Starting phenix.real_space_refine on Sat Jun 6 10:25:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx0_47276/06_2026/9dx0_47276.map" } resolution = 3.47 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= 0.001 sd= 0.011 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 200 5.16 5 C 17023 2.51 5 N 4858 2.21 5 O 4972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 27053 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8290 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 43, 'TRANS': 1059} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 473 Unresolved non-hydrogen angles: 574 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 24, 'ASN:plan1': 9, 'ARG:plan': 10, 'ASP:plan': 18, 'TYR:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 276 Chain: "B" Number of atoms: 7352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 7352 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 373} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1046} Chain breaks: 7 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1341 Unresolved non-hydrogen angles: 1706 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'ASP:plan': 35, 'TRP:plan': 9, 'HIS:plan': 10, 'ARG:plan': 24, 'PHE:plan': 13, 'GLU:plan': 30, 'TYR:plan': 10, 'ASN:plan1': 20, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 740 Chain: "C" Number of atoms: 6746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 6746 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 31, 'TRANS': 873} Chain breaks: 5 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 349 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 13, 'ARG:plan': 17, 'GLN:plan1': 8, 'PHE:plan': 5, 'GLU:plan': 20, 'HIS:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 284 Chain: "D" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4665 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 27, 'TRANS': 605} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 2, 'GLN:plan1': 6, 'HIS:plan': 4, 'GLU:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 193 Time building chain proxies: 6.46, per 1000 atoms: 0.24 Number of scatterers: 27053 At special positions: 0 Unit cell: (233.08, 171.331, 170.461, 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 200 16.00 O 4972 8.00 N 4858 7.00 C 17023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 550 " distance=2.03 Simple disulfide: pdb=" SG CYS B1110 " - pdb=" SG CYS B1145 " distance=2.04 Simple disulfide: pdb=" SG CYS B1197 " - pdb=" SG CYS B1200 " distance=2.03 Simple disulfide: pdb=" SG CYS D1248 " - pdb=" SG CYS D1257 " distance=2.02 Simple disulfide: pdb=" SG CYS D1248 " - pdb=" SG CYS D1260 " distance=2.03 Simple disulfide: pdb=" SG CYS D1257 " - pdb=" SG CYS D1260 " distance=2.03 Simple disulfide: pdb=" SG CYS D1267 " - pdb=" SG CYS D1270 " distance=2.03 Simple disulfide: pdb=" SG CYS D1284 " - pdb=" SG CYS D1309 " distance=2.03 Simple disulfide: pdb=" SG CYS D1307 " - pdb=" SG CYS D1309 " distance=2.04 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: 2.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7030 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 55 sheets defined 23.1% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 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: 3.530A pdb=" N LEU A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) removed outlier: 3.887A 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 786 removed outlier: 3.590A pdb=" N LEU A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 811 removed outlier: 3.625A pdb=" N THR A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 removed outlier: 3.548A pdb=" N ILE A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 857 through 867 Processing helix chain 'A' and resid 878 through 889 removed outlier: 3.640A pdb=" N VAL A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.597A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.743A pdb=" N GLN A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.906A pdb=" N VAL A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 933 " --> pdb=" O MET A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 948 through 953 removed outlier: 3.849A pdb=" N LEU A 951 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 953 " --> pdb=" O ARG A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.615A pdb=" N CYS A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.732A pdb=" N LYS A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1014 removed outlier: 3.849A pdb=" N ASN A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A1001 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A1008 " --> pdb=" O GLU A1004 " (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: 3.661A pdb=" N ASP A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1051 removed outlier: 3.935A pdb=" N ALA A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A1049 " --> pdb=" O ALA A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1060 through 1077 removed outlier: 3.525A pdb=" N GLN A1064 " --> pdb=" O ASP A1060 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1094 removed outlier: 3.502A pdb=" N GLU A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A1093 " --> pdb=" O HIS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.760A pdb=" N ASN A1192 " --> pdb=" O GLN A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1213 removed outlier: 3.720A pdb=" N SER A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1232 removed outlier: 3.597A pdb=" N LEU A1231 " --> pdb=" O CYS A1228 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A1232 " --> pdb=" O MET A1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1228 through 1232' Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.501A pdb=" N PHE B 455 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 759 through 770 removed outlier: 3.569A pdb=" N LEU B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) 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 removed outlier: 3.894A pdb=" N LEU B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 813 removed outlier: 4.307A pdb=" N LYS B 813 " --> pdb=" O ASP B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 824 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.817A pdb=" N ASP B 848 " --> pdb=" O SER B 845 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 849 " --> pdb=" O GLY B 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 845 through 849' Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.596A pdb=" N LEU B 856 " --> pdb=" O ASP B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 868 removed outlier: 3.616A pdb=" N ALA B 863 " --> pdb=" O GLU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 889 removed outlier: 3.661A pdb=" N SER B 884 " --> pdb=" O PRO B 880 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 901 removed outlier: 3.512A pdb=" N ALA B 896 " --> pdb=" O GLU B 892 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 917 removed outlier: 3.576A pdb=" N ALA B 907 " --> pdb=" O ASP B 903 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 932 removed outlier: 3.794A pdb=" N VAL B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 950 removed outlier: 4.277A pdb=" N THR B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 950 " --> pdb=" O CYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 955 through 967 removed outlier: 3.894A pdb=" N LEU B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 977 removed outlier: 3.763A pdb=" N TYR B 977 " --> pdb=" O ASP B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 994 removed outlier: 3.688A pdb=" N ARG B 986 " --> pdb=" O ALA B 982 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 992 " --> pdb=" O ALA B 988 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 993 " --> pdb=" O PHE B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1014 removed outlier: 3.705A pdb=" N ASN B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B1010 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B1012 " --> pdb=" O ASN B1008 " (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 1025 through 1040 removed outlier: 3.733A pdb=" N ASP B1030 " --> pdb=" O LYS B1026 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1031 " --> pdb=" O ASP B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1048 Processing helix chain 'B' and resid 1049 through 1051 No H-bonds generated for 'chain 'B' and resid 1049 through 1051' Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1060 through 1077 removed outlier: 3.617A pdb=" N ALA B1076 " --> pdb=" O ASN B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1094 removed outlier: 3.603A pdb=" N LYS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B1093 " --> pdb=" O HIS