVERT: E 114 MET cc_start: 0.2764 (mmp) cc_final: 0.2301 (mmm) REVERT: F 1 MET cc_start: 0.4805 (tpp) cc_final: 0.4379 (tpp) REVERT: F 36 ARG cc_start: 0.6457 (ttp-110) cc_final: 0.6118 (ttt90) REVERT: F 175 HIS cc_start: 0.5477 (m-70) cc_final: 0.4818 (p-80) REVERT: F 178 GLN cc_start: 0.7750 (tm-30) cc_final: 0.6718 (pp30) REVERT: F 264 ARG cc_start: 0.8298 (ptm160) cc_final: 0.8033 (ptm160) REVERT: F 265 MET cc_start: -0.1558 (mmp) cc_final: -0.2497 (mmt) REVERT: F 267 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7742 (mtt90) REVERT: G 36 ARG cc_start: 0.4151 (ptm-80) cc_final: 0.3826 (ptm-80) REVERT: G 54 MET cc_start: 0.1190 (mpp) cc_final: -0.0661 (tpp) REVERT: G 190 ASP cc_start: 0.8303 (m-30) cc_final: 0.8061 (t70) REVERT: H 196 MET cc_start: 0.5068 (pmm) cc_final: 0.4811 (pmm) REVERT: H 518 MET cc_start: 0.7195 (pmm) cc_final: 0.6902 (pmm) REVERT: H 625 MET cc_start: 0.8813 (mmm) cc_final: 0.8578 (mmm) REVERT: H 1022 MET cc_start: 0.8512 (ttp) cc_final: 0.7863 (tmm) outliers start: 87 outliers final: 58 residues processed: 243 average time/residue: 0.2143 time to fit residues: 85.0029 Evaluate side-chains 227 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 545 CYS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 668 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 612 ILE Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 305 optimal weight: 40.0000 chunk 118 optimal weight: 1.9990 chunk 422 optimal weight: 50.0000 chunk 297 optimal weight: 50.0000 chunk 291 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 433 optimal weight: 50.0000 chunk 277 optimal weight: 50.0000 chunk 404 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 654 HIS ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN F 246 GLN F 321 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN H 755 HIS H 760 HIS H 832 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.087405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.064621 restraints weight = 239538.749| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 8.62 r_work: 0.2972 rms_B_bonded: 7.22 restraints_weight: 2.0000 r_work: 0.3052 rms_B_bonded: 5.75 restraints_weight: 4.0000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 35093 Z= 0.336 Angle : 0.713 9.038 47938 Z= 0.373 Chirality : 0.048 0.190 5536 Planarity : 0.005 0.106 6100 Dihedral : 5.225 58.715 4906 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.99 % Allowed : 12.03 % Favored : 84.97 % 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: -1.39 (0.12), residues: 4548 helix: -0.17 (0.17), residues: 870 sheet: -0.11 (0.15), residues: 1286 loop : -1.70 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 145 TYR 0.029 0.002 TYR B 823 PHE 0.031 0.002 PHE A 405 TRP 0.023 0.003 TRP A1196 HIS 0.017 0.002 HIS C1119 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.34 (35087) covalent geometry : angle 0.71226 / 0.37 (47926) SS BOND : bond 0.00907 / 0.54 ( 6) SS BOND : angle 1.92971 / 0.97 ( 12) hydrogen bonds : bond 0.05470 / 3.71 ( 1067) hydrogen bonds : angle 5.29759 / 3.68 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 170 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 843 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9155 (p0) REVERT: B 412 MET cc_start: 0.8757 (pmm) cc_final: 0.8331 (pmm) REVERT: B 1148 CYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5547 (m) REVERT: B 1209 MET cc_start: 0.8205 (mtt) cc_final: 0.7999 (mtt) REVERT: C 623 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8503 (m) REVERT: D 943 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8357 (p) REVERT: E 114 MET cc_start: 0.3084 (mmp) cc_final: 0.2289 (mmm) REVERT: F 1 MET cc_start: 0.4991 (tpp) cc_final: 0.4515 (tpp) REVERT: F 36 ARG cc_start: 0.6307 (ttp-110) cc_final: 0.5893 (ttt90) REVERT: F 175 HIS cc_start: 0.4596 (m-70) cc_final: 0.4055 (p-80) REVERT: F 178 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7103 (pp30) REVERT: F 308 VAL cc_start: 0.4447 (OUTLIER) cc_final: 0.4212 (m) REVERT: G 36 ARG cc_start: 0.3585 (ptm-80) cc_final: 0.3248 (ptm-80) REVERT: G 54 MET cc_start: 0.1248 (mpp) cc_final: -0.0543 (tpp) REVERT: G 190 ASP cc_start: 0.8251 (m-30) cc_final: 0.7964 (t70) REVERT: H 518 MET cc_start: 0.7648 (pmm) cc_final: 0.7307 (pmm) REVERT: H 1022 MET cc_start: 0.8483 (ttp) cc_final: 0.8053 (tmm) outliers start: 101 outliers final: 67 residues processed: 260 average time/residue: 0.2221 time to fit residues: 94.5710 Evaluate side-chains 234 