Starting phenix.real_space_refine on Sat Jun 6 20:37:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx1_47277/06_2026/9dx1_47277.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 218 5.16 5 C 19210 2.51 5 N 5454 2.21 5 O 5617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 30499 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6027 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 24, 'TRANS': 766} Chain breaks: 4 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 13, 'PHE:plan': 1, 'ARG:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'TYR:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 7467 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 344} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1049} Chain breaks: 7 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1248 Unresolved non-hydrogen angles: 1593 Unresolved non-hydrogen dihedrals: 1060 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'ASP:plan': 29, 'TRP:plan': 9, 'HIS:plan': 10, 'ARG:plan': 20, 'PHE:plan': 14, 'GLU:plan': 25, 'TYR:plan': 10, 'ASN:plan1': 19, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 685 Chain: "C" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4577 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 575} Chain breaks: 5 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4244 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'TYR:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 6, 'TRP:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "E" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2682 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5502 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 36, 'TRANS': 692} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 15, 'ASN:plan1': 4, 'ARG:plan': 11, 'ASP:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 7.18, per 1000 atoms: 0.24 Number of scatterers: 30499 At special positions: 0 Unit cell: (227.861, 173.94, 171.331, 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 218 16.00 O 5617 8.00 N 5454 7.00 C 19210 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=2.03 Simple disulfide: pdb=" SG CYS B1197 " - pdb=" SG CYS B1200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 663 " - pdb=" SG CYS F 672 " distance=2.02 Simple disulfide: pdb=" SG CYS F 663 " - pdb=" SG CYS F 675 " distance=2.03 Simple disulfide: pdb=" SG CYS F 672 " - pdb=" SG CYS F 675 " distance=2.04 Simple disulfide: pdb=" SG CYS F 682 " - pdb=" SG CYS F 685 " distance=2.04 Simple disulfide: pdb=" SG CYS F 699 " - pdb=" SG CYS F 724 " distance=2.04 Simple disulfide: pdb=" SG CYS F 722 " - pdb=" SG CYS F 724 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7736 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 55 sheets defined 26.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.547A pdb=" N MET A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 770 removed outlier: 3.775A pdb=" N LEU A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 781 through 787 removed outlier: 4.076A pdb=" N GLY A 787 " --> pdb=" O HIS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.509A pdb=" N TYR A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 857 through 867 removed outlier: 3.592A pdb=" N ALA A 863 " --> pdb=" O GLU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 889 removed outlier: 3.538A pdb=" N GLN A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.642A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 916 Processing helix chain 'A' and resid 921 through 933 removed outlier: 3.797A pdb=" N ASN A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 933 " --> pdb=" O MET A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 950 removed outlier: 4.587A pdb=" N SER A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.656A pdb=" N PHE A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.533A pdb=" N LYS A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1014 removed outlier: 3.711A pdb=" N ASN A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 3.517A pdb=" N SER A1034 " --> pdb=" O ASP A1030 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1051 removed outlier: 3.779A pdb=" N ALA A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A1051 " --> pdb=" O TYR A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1059 Processing helix chain 'A' and resid 1060 through 1077 removed outlier: 3.556A pdb=" N ASP A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1076 " --> pdb=" O ASN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1094 removed outlier: 3.523A pdb=" N ALA A1084 " --> pdb=" O TRP A1080 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1093 " --> pdb=" O HIS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1192 removed outlier: 3.749A pdb=" N ASN A1192 " --> pdb=" O GLN A1189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1189 through 1192' Processing helix chain 'A' and resid 1206 through 1214 removed outlier: 3.513A pdb=" N SER A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.601A pdb=" N GLY B 512 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 770 removed outlier: 3.599A pdb=" N ALA B 768 " --> pdb=" O MET B 764 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 784 removed outlier: 3.867A pdb=" N HIS B 783 " --> pdb=" O TRP B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 813 removed outlier: 3.520A pdb=" N LYS B 794 " --> pdb=" O ASP B 790 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 801 " --> pdb=" O TRP B 797 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 805 " --> pdb=" O HIS B 801 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 811 " --> pdb=" O THR B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 830 removed outlier: 3.527A pdb=" N ILE B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 830 " --> pdb=" O ILE B 826 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 825 through 830' Processing helix chain 'B' and resid 850 through 856 removed outlier: 4.617A pdb=" N GLN B 854 " --> pdb=" O GLN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.638A pdb=" N ILE B 861 " --> pdb=" O ASN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 889 removed outlier: 3.521A pdb=" N GLN B 887 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 901 removed outlier: 3.648A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 914 removed outlier: 3.578A pdb=" N ALA B 907 " --> pdb=" O ASP B 903 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 914 " --> pdb=" O ILE B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 932 removed outlier: 4.334A pdb=" N VAL B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 950 removed outlier: 3.580A pdb=" N GLU B 944 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.653A pdb=" N CYS B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 994 Processing helix chain 'B' and resid 995 through 1014 removed outlier: 3.581A pdb=" N ASN B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B1001 " --> pdb=" O THR B 997 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 4.071A 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: 3.632A pdb=" N ASP B1030 " --> pdb=" O LYS B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1050 removed outlier: 3.750A pdb=" N SER B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B1050 " --> pdb=" O SER B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.766A pdb=" N LEU B1058 " --> pdb=" O PRO B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1077 removed outlier: 3.522A pdb=" N GLN B1064 " --> pdb=" O ASP B1060 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B1067 " --> pdb=" O VAL B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1092 removed outlier: 3.718A pdb=" N ALA B1084 " --> pdb=" O TRP B1080 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1098 removed outlier: 3.599A pdb=" N LYS B1098 " --> pdb=" O PRO B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1191 removed outlier: 3.580A pdb=" N ASN B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1213 removed outlier: 3.652A pdb=" N SER B1211 " --> pdb=" O GLY B1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 780 through 790 Processing helix chain 'C' and resid 796 through 812 removed outlier: 3.528A pdb=" N VAL C 807 " --> pdb=" O HIS C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 828 removed outlier: 3.573A pdb=" N TYR C 827 