B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1095 through 1098 Processing helix chain 'B' and resid 1185 through 1191 removed outlier: 4.099A pdb=" N ASN B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1214 removed outlier: 3.624A pdb=" N SER B1211 " --> pdb=" O GLY B1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' 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 788 removed outlier: 3.829A pdb=" N THR C 786 " --> pdb=" O TRP C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 811 removed outlier: 3.643A pdb=" N ASP C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 811 " --> pdb=" O VAL C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 828 removed outlier: 3.703A pdb=" N TRP C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 824 " --> pdb=" O TRP C 820 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 825 " --> pdb=" O THR C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.536A pdb=" N LEU C1012 " --> pdb=" O VAL C1008 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS C1013 " --> pdb=" O ARG C1009 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C1017 " --> pdb=" O HIS C1013 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1032 removed outlier: 3.805A pdb=" N ALA C1024 " --> pdb=" O ASP C1020 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C1028 " --> pdb=" O ALA C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1039 removed outlier: 3.769A pdb=" N ARG C1036 " --> pdb=" O GLU C1033 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS C1037 " --> pdb=" O ARG C1034 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C1039 " --> pdb=" O ARG C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1058 Processing helix chain 'C' and resid 1060 through 1071 removed outlier: 3.613A pdb=" N VAL C1067 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C1068 " --> pdb=" O SER C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1146 removed outlier: 3.618A pdb=" N MET C1141 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C1145 " --> pdb=" O MET C1141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C1146 " --> pdb=" O LYS C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 702 Processing helix chain 'D' and resid 723 through 727 Processing helix chain 'D' and resid 1002 through 1009 removed outlier: 3.675A pdb=" N GLY D1006 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D1007 " --> pdb=" O LYS D1003 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D1008 " --> pdb=" O SER D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1031 removed outlier: 3.608A pdb=" N ALA D1024 " --> pdb=" O CYS D1020 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D1025 " --> pdb=" O GLN D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1046 removed outlier: 3.904A pdb=" N VAL D1036 " --> pdb=" O ARG D1032 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL D1044 " --> pdb=" O SER D1040 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D1046 " --> pdb=" O ALA D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1051 removed outlier: 3.932A pdb=" N LEU D1050 " --> pdb=" O ASP D1047 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D1051 " --> pdb=" O LEU D1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1047 through 1051' Processing helix chain 'D' and resid 1061 through 1065 Processing helix chain 'D' and resid 1068 through 1081 removed outlier: 3.503A pdb=" N LEU D1072 " --> pdb=" O GLY D1068 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1077 " --> pdb=" O GLU D1073 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 3.576A pdb=" N LEU D1088 " --> pdb=" O ASP D1084 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1095 " --> pdb=" O LEU D1091 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D1096 " --> pdb=" O CYS D1092 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D1099 " --> pdb=" O PHE D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1179 through 1192 removed outlier: 3.662A pdb=" N LYS D1189 " --> pdb=" O ASP D1185 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D1191 " --> pdb=" O HIS D1187 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG D1192 " --> pdb=" O ASP D1188 " (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 1217 removed outlier: 3.627A pdb=" N LYS D1206 " --> pdb=" O PHE D1202 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D1212 " --> pdb=" O CYS D1208 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D1213 " --> pdb=" O TYR D1209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.701A pdb=" N GLU D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D1225 " --> pdb=" O LYS D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1297 removed outlier: 3.663A pdb=" N GLU D1295 " --> pdb=" O SER D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1310 through 1316 removed outlier: 3.508A pdb=" N GLU D1314 " --> pdb=" O HIS D1310 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D1316 " --> pdb=" O LEU D1312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.550A pdb=" N SER A 26 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 25 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 56 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 27 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 68 removed outlier: 4.173A pdb=" N CYS A 65 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.889A pdb=" N THR A 118 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER A 141 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 182 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.630A pdb=" N SER A 189 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 202 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 232 removed outlier: 3.550A pdb=" N GLN A 228 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 230 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 241 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 232 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ARG A 239 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 261 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.774A pdb=" N LEU A 286 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 273 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 284 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP A 275 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 282 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 314 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330 removed outlier: 3.702A pdb=" N SER A 327 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 359 removed outlier: 3.679A pdb=" N HIS A 373 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 376 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 405 removed outlier: 6.491A pdb=" N CYS A 415 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 403 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 413 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 405 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 411 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 421 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 437 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 423 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 445 through 449 removed outlier: 7.074A pdb=" N CYS A 462 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 448 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 460 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 468 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR A 493 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 470 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 501 through 506 removed outlier: 3.988A pdb=" N ASP A 503 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS A 542 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 528 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 540 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.074A pdb=" N CYS A 552 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 582 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR A 599 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 584 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 593 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 609 through 612 removed outlier: 4.048A pdb=" N ASP A 609 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 630 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A 658 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 632 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 666 through 671 removed outlier: 7.027A pdb=" N SER A 681 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 669 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 679 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 682 " --> pdb=" O CYS A 686 