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1018 GLN Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 310 MET Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 612 ILE Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 154 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 323 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 318 optimal weight: 50.0000 chunk 314 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS B1208 HIS C1118 HIS F 246 GLN F 321 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 832 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.088079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.063352 restraints weight = 241133.668| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 7.86 r_work: 0.2998 rms_B_bonded: 6.44 restraints_weight: 2.0000 r_work: 0.3078 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35093 Z= 0.186 Angle : 0.557 10.491 47938 Z= 0.290 Chirality : 0.044 0.153 5536 Planarity : 0.004 0.067 6100 Dihedral : 4.735 58.395 4900 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.22 % Allowed : 13.04 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.14 (0.12), residues: 4548 helix: 0.28 (0.18), residues: 875 sheet: -0.02 (0.15), residues: 1275 loop : -1.60 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 183 TYR 0.026 0.001 TYR G 51 PHE 0.015 0.001 PHE A1194 TRP 0.020 0.001 TRP B1196 HIS 0.009 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (35087) covalent geometry : angle 0.55680 / 0.29 (47926) SS BOND : bond 0.01029 / 0.52 ( 6) SS BOND : angle 1.51149 / 0.72 ( 12) hydrogen bonds : bond 0.04153 / 2.82 ( 1067) hydrogen bonds : angle 4.83696 / 3.35 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 MET cc_start: 0.7839 (ppp) cc_final: 0.7570 (ppp) REVERT: A 843 ASN cc_start: 0.9519 (OUTLIER) cc_final: 0.9194 (p0) REVERT: B 412 MET cc_start: 0.8870 (pmm) cc_final: 0.8353 (pmm) REVERT: B 1148 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5746 (m) REVERT: B 1209 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7881 (mtt) REVERT: C 623 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8381 (p) REVERT: D 943 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (p) REVERT: E 114 MET cc_start: 0.3195 (mmp) cc_final: 0.2443 (mmm) REVERT: F 1 MET cc_start: 0.5037 (tpp) cc_final: 0.4607 (tpp) REVERT: F 175 HIS cc_start: 0.5403 (m-70) cc_final: 0.4507 (p-80) REVERT: F 178 GLN cc_start: 0.7786 (tm-30) cc_final: 0.6855 (pp30) REVERT: F 181 GLN cc_start: 0.8450 (mm110) cc_final: 0.8048 (mp10) REVERT: F 267 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7670 (mtt90) REVERT: G 54 MET cc_start: 0.1008 (mpp) cc_final: -0.0643 (tpp) REVERT: G 190 ASP cc_start: 0.8323 (m-30) cc_final: 0.8090 (t70) REVERT: H 518 MET cc_start: 0.7778 (pmm) cc_final: 0.7418 (pmm) REVERT: H 634 MET cc_start: 0.8648 (mpp) cc_final: 0.8196 (mpp) REVERT: H 1022 MET cc_start: 0.8477 (ttp) cc_final: 0.7961 (tmm) outliers start: 75 outliers final: 56 residues processed: 230 average time/residue: 0.2152 time to fit residues: 80.9181 Evaluate side-chains 220 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 124 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 378 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 chunk 369 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN F 246 GLN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 832 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.087971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.064900 restraints weight = 240549.411| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 8.39 r_work: 0.2980 rms_B_bonded: 7.03 restraints_weight: 2.0000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35093 Z= 0.188 Angle : 0.562 8.631 47938 Z= 0.291 Chirality : 0.044 0.150 5536 Planarity : 0.004 0.080 6100 Dihedral : 4.653 59.271 4900 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.49 % Allowed : 12.86 % Favored : 84.65 % 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: -1.05 (0.13), residues: 4548 helix: 0.42 (0.18), residues: 885 sheet: 0.02 (0.15), residues: 1271 loop : -1.56 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 586 TYR 0.019 0.001 TYR G 51 PHE 0.016 0.001 PHE A 405 TRP 0.018 0.001 TRP B1196 HIS 0.040 0.001 HIS B 842 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (35087) covalent geometry : angle 0.56137 / 0.29 (47926) SS BOND : bond 0.00465 / 0.24 ( 6) SS BOND : angle 1.18671 / 0.58 ( 12) hydrogen bonds : bond 0.04120 / 2.80 ( 1067) hydrogen bonds : angle 4.73777 / 3.27 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 161 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 MET cc_start: 0.7982 (ppp) cc_final: 0.7746 (ppp) REVERT: A 843 ASN cc_start: 0.9517 (OUTLIER) cc_final: 0.9153 (p0) REVERT: B 412 MET cc_start: 0.8921 (pmm) cc_final: 0.8351 (pmm) REVERT: B 678 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8777 (tt) REVERT: B 1148 CYS cc_start: 0.6375 (OUTLIER) cc_final: 0.6095 (m) REVERT: C 623 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8333 (p) REVERT: D 943 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8372 (p) REVERT: E 114 MET cc_start: 0.3175 (mmp) cc_final: 0.2383 (mmm) REVERT: F 1 MET cc_start: 0.5003 (tpp) cc_final: 0.4633 (tpp) REVERT: F 175 HIS cc_start: 0.4748 (m-70) cc_final: 0.4107 (p-80) REVERT: F 178 GLN cc_start: 0.7635 (tm-30) cc_final: 0.6547 (pp30) REVERT: F 181 GLN cc_start: 0.8321 (mm110) cc_final: 0.7809 (mp10) REVERT: F 267 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7761 (mtt90) REVERT: G 54 MET cc_start: 0.1241 (mpp) cc_final: -0.0486 (tpp) REVERT: G 190 ASP cc_start: 0.8279 (m-30) cc_final: 0.7985 (t70) REVERT: H 634 MET cc_start: 0.8777 (mpp) cc_final: 0.8386 (mpp) REVERT: H 918 MET cc_start: 0.7784 (tmm) cc_final: 0.7584 (tmm) REVERT: H 1022 MET cc_start: 0.8812 (ttp) cc_final: 0.8308 (tmm) outliers start: 84 outliers final: 63 residues processed: 238 average time/residue: 0.2145 time to fit residues: 84.8304 Evaluate side-chains 226 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain D residue 545 CYS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 254 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 444 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 370 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 453 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 832 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.088156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.063105 restraints weight = 241568.710| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 7.87 r_work: 0.3075 rms_B_bonded: 7.15 restraints_weight: 2.0000 r_work: 0.3114 rms_B_bonded: 5.16 restraints_weight: 4.0000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35093 Z= 0.158 Angle : 0.540 10.134 47938 Z= 0.278 Chirality : 0.043 0.158 5536 Planarity : 0.004 0.059 6100 Dihedral : 4.537 58.827 4899 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 2.07 % Allowed : 13.22 % Favored : 84.71 % 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: -0.94 (0.13), residues: 4548 helix: 0.53 (0.18), residues: 892 sheet: 0.06 (0.15), residues: 1277 loop : -1.50 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.017 0.001 TYR G 51 PHE 0.013 0.001 PHE A1194 TRP 0.019 0.001 TRP F 263 HIS 0.011 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (35087) covalent geometry : angle 0.53957 / 0.28 (47926) SS BOND : bond 0.00347 / 0.18 ( 6) SS BOND : angle 0.94726 / 0.48 ( 12) hydrogen bonds : bond 0.03773 / 2.56 ( 1067) hydrogen bonds : angle 4.64025 / 3.20 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 MET cc_start: 0.8181 (ppp) cc_final: 0.7972 (ppp) REVERT: A 843 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9111 (p0) REVERT: B 412 MET cc_start: 0.8959 (pmm) cc_final: 0.8385 (pmm) REVERT: B 836 MET cc_start: 0.5699 (tpp) cc_final: 0.5099 (ttt) REVERT: B 1148 CYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6193 (m) REVERT: C 623 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8228 (p) REVERT: D 943 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8381 (p) REVERT: E 114 MET cc_start: 0.3087 (mmp) cc_final: 0.2587 (mmm) REVERT: F 1 MET cc_start: 0.5210 (tpp) cc_final: 0.4897 (tpp) REVERT: F 175 HIS cc_start: 0.4746 (m-70) cc_final: 0.4121 (p-80) REVERT: F 178 GLN cc_start: 0.7661 (tm-30) cc_final: 0.6612 (pp30) REVERT: F 181 GLN cc_start: 0.8316 (mm110) cc_final: 0.7738 (mp10) REVERT: F 267 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7695 (mtt90) REVERT: H 1022 MET cc_start: 0.8466 (ttp) cc_final: 0.7954 (tmm) outliers start: 70 outliers final: 62 residues processed: 224 average time/residue: 0.2129 time to fit residues: 78.0504 Evaluate side-chains 224 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1148 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain D residue 545 CYS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 53 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 312 optimal weight: 20.0000 chunk 360 optimal weight: 50.0000 