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 687 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE A 703 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 689 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1104 through 1105 Processing sheet with id=AB7, first strand: chain 'A' and resid 1194 through 1197 removed outlier: 3.997A pdb=" N PHE A1194 " --> pdb=" O TRP C1127 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP C1127 " --> pdb=" O PHE A1194 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP A1196 " --> pdb=" O PHE C1125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.506A pdb=" N LEU B 25 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE B 56 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 27 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 68 removed outlier: 4.314A pdb=" N CYS B 65 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 90 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 80 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 6.855A pdb=" N GLY B 132 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 119 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 130 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TRP B 121 " --> pdb=" O TRP B 128 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TRP B 128 " --> pdb=" O TRP B 121 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 141 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE B 140 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN B 183 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.545A pdb=" N LEU B 208 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B 221 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 210 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 228 through 232 removed outlier: 4.613A pdb=" N GLY B 229 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 243 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.553A pdb=" N LEU B 286 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL B 273 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA B 284 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TRP B 275 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 282 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 327 through 330 Processing sheet with id=AC6, first strand: chain 'B' and resid 357 through 360 removed outlier: 3.847A pdb=" N SER B 357 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 366 " --> pdb=" O CYS B 377 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 378 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 405 removed outlier: 6.947A pdb=" N CYS B 415 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 403 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA B 413 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 405 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 411 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 421 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 437 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 423 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 433 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.813A pdb=" N CYS B 462 " --> pdb=" O TRP B 446 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 448 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 460 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 459 " --> pdb=" O TRP B 471 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 471 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 492 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 501 through 506 removed outlier: 4.646A pdb=" N ASP B 503 " --> pdb=" O CYS B 518 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS B 518 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 524 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU B 543 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 526 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 553 through 555 removed outlier: 7.523A pdb=" N VAL B 582 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR B 599 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE B 584 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 593 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 609 through 612 removed outlier: 3.730A pdb=" N ASP B 609 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 630 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN B 658 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 632 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 666 through 671 removed outlier: 3.553A pdb=" N ARG B 668 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 682 " --> pdb=" O CYS B 686 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS B 686 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 691 " --> pdb=" O CYS B 700 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N CYS B 700 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1103 through 1107 Processing sheet with id=AD5, first strand: chain 'B' and resid 1196 through 1197 Processing sheet with id=AD6, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.464A pdb=" N SER C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 324 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 316 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE C 313 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 306 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.920A pdb=" N ALA C 31 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 44 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 49 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN C 64 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 51 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 77 through 82 removed outlier: 6.982A pdb=" N ALA C 93 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C 80 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA C 91 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP C 82 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU C 89 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 100 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 99 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU C 115 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR C 101 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 128 removed outlier: 6.791A pdb=" N GLY C 139 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 126 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 137 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 171 removed outlier: 4.157A pdb=" N ASP C 168 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 187 through 189 removed outlier: 4.134A pdb=" N PHE C 203 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 210 through 215 removed outlier: 3.505A pdb=" N CYS C 212 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL C 232 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS C 247 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 234 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 254 through 259 removed outlier: 6.873A pdb=" N CYS C 270 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 257 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 268 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 291 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.564A pdb=" N ALA C 355 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C 397 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 424 through 429 removed outlier: 6.993A pdb=" N CYS C 439 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 427 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 437 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE C 429 " --> pdb=" O ARG C 435 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 435 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 440 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER C 444 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 445 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER C 461 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 447 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 469 through 474 removed outlier: 7.017A pdb=" N CYS C 486 " --> pdb=" O TRP C 470 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 472 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 484 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP C 474 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 482 " --> pdb=" O TRP C 474 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 492 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR C 517 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 494 " --> pdb=" O ARG C 515 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.888A pdb=" N CYS C 542 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL C 528 " --> pdb=" O ALA C 540 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 540 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE C 530 " --> pdb=" O MET C 538 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET C 538 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 566 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU C 552 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU C 564 " --> pdb=" O GLU C 552 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 577 through 579 removed outlier: 7.281A pdb=" N VAL C 606 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR C 623 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.643A pdb=" N ASP C 633 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 681 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR C 658 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE C 679 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LYS C 660 " --> pdb=" O ILE C 677 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE C 677 " --> pdb=" O LYS C 660 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 690 through 695 removed outlier: 3.909A pdb=" N ARG C 692 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 706 " --> pdb=" O CYS C 710 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N CYS C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 711 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 727 " --> pdb=" O VAL C 711 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU C 713 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.703A pdb=" N GLY D 541 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 553 " --> pdb=" O GLY D 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 647 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 672 through 677 removed outlier: 6.836A pdb=" N CYS D 687 " --> pdb=" O HIS D 673 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA D 675 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA D 685 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET D 677 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG D 683 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 684 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 695 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 707 " --> pdb=" O ILE D 695 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 716 through 721 removed outlier: 6.985A pdb=" N CYS D 733 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL D 719 " --> pdb=" O ALA D 731 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 731 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP D 721 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE D 729 " --> pdb=" O TRP D 721 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 739 " --> pdb=" O GLU D 754 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU D 754 " --> pdb=" O VAL D 739 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 741 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 762 through 767 removed outlier: 6.777A pdb=" N GLY D 779 " --> pdb=" O ASN D 763 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL D 765 " --> pdb=" O ALA D 777 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA D 777 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP D 767 " --> pdb=" O ILE D 775 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE D 775 " --> pdb=" O TRP D 767 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D 795 " --> pdb=" O THR D 791 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 809 through 814 removed outlier: 6.804A pdb=" N GLY D 841 " --> pdb=" O ASN D 810 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 812 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA D 839 " --> pdb=" O VAL D 812 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP D 814 " --> pdb=" O ARG D 837 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ARG D 837 " --> pdb=" O TRP D 814 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 847 " --> pdb=" O LYS D 863 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS D 863 " --> pdb=" O ILE D 847 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU D 849 " --> pdb=" O GLU D 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 871 through 875 removed outlier: 6.918A pdb=" N CYS D 890 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL D 874 " --> pdb=" O ALA D 888 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA D 888 " --> pdb=" O VAL D 874 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 885 " --> pdb=" O CYS D 901 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 887 " --> pdb=" O TRP D 899 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 891 " --> pdb=" O ARG D 895 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG D 895 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL D 896 " --> pdb=" O LEU D 914 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 921 through 925 removed outlier: 3.639A pdb=" N HIS D 923 " --> pdb=" O SER D 936 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2418 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: 6.94 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9052 1.35 - 1.47: 7067 1.47 - 1.59: 11289 1.59 - 1.72: 0 1.72 - 1.84: 273 Bond restraints: 27681 Sorted by residual: bond pdb=" C VAL B 352 " pdb=" N PHE B 353 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.30e-02 5.92e+03 2.97e+00 bond pdb=" N CYS B1148 " pdb=" CA CYS B1148 " ideal model delta sigma weight residual 1.459 1.475 -0.016 1.25e-02 6.40e+03 1.66e+00 bond pdb=" N GLY B1147 " pdb=" CA GLY B1147 " ideal model delta sigma weight residual 1.449 1.467 -0.018 1.45e-02 4.76e+03 1.48e+00 bond pdb=" C HIS C 587 " pdb=" N SER C 588 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.83e-02 1.25e+03 1.31e+00 bond pdb=" CA PHE C 389 " pdb=" C PHE C 389 " ideal model delta sigma weight residual 1.525 1.501 0.024 2.10e-02 2.27e+03 1.30e+00 ... (remaining 27676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 37114 1.46 - 2.92: 585 2.92 - 4.38: 88 4.38 - 5.85: 5 5.85 - 7.31: 2 Bond angle restraints: 37794 Sorted by residual: angle pdb=" C GLU C 665 " pdb=" CA GLU C 665 " pdb=" CB GLU C 665 " ideal model delta sigma weight residual 117.23 110.53 6.70 1.36e+00 5.41e-01 2.43e+01 angle pdb=" N VAL B 878 " pdb=" CA VAL B 878 " pdb=" C VAL B 878 " ideal model delta sigma weight residual 112.29 107.95 4.34 9.40e-01 1.13e+00 2.13e+01 angle pdb=" CA GLU C 665 " pdb=" C GLU C 665 " pdb=" N LEU C 666 " ideal model delta sigma weight residual 119.98 116.79 3.19 8.50e-01 1.38e+00 1.41e+01 angle pdb=" C VAL B 352 " pdb=" N PHE B 353 " pdb=" CA PHE B 353 " ideal model delta sigma weight residual 123.23 119.03 4.20 1.54e+00 4.22e-01 7.43e+00 angle pdb=" N VAL C 156 " pdb=" CA VAL C 156 " pdb=" C VAL C 156 " ideal model delta sigma weight residual 111.81 109.55 2.26 8.60e-01 1.35e+00 6.89e+00 ... (remaining 37789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 15243 15.18 - 30.36: 716 30.36 - 45.54: 153 45.54 - 60.72: 57 60.72 - 75.89: 4 Dihedral angle restraints: 16173 sinusoidal: 5370 harmonic: 10803 Sorted by residual: dihedral pdb=" CB CYS D1248 " pdb=" SG CYS D1248 " pdb=" SG CYS D1257 " pdb=" CB CYS D1257 " ideal model delta sinusoidal sigma weight residual -86.00 -161.89 75.89 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS D1248 " pdb=" SG CYS D1248 " pdb=" SG CYS D1260 " pdb=" CB CYS D1260 " ideal model delta sinusoidal sigma weight residual -86.00 -10.50 -75.50 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS D1257 " pdb=" SG CYS D1257 " pdb=" SG CYS D1260 " pdb=" CB CYS D1260 " ideal model delta sinusoidal sigma weight residual 93.00 154.12 -61.12 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 16170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2543 0.031 - 0.062: 1186 0.062 - 0.092: 325 0.092 - 0.123: 264 0.123 - 0.154: 10 Chirality restraints: 4328 Sorted by residual: chirality pdb=" CA ILE A 474 " pdb=" N ILE A 474 " pdb=" C ILE A 474 " pdb=" CB ILE A 474 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE B 610 " pdb=" N ILE B 610 " pdb=" C ILE B 610 " pdb=" CB ILE B 610 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE C 656 " pdb=" N ILE C 656 " pdb=" C ILE C 656 " pdb=" CB ILE C 656 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 4325 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 353 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE B 353 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE B 353 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU B 354 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 810 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C MET B 810 " -0.031 2.00e-02 2.50e+03 pdb=" O MET B 810 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 