chunk 252 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 450 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN B1199 ASN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 HIS H 832 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.086493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.057942 restraints weight = 189595.118| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 9.09 r_work: 0.2970 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 35093 Z= 0.346 Angle : 0.719 12.478 47938 Z= 0.372 Chirality : 0.049 0.413 5536 Planarity : 0.005 0.066 6100 Dihedral : 5.108 58.773 4899 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 2.25 % Allowed : 12.92 % Favored : 84.83 % 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: -1.33 (0.12), residues: 4548 helix: -0.09 (0.17), residues: 882 sheet: -0.13 (0.15), residues: 1274 loop : -1.64 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 9 TYR 0.022 0.002 TYR B 823 PHE 0.029 0.002 PHE A 405 TRP 0.025 0.003 TRP A 471 HIS 0.017 0.002 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.35 (35087) covalent geometry : angle 0.71841 / 0.37 (47926) SS BOND : bond 0.00847 / 0.48 ( 6) SS BOND : angle 1.63873 / 0.85 ( 12) hydrogen bonds : bond 0.05457 / 3.69 ( 1067) hydrogen bonds : angle 5.19052 / 3.59 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 158 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.8924 (p0) REVERT: B 412 MET cc_start: 0.8973 (pmm) cc_final: 0.8368 (pmm) REVERT: B 1069 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8837 (m110) REVERT: C 623 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8481 (p) REVERT: E 114 MET cc_start: 0.3020 (mmp) cc_final: 0.2520 (mmm) REVERT: F 1 MET cc_start: 0.5469 (tpp) cc_final: 0.5032 (tpp) REVERT: F 175 HIS cc_start: 0.3810 (m-70) cc_final: 0.3460 (p-80) REVERT: F 178 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6595 (pp30) REVERT: F 183 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6429 (tpt90) REVERT: F 267 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7461 (mtt90) REVERT: G 126 ARG cc_start: 0.2474 (mmp80) cc_final: 0.2092 (mmp80) REVERT: H 1022 MET cc_start: 0.8777 (ttp) cc_final: 0.8297 (tmm) outliers start: 76 outliers final: 63 residues processed: 230 average time/residue: 0.2158 time to fit residues: 82.2278 Evaluate side-chains 223 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 843 ASN Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 934 TYR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1069 ASN Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 836 LYS Chi-restraints excluded: chain D residue 922 TRP Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1174 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 167 CYS Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 556 LYS Chi-restraints excluded: chain H residue 605 VAL Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 833 ASN Chi-restraints excluded: chain H residue 1012 CYS Chi-restraints excluded: chain H residue 1021 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 247 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 268 optimal weight: 30.0000 chunk 172 optimal weight: 0.9990 chunk 157 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN ** H 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.095495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.066621 restraints weight = 119865.896| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 6.57 r_work: 0.3014 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 35093 Z= 0.292 Angle : 0.795 59.188 47938 Z= 0.430 Chirality : 0.048 1.039 5536 Planarity : 0.005 0.066 6100 Dihedral : 5.095 58.796 4898 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 2.22 % Allowed : 12.83 % Favored : 84.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.36 (0.12), residues: 4548 helix: -0.15 (0.17), residues: 882 sheet: -0.14 (0.15), residues: 1276 loop : -1.65 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG G 35 TYR 0.021 0.002 TYR B 823 PHE 0.024 0.002 PHE A 405 TRP 0.021 0.002 TRP A 471 HIS 0.013 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (35087) covalent geometry : angle 0.79166 / 0.43 (47926) SS BOND : bond 0.01160 / 0.60 ( 6) SS BOND : angle 4.35785 / 2.36 ( 12) hydrogen bonds : bond 0.05231 / 3.52 ( 1067) hydrogen bonds : angle 5.17812 / 3.58 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20324.94 seconds wall clock time: 344 minutes 39.20 seconds (20679.20 seconds total)