811 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B1110 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C CYS B1110 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS B1110 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B1111 " -0.010 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1000 2.72 - 3.26: 25131 3.26 - 3.81: 38416 3.81 - 4.35: 45047 4.35 - 4.90: 81231 Nonbonded interactions: 190825 Sorted by model distance: nonbonded pdb=" OG1 THR A 342 " pdb=" OG1 THR A 346 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR B 499 " pdb=" OG SER B 519 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN A 588 " pdb=" OG1 THR A 591 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 523 " pdb=" OD1 ASP C 545 " model vdw 2.225 3.040 nonbonded pdb=" O MET A 929 " pdb=" OG SER A 932 " model vdw 2.227 3.040 ... (remaining 190820 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 4 through 40 and (name N or name CA or name C or name O o \ r name CB )) or (resid 41 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 or (resid 82 through 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 or (resid 86 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 or (resid 94 through 104 and \ (name N or name CA or name C or name O or name CB )) or (resid 105 through 131 \ and (name N or name CA or name C or name O or name CB )) or resid 132 or (resid \ 133 through 181 and (name N or name CA or name C or name O or name CB )) or (res \ id 182 through 202 and (name N or name CA or name C or name O or name CB )) or r \ esid 203 or (resid 204 through 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 or (resid 230 through 245 and (name N or name CA or nam \ e C or name O or name CB )) or resid 246 or (resid 247 through 280 and (name N o \ r name CA or name C or name O or name CB )) or resid 281 or (resid 282 through 2 \ 99 and (name N or name CA or name C or name O or name CB )) or (resid 312 throug \ h 352 and (name N or name CA or name C or name O or name CB )) or resid 353 or ( \ resid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 through 379 or resid 387 through 391 or (resid 392 through 395 a \ nd (name N or name CA or name C or name O or name CB )) or resid 396 or (resid 3 \ 97 and (name N or name CA or name C or name O or name CB )) or resid 398 through \ 424 or (resid 425 through 426 and (name N or name CA or name C or name O or nam \ e CB )) or resid 427 through 428 or (resid 429 and (name N or name CA or name C \ or name O or name CB )) or resid 430 through 438 or (resid 439 and (name N or na \ me CA or name C or name O or name CB )) or resid 440 through 463 or (resid 464 a \ nd (name N or name CA or name C or name O or name CB )) or resid 465 through 474 \ or (resid 486 through 487 and (name N or name CA or name C or name O or name CB \ )) or resid 488 through 497 or (resid 498 and (name N or name CA or name C or n \ ame O or name CB )) or resid 499 through 524 or (resid 525 and (name N or name C \ A or name C or name O or name CB )) or resid 526 through 536 or (resid 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 through 542 or \ (resid 543 and (name N or name CA or name C or name O or name CB )) or resid 544 \ through 578 or (resid 579 through 580 and (name N or name CA or name C or name \ O or name CB )) or resid 581 through 589 or (resid 590 and (name N or name CA or \ name C or name O or name CB )) or resid 591 or (resid 592 through 593 and (name \ N or name CA or name C or name O or name CB )) or resid 594 through 600 or (res \ id 601 and (name N or name CA or name C or name O or name CB )) or resid 602 thr \ ough 649 or (resid 650 and (name N or name CA or name C or name O or name CB )) \ or resid 651 or (resid 652 and (name N or name CA or name C or name O or name CB \ )) or resid 653 through 683 or (resid 684 and (name N or name CA or name C or n \ ame O or name CB )) or resid 685 or (resid 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 698 or (resid 699 and (name N or na \ me CA or name C or name O or name CB )) or resid 700 through 704 or (resid 705 a \ nd (name N or name CA or name C or name O or name CB )) or resid 706 or (resid 7 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 708 or resi \ d 757 through 776 or (resid 777 and (name N or name CA or name C or name O or na \ me CB )) or resid 778 through 789 or (resid 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 833 or (resid 834 and (name N or n \ ame CA or name C or name O or name CB )) or resid 835 through 836 or (resid 837 \ through 841 and (name N or name CA or name C or name O or name CB )) or resid 84 \ 2 through 857 or (resid 858 and (name N or name CA or name C or name O or name C \ B )) or resid 859 through 889 or (resid 890 and (name N or name CA or name C or \ name O or name CB )) or resid 891 through 939 or (resid 940 and (name N or name \ CA or name C or name O or name CB )) or resid 941 through 944 or (resid 945 thro \ ugh 947 and (name N or name CA or name C or name O or name CB )) or resid 948 th \ rough 967 or (resid 968 through 969 and (name N or name CA or name C or name O o \ r name CB )) or resid 970 through 995 or (resid 996 and (name N or name CA or na \ me C or name O or name CB )) or resid 997 through 1111 or (resid 1112 and (name \ N or name CA or name C or name O or name CB )) or resid 1113 through 1114 or (re \ sid 1115 through 1141 and (name N or name CA or name C or name O or name CB )) o \ r resid 1142 through 1165 or (resid 1166 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1184 through 1200 or (resid 1201 and (name N or name \ CA or name C or name O or name CB )) or resid 1202 through 1233)) selection = (chain 'B' and (resid 4 through 147 or resid 177 through 378 or (resid 379 throu \ gh 387 and (name N or name CA or name C or name O or name CB )) or resid 388 thr \ ough 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) \ or resid 432 through 808 or (resid 809 through 815 and (name N or name CA or nam \ e C or name O or name CB )) or resid 816 or (resid 817 through 818 and (name N o \ r name CA or name C or name O or name CB )) or resid 819 through 838 or (resid 8 \ 39 through 841 and (name N or name CA or name C or name O or name CB )) or resid \ 842 through 844 or (resid 845 and (name N or name CA or name C or name O or nam \ e CB )) or resid 852 through 873 or (resid 874 through 877 and (name N or name C \ A or name C or name O or name CB )) or resid 878 through 908 or (resid 909 and ( \ name N or name CA or name C or name O or name CB )) or resid 910 through 921 or \ (resid 922 and (name N or name CA or name C or name O or name CB )) or resid 923 \ through 935 or (resid 936 through 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 942 or (resid 943 through 947 and (name N o \ r name CA or name C or name O or name CB )) or resid 948 through 1011 or (resid \ 1012 through 1013 and (name N or name CA or name C or name O or name CB )) or re \ sid 1014 through 1097 or (resid 1098 and (name N or name CA or name C or name O \ or name CB )) or resid 1099 through 1115 or (resid 1116 through 1141 and (name N \ or name CA or name C or name O or name CB )) or resid 1142 through 1166 or (res \ id 1184 through 1185 and (name N or name CA or name C or name O or name CB )) or \ resid 1186 through 1233)) } 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.720 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 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 : 0.004 0.057 27690 Z= 0.179 Angle : 0.481 7.307 37812 Z= 0.264 Chirality : 0.043 0.154 4328 Planarity : 0.003 0.048 4858 Dihedral : 10.035 74.229 9116 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 5.24 % Allowed : 6.96 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.95 (0.14), residues: 3673 helix: -0.31 (0.20), residues: 626 sheet: 0.32 (0.17), residues: 978 loop : -1.23 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1149 TYR 0.011 0.001 TYR D 552 PHE 0.011 0.001 PHE B1109 TRP 0.017 0.001 TRP D 922 HIS 0.004 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (27681) covalent geometry : angle 0.47892 / 0.26 (37794) SS BOND : bond 0.00499 / 0.26 ( 9) SS BOND : angle 2.27863 / 1.75 ( 18) hydrogen bonds : bond 0.31142 / 21.68 ( 875) hydrogen bonds : angle 7.98302 / 5.57 ( 2418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 201 time to evaluate : 1.170 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: A 63 MET cc_start: 0.4597 (ttm) cc_final: 0.4161 (mtm) REVERT: A 215 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7381 (p0) REVERT: A 221 PHE cc_start: 0.9411 (p90) cc_final: 0.9024 (p90) REVERT: B 627 THR cc_start: 0.0215 (OUTLIER) cc_final: -0.0734 (p) REVERT: B 1062 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7443 (mtm180) REVERT: B 1144 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 1221 VAL cc_start: 0.7670 (t) cc_final: 0.7434 (p) REVERT: C 237 MET cc_start: 0.2384 (OUTLIER) cc_final: 0.1640 (ptt) REVERT: C 266 HIS cc_start: 0.6137 (OUTLIER) cc_final: 0.5893 (m90) REVERT: C 282 ASP cc_start: 0.6175 (OUTLIER) cc_final: 0.5515 (p0) REVERT: C 819 THR cc_start: 0.6574 (t) cc_final: 0.4993 (p) REVERT: C 1126 VAL cc_start: 0.5871 (OUTLIER) cc_final: 0.4857 (p) REVERT: C 1159 GLU cc_start: 0.4445 (OUTLIER) cc_final: 0.2321 (pm20) REVERT: D 539 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7382 (m) outliers start: 134 outliers final: 17 residues processed: 325 average time/residue: 0.1920 time to fit residues: 96.9869 Evaluate side-chains 149 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 1062 ARG Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 896 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1270 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 373 HIS ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN A1208 HIS B 408 HIS ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B1205 HIS C 206 HIS C 561 GLN C 565 GLN C 601 ASN ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1187 HIS D1200 GLN D1236 HIS D1310 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.092508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064375 restraints weight = 132153.678| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 6.16 r_work: 0.3175 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 27690 Z= 0.317 Angle : 0.746 11.684 37812 Z= 0.399 Chirality : 0.051 0.253 4328 Planarity : 0.005 0.085 4858 Dihedral : 5.576 58.392 3971 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 3.95 % Allowed : 10.64 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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 (0.13), residues: 3673 helix: -1.01 (0.18), residues: 665 sheet: 0.09 (0.16), residues: 1021 loop : -1.37 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 194 TYR 0.040 0.003 TYR A 375 PHE 0.025 0.003 PHE A1190 TRP 0.045 0.003 TRP A 368 HIS 0.012 0.002 HIS A1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.32 (27681) covalent geometry : angle 0.74250 / 0.40 (37794) SS BOND : bond 0.04095 / 2.82 ( 9) SS BOND : angle 3.23510 / 2.49 ( 18) hydrogen bonds : bond 0.05685 / 3.88 ( 875) hydrogen bonds : angle 5.67377 / 4.04 ( 2418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 115 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.4590 (ttm) cc_final: 0.4176 (mtm) REVERT: A 215 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7354 (p0) REVERT: A 367 MET cc_start: 0.8678 (ttm) cc_final: 0.8332 (ttp) REVERT: B 627 THR cc_start: 0.2580 (OUTLIER) cc_final: 0.1692 (p) REVERT: B 836 MET cc_start: 0.2482 (tpp) cc_final: 0.1977 (ppp) REVERT: B 1032 MET cc_start: 0.8805 (tpt) cc_final: 0.8557 (mmm) REVERT: B 1196 TRP cc_start: 0.7837 (t60) cc_final: 0.7277 (t-100) REVERT: B 1212 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8277 (t-100) REVERT: C 237 MET cc_start: 0.2346 (OUTLIER) cc_final: 0.1541 (ptt) REVERT: C 603 MET cc_start: 0.8521 (mtm) cc_final: 0.7866 (mtm) REVERT: C 1031 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8411 (mp) REVERT: C 1159 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6019 (pt0) REVERT: D 1294 MET cc_start: 0.9079 (ttm) cc_final: 0.8876 (tpp) REVERT: D 1298 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8644 (tmm-80) outliers start: 101 outliers final: 40 residues processed: 206 average time/residue: 0.1613 time to fit residues: 54.7384 Evaluate side-chains 148 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1212 TRP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1274 VAL Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 214 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 55 optimal weight: 0.0170 chunk 31 optimal weight: 30.0000 chunk 200 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 303 optimal weight: 0.0040 overall best weight: 1.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS A1199 ASN A1208 HIS B1198 HIS B1205 HIS C 420 HIS ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 HIS C1108 HIS ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.091760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.065868 restraints weight = 154112.833| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 6.98 r_work: 0.3067 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27690 Z= 0.100 Angle : 0.484 8.406 37812 Z= 0.257 Chirality : 0.042 0.160 4328 Planarity : 0.003 0.047 4858 Dihedral : 4.526 59.343 3943 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 11.85 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.78 (0.14), residues: 3673 helix: 0.01 (0.20), residues: 671 sheet: 0.34 (0.16), residues: 1030 loop : -1.18 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 616 TYR 0.011 0.001 TYR C 718 PHE 0.011 0.001 PHE C1058 TRP 0.025 0.001 TRP B 368 HIS 0.005 0.001 HIS B 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (27681) covalent geometry : angle 0.48167 / 0.26 (37794) SS BOND : bond 0.00460 / 0.23 ( 9) SS BOND : angle 2.37210 / 1.80 ( 18) hydrogen bonds : bond 0.03831 / 2.62 ( 875) hydrogen bonds : angle 4.81188 / 3.43 ( 2418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.4366 (ttm) cc_final: 0.4007 (mtm) REVERT: A 215 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 244 TYR cc_start: 0.9032 (t80) cc_final: 0.8778 (m-80) REVERT: A 314 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 367 MET cc_start: 0.8697 (ttm) cc_final: 0.8405 (ttp) REVERT: A 790 ASP cc_start: 0.7825 (m-30) cc_final: 0.7615 (m-30) REVERT: A 1162 MET cc_start: 0.8474 (mtm) cc_final: 0.7975 (mtp) REVERT: B 367 MET cc_start: 0.8846 (tpp) cc_final: 0.8447 (tpp) REVERT: B 836 MET cc_start: 0.3061 (tpp) cc_final: 0.2012 (ppp) REVERT: C 552 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: C 603 MET cc_start: 0.8239 (mtm) cc_final: 0.7851 (mtm) REVERT: C 780 MET cc_start: 0.7889 (mmp) cc_final: 0.7584 (mmt) REVERT: C 1031 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 1159 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5286 (pm20) REVERT: D 1041 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8234 (mp) REVERT: D 1294 MET cc_start: 0.9095 (ttm) cc_final: 0.8828 (tpp) outliers start: 64 outliers final: 28 residues processed: 163 average time/residue: 0.1706 time to fit residues: 46.0712 Evaluate side-chains 135 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 255 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 357 optimal weight: 0.8980 chunk 337 optimal weight: 20.0000 chunk 352 optimal weight: 0.0970 chunk 225 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 355 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 161 optimal weight: 30.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 HIS B 542 HIS B1102 GLN B1208 HIS C 561 GLN ** D1271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.090540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.063880 restraints weight = 151771.282| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 5.99 r_work: 0.3031 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27690 Z= 0.140 Angle : 0.501 8.361 37812 Z= 0.265 Chirality : 0.043 0.206 4328 Planarity : 0.004 0.044 4858 Dihedral : 4.164 56.736 3933 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 2.82 % Allowed : 12.05 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.64 (0.14), residues: 3673 helix: 0.24 (0.20), residues: 676 sheet: 0.42 (0.16), residues: 1044 loop : -1.14 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 906 TYR 0.014 0.001 TYR C1160 PHE 0.014 0.001 PHE C 293 TRP 0.014 0.001 TRP A 145 HIS 0.019 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (27681) covalent geometry : angle 0.49790 / 0.26 (37794) SS BOND : bond 0.00476 / 0.30 ( 9) SS BOND : angle 2.51459 / 1.85 ( 18) hydrogen bonds : bond 0.03927 / 2.69 ( 875) hydrogen bonds : angle 4.56394 / 3.24 ( 2418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 102 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.4488 (ttm) cc_final: 0.4248 (mtm) REVERT: A 215 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7517 (p0) REVERT: A 244 TYR cc_start: 0.9056 (t80) cc_final: 0.8793 (m-80) REVERT: A 314 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 367 MET cc_start: 0.8779 (ttm) cc_final: 0.8460 (ttp) REVERT: A 790 ASP cc_start: 0.7990 (m-30) cc_final: 0.7747 (m-30) REVERT: A 1197 CYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 836 MET cc_start: 0.4212 (tpp) cc_final: 0.2467 (ppp) REVERT: B 929 MET cc_start: 0.5949 (mmt) cc_final: 0.5704 (mmt) REVERT: C 561 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: C 603 MET cc_start: 0.8061 (mtm) cc_final: 0.7606 (mtm) REVERT: C 633 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.5535 (m-30) REVERT: C 780 MET cc_start: 0.7813 (mmp) cc_final: 0.7563 (mmt) REVERT: C 1023 MET cc_start: 0.8849 (tpt) cc_final: 0.8590 (tpt) REVERT: C 1031 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 1159 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5771 (mt-10) outliers start: 72 outliers final: 43 residues processed: 167 average time/residue: 0.1576 time to fit residues: 44.6815 Evaluate side-chains 151 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1195 THR Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 111 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 chunk 313 optimal weight: 40.0000 chunk 224 optimal weight: 9.9990 chunk 291 optimal weight: 30.0000 chunk 359 optimal weight: 0.6980 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS B 621 HIS B 693 ASN B 697 ASN C 296 HIS C 511 HIS ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 HIS D1065 HIS D1300 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.088480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.061613 restraints weight = 150628.229| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 6.89 r_work: 0.2916 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 27690 Z= 0.301 Angle : 0.673 9.379 37812 Z= 0.359 Chirality : 0.048 0.165 4328 Planarity : 0.005 0.079 4858 Dihedral : 4.980 50.804 3933 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 3.48 % Allowed : 12.91 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3673 helix: -0.27 (0.20), residues: 668 sheet: 0.16 (0.16), residues: 1068 loop : -1.25 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 691 TYR 0.033 0.002 TYR C1160 PHE 0.022 0.002 PHE D1263 TRP 0.039 0.002 TRP C 562 HIS 0.009 0.002 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (27681) covalent geometry : angle 0.67012 / 0.36 (37794) SS BOND : bond 0.00526 / 0.34 ( 9) SS BOND : angle 3.09864 / 2.17 ( 18) hydrogen bonds : bond 0.05812 / 4.06 ( 875) hydrogen bonds : angle 5.22047 / 3.72 ( 2418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 101 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.4565 (ttm) cc_final: 0.4219 (mtm) REVERT: A 215 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7310 (p0) REVERT: A 244 TYR cc_start: 0.9117 (t80) cc_final: 0.8839 (m-80) REVERT: A 314 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 347 MET cc_start: 0.6722 (mpp) cc_final: 0.6363 (mpp) REVERT: A 367 MET cc_start: 0.8811 (ttm) cc_final: 0.8539 (ttp) REVERT: A 923 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8038 (p0) REVERT: A 1197 CYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 836 MET cc_start: 0.4631 (tpp) cc_final: 0.3094 (ppp) REVERT: C 292 MET cc_start: 0.6569 (mmp) cc_final: 0.5618 (tmm) REVERT: C 552 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 603 MET cc_start: 0.8418 (mtm) cc_final: 0.7992 (mtm) REVERT: C 780 MET cc_start: 0.8029 (mmp) cc_final: 0.7759 (mmt) REVERT: C 1031 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 1159 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: D 1263 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6790 (t80) outliers start: 89 outliers final: 49 residues processed: 185 average time/residue: 0.1570 time to fit residues: 49.2632 Evaluate side-chains 155 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 98 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1195 THR Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1079 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1263 PHE Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1271 HIS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 256 optimal weight: 0.0050 chunk 86 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 356 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 123 optimal weight: 50.0000 chunk 358 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A1208 HIS B1102 GLN C 601 ASN D1300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.090259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063761 restraints weight = 149933.056| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 6.16 r_work: 0.3014 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27690 Z= 0.082 Angle : 0.471 9.665 37812 Z= 0.247 Chirality : 0.042 0.147 4328 Planarity : 0.003 0.052 4858 Dihedral : 4.086 50.673 3933 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 14.82 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.48 (0.14), residues: 3673 helix: 0.56 (0.21), residues: 669 sheet: 0.46 (0.16), residues: 1049 loop : -1.08 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 585 TYR 0.013 0.001 TYR C 718 PHE 0.013 0.001 PHE C1058 TRP 0.018 0.001 TRP B1077 HIS 0.006 0.001 HIS D 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (27681) covalent geometry : angle 0.46832 / 0.25 (37794) SS BOND : bond 0.00415 / 0.31 ( 9) SS BOND : angle 2.26501 / 1.77 ( 18) hydrogen bonds : bond 0.02989 / 2.03 ( 875) hydrogen bonds : angle 4.35712 / 3.10 ( 2418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7426 (p0) REVERT: A 244 TYR cc_start: 0.9077 (t80) cc_final: 0.8793 (m-80) REVERT: A 314 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8349 (mp) REVERT: A 347 MET cc_start: 0.6843 (mpp) cc_final: 0.6524 (mpp) REVERT: A 367 MET cc_start: 0.8788 (ttm) cc_final: 0.8544 (ttp) REVERT: A 790 ASP cc_start: 0.8237 (m-30) cc_final: 0.8005 (m-30) REVERT: B 367 MET cc_start: 0.9380 (mmm) cc_final: 0.8603 (tpp) REVERT: B 836 MET cc_start: 0.4777 (tpp) cc_final: 0.3097 (ppp) REVERT: C 292 MET cc_start: 0.6582 (mmp) cc_final: 0.5463 (tmm) REVERT: C 603 MET cc_start: 0.8229 (mtm) cc_final: 0.7775 (mtm) REVERT: C 780 MET cc_start: 0.8104 (mmp) cc_final: 0.7884 (mmt) REVERT: C 1031 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 1159 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: D 670 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.7885 (t0) REVERT: D 1263 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6546 (t80) outliers start: 47 outliers final: 29 residues processed: 139 average time/residue: 0.1508 time to fit residues: 37.0133 Evaluate side-chains 133 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1263 PHE Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 195 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 182 optimal weight: 0.0010 chunk 75 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 141 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 HIS B1102 GLN C 185 ASN C 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.088679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061616 restraints weight = 147918.272| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.43 r_work: 0.2945 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27690 Z= 0.214 Angle : 0.551 10.029 37812 Z= 0.291 Chirality : 0.045 0.151 4328 Planarity : 0.004 0.057 4858 Dihedral : 4.271 53.201 3931 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 2.23 % Allowed : 14.24 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.67 (0.14), residues: 3673 helix: 0.28 (0.20), residues: 675 sheet: 0.30 (0.16), residues: 1055 loop : -1.13 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 585 TYR 0.020 0.001 TYR C1160 PHE 0.016 0.001 PHE B 962 TRP 0.014 0.001 TRP A 671 HIS 0.013 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (27681) covalent geometry : angle 0.54862 / 0.29 (37794) SS BOND : bond 0.00503 / 0.32 ( 9) SS BOND : angle 2.63068 / 1.87 ( 18) hydrogen bonds : bond 0.04555 / 3.16 ( 875) hydrogen bonds : angle 4.66813 / 3.32 ( 2418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 244 TYR cc_start: 0.9065 (t80) cc_final: 0.8786 (m-80) REVERT: A 314 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 347 MET cc_start: 0.6876 (mpp) cc_final: 0.6600 (mpp) REVERT: A 367 MET cc_start: 0.8722 (ttm) cc_final: 0.8476 (ttp) REVERT: A 790 ASP cc_start: 0.8636 (m-30) cc_final: 0.8421 (m-30) REVERT: B 836 MET cc_start: 0.4949 (tpp) cc_final: 0.3505 (ppp) REVERT: C 292 MET cc_start: 0.6683 (mmp) cc_final: 0.5729 (tmm) REVERT: C 603 MET cc_start: 0.8367 (mtm) cc_final: 0.8070 (mtm) REVERT: C 780 MET cc_start: 0.8045 (mmp) cc_final: 0.7777 (mmt) REVERT: C 1031 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8263 (mp) REVERT: C 1159 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: D 1263 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6656 (t80) outliers start: 57 outliers final: 37 residues processed: 152 average time/residue: 0.1529 time to fit residues: 40.6015 Evaluate side-chains 141 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1263 PHE Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 171 optimal weight: 7.9990 chunk 222 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 335 optimal weight: 8.9990 chunk 370 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 228 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 overall best weight: 2.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.088978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.062232 restraints weight = 149175.012| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 6.80 r_work: 0.2952 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27690 Z= 0.142 Angle : 0.495 10.844 37812 Z= 0.258 Chirality : 0.043 0.149 4328 Planarity : 0.003 0.055 4858 Dihedral : 4.073 51.209 3931 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.15 % Allowed : 14.39 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.49 (0.14), residues: 3673 helix: 0.59 (0.21), residues: 668 sheet: 0.47 (0.16), residues: 1011 loop : -1.08 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 585 TYR 0.020 0.001 TYR C1160 PHE 0.010 0.001 PHE C 431 TRP 0.022 0.001 TRP B1077 HIS 0.007 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (27681) covalent geometry : angle 0.49247 / 0.26 (37794) SS BOND : bond 0.00406 / 0.29 ( 9) SS BOND : angle 2.38838 / 1.76 ( 18) hydrogen bonds : bond 0.03581 / 2.47 ( 875) hydrogen bonds : angle 4.39939 / 3.12 ( 2418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7448 (p0) REVERT: A 244 TYR cc_start: 0.9127 (t80) cc_final: 0.8867 (m-80) REVERT: A 314 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 347 MET cc_start: 0.7063 (mpp) cc_final: 0.6795 (mpp) REVERT: A 367 MET cc_start: 0.8766 (ttm) cc_final: 0.8426 (ttp) REVERT: A 790 ASP cc_start: 0.8491 (m-30) cc_final: 0.8273 (m-30) REVERT: B 367 MET cc_start: 0.9444 (mmm) cc_final: 0.8832 (tpp) REVERT: B 836 MET cc_start: 0.4946 (tpp) cc_final: 0.3791 (ppp) REVERT: C 292 MET cc_start: 0.6703 (mmp) cc_final: 0.5751 (tmm) REVERT: C 603 MET cc_start: 0.8354 (mtm) cc_final: 0.8046 (mtm) REVERT: C 1031 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8331 (mp) outliers start: 55 outliers final: 41 residues processed: 147 average time/residue: 0.1435 time to fit residues: 37.6401 Evaluate side-chains 142 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1195 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1284 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 131 optimal weight: 50.0000 chunk 301 optimal weight: 5.9990 chunk 368 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 347 optimal weight: 0.5980 chunk 352 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.088884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061827 restraints weight = 148891.989| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 6.21 r_work: 0.2966 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27690 Z= 0.136 Angle : 0.492 11.956 37812 Z= 0.256 Chirality : 0.043 0.160 4328 Planarity : 0.003 0.056 4858 Dihedral : 3.985 56.481 3931 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 1.96 % Allowed : 14.31 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.42 (0.14), residues: 3673 helix: 0.65 (0.21), residues: 672 sheet: 0.49 (0.16), residues: 1011 loop : -1.02 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.014 0.001 TYR B 957 PHE 0.012 0.001 PHE B 962 TRP 0.013 0.001 TRP B1077 HIS 0.008 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (27681) covalent geometry : angle 0.48929 / 0.25 (37794) SS BOND : bond 0.00419 / 0.29 ( 9) SS BOND : angle 2.29890 / 1.71 ( 18) hydrogen bonds : bond 0.03600 / 2.46 ( 875) hydrogen bonds : angle 4.29641 / 3.04 ( 2418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7430 (p0) REVERT: A 244 TYR cc_start: 0.9079 (t80) cc_final: 0.8804 (m-80) REVERT: A 314 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 367 MET cc_start: 0.9472 (mmm) cc_final: 0.8777 (tpp) REVERT: B 836 MET cc_start: 0.5539 (tpp) cc_final: 0.4192 (ppp) REVERT: B 864 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8437 (mm) REVERT: C 292 MET cc_start: 0.6784 (mmp) cc_final: 0.5835 (tmm) REVERT: C 603 MET cc_start: 0.8354 (mtm) cc_final: 0.8034 (mtm) REVERT: C 1031 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 1159 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: D 1263 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6738 (t80) outliers start: 50 outliers final: 38 residues processed: 142 average time/residue: 0.1562 time to fit residues: 38.7052 Evaluate side-chains 139 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1195 THR Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1263 PHE Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1284 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 228 optimal weight: 40.0000 chunk 260 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 240 optimal weight: 50.0000 chunk 214 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN A1205 HIS A1208 HIS ** B 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 GLN ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.087752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061380 restraints weight = 150091.080| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.57 r_work: 0.2949 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27690 Z= 0.253 Angle : 0.600 12.100 37812 Z= 0.314 Chirality : 0.046 0.166 4328 Planarity : 0.004 0.064 4858 Dihedral : 4.460 59.260 3930 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 2.15 % Allowed : 14.39 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.74 (0.14), residues: 3673 helix: 0.13 (0.20), residues: 675 sheet: 0.22 (0.16), residues: 1034 loop : -1.10 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.015 0.002 TYR A1047 PHE 0.016 0.002 PHE A 506 TRP 0.017 0.002 TRP B1196 HIS 0.015 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (27681) covalent geometry : angle 0.59693 / 0.31 (37794) SS BOND : bond 0.00583 / 0.39 ( 9) SS BOND : angle 2.71178 / 1.89 ( 18) hydrogen bonds : bond 0.04844 / 3.38 ( 875) hydrogen bonds : angle 4.75688 / 3.37 ( 2418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7346 Ramachandran restraints generated. 3673 Oldfield, 0 Emsley, 3673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 95 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7271 (p0) REVERT: A 244 TYR cc_start: 0.9048 (t80) cc_final: 0.8749 (m-80) REVERT: A 314 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 367 MET cc_start: 0.8718 (ttm) cc_final: 0.8507 (ttp) REVERT: B 367 MET cc_start: 0.9489 (mmm) cc_final: 0.8741 (tpp) REVERT: B 864 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8417 (mm) REVERT: C 292 MET cc_start: 0.7067 (mmp) cc_final: 0.6044 (tmm) REVERT: C 603 MET cc_start: 0.8323 (mtm) cc_final: 0.7967 (mtm) REVERT: C 1031 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 670 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7965 (t0) REVERT: D 1263 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6745 (t80) outliers start: 55 outliers final: 39 residues processed: 143 average time/residue: 0.1536 time to fit residues: 38.4675 Evaluate side-chains 140 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1195 THR Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1159 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1257 CYS Chi-restraints excluded: chain D residue 1263 PHE Chi-restraints excluded: chain D residue 1270 CYS Chi-restraints excluded: chain D residue 1298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 330 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 HIS B 783 HIS B1102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.088743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061986 restraints weight = 149347.668| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.91 r_work: 0.2978 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27690 Z= 0.099 Angle : 0.483 12.561 37812 Z= 0.249 Chirality : 0.042 0.153 4328 Planarity : 0.003 0.060 4858 Dihedral : 4.058 59.832 3930 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 1.64 % Allowed : 14.86 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % 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: -0.43 (0.14), residues: 3673 helix: 0.65 (0.21), residues: 676 sheet: 0.46 (0.16), residues: 1004 loop : -1.01 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 585 TYR 0.011 0.001 TYR C 718 PHE 0.011 0.001 PHE C1058 TRP 0.016 0.001 TRP B1077 HIS 0.004 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (27681) covalent geometry : angle 0.48055 / 0.25 (37794) SS BOND : bond 0.00383 / 0.28 ( 9) SS BOND : angle 2.22736 / 1.66 ( 18) hydrogen bonds : bond 0.03218 / 2.20 ( 875) hydrogen bonds : angle 4.26010 / 3.01 ( 2418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10264.41 seconds wall clock time: 175 minutes 12.07 seconds (10512.07 seconds total)