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.823A pdb=" N GLN C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1032 removed outlier: 3.717A pdb=" N ALA C1024 " --> pdb=" O ASP C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1039 removed outlier: 4.128A pdb=" N ARG C1036 " --> pdb=" O GLU C1033 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS C1037 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1058 removed outlier: 3.586A pdb=" N HIS C1046 " --> pdb=" O GLN C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1070 Processing helix chain 'C' and resid 1136 through 1145 removed outlier: 3.567A pdb=" N MET C1141 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C1145 " --> pdb=" O MET C1141 " (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 1007 removed outlier: 3.761A pdb=" N GLY D1006 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D1007 " --> pdb=" O LYS D1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1002 through 1007' Processing helix chain 'D' and resid 1015 through 1031 removed outlier: 3.599A pdb=" N THR D1019 " --> pdb=" O ASP D1015 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D1021 " --> pdb=" O GLN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1046 removed outlier: 3.768A pdb=" N VAL D1036 " --> pdb=" O ARG D1032 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D1044 " --> pdb=" O SER D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1051 removed outlier: 3.655A pdb=" N LEU D1050 " --> pdb=" O ASP D1047 " (cutoff:3.500A) removed outlier: 4.041A 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 1082 removed outlier: 3.565A pdb=" N ARG D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1100 removed outlier: 3.564A pdb=" N GLN D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1192 removed outlier: 3.563A pdb=" N ASP D1185 " --> pdb=" O GLU D1181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D1189 " --> pdb=" O ASP D1185 " (cutoff:3.500A) removed outlier: 3.981A 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 1216 removed outlier: 3.616A pdb=" N LYS D1206 " --> pdb=" O PHE D1202 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D1212 " --> pdb=" O CYS D1208 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1227 removed outlier: 3.746A pdb=" N ARG D1222 " --> pdb=" O LEU D1218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D1223 " --> pdb=" O ARG D1219 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.522A pdb=" N VAL E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 86 through 103 removed outlier: 3.766A pdb=" N SER E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.530A pdb=" N HIS E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.585A pdb=" N ALA E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 152 removed outlier: 6.376A pdb=" N LEU E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS E 150 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 151 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.502A pdb=" N HIS E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 removed outlier: 3.660A pdb=" N ILE E 173 " --> pdb=" O PRO E 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 173' Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.891A pdb=" N ILE E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 215 removed outlier: 3.682A pdb=" N GLN E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 209 " --> pdb=" O HIS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.530A pdb=" N CYS E 314 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 316 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 347 through 356 removed outlier: 3.522A pdb=" N LEU E 351 " --> pdb=" O HIS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 371 removed outlier: 3.707A pdb=" N GLN E 361 " --> pdb=" O PRO E 357 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR E 371 " --> pdb=" O PHE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 402 removed outlier: 3.696A pdb=" N LEU E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 417 removed outlier: 3.864A pdb=" N GLN E 415 " --> pdb=" O GLY E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 431 Processing helix chain 'E' and resid 432 through 435 removed outlier: 3.661A pdb=" N THR E 435 " --> pdb=" O PRO E 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'E' and resid 436 through 443 removed outlier: 3.653A pdb=" N TYR E 440 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 443 " --> pdb=" O MET E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 480 removed outlier: 3.805A pdb=" N LYS E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 474 " --> pdb=" O TYR E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 386 Processing helix chain 'F' and resid 640 through 642 No H-bonds generated for 'chain 'F' and resid 640 through 642' Processing helix chain 'F' and resid 705 through 712 Processing helix chain 'F' and resid 725 through 731 removed outlier: 3.856A pdb=" N GLU F 729 " --> pdb=" O HIS F 725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.637A pdb=" N ALA A 369 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 405 removed outlier: 6.739A pdb=" N CYS A 415 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 403 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 413 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE A 405 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG A 411 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 421 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 437 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 423 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 450 removed outlier: 4.408A pdb=" N ARG A 447 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 462 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 468 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A 493 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 470 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 501 through 506 removed outlier: 4.010A pdb=" N ASP A 503 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 542 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLU A 528 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 540 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 555 removed outlier: 6.698A pdb=" N GLY A 570 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 553 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 568 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP A 555 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET A 566 " --> pdb=" O TRP A 555 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 582 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A 599 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE A 584 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 612 removed outlier: 3.644A pdb=" N ASP A 609 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 631 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 630 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 658 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 632 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 671 removed outlier: 6.926A pdb=" N SER A 681 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 669 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 679 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 682 " --> pdb=" O CYS A 686 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 687 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 703 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 689 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1104 through 1106 removed outlier: 4.734A pdb=" N HIS C1087 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C1095 " --> pdb=" O CYS C1090 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1203 through 1205 removed outlier: 4.114A pdb=" N PHE A1194 " --> pdb=" O TRP C1127 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP C1127 " --> pdb=" O PHE A1194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.489A pdb=" N LEU B 25 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 56 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 27 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.624A pdb=" N THR B 90 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 80 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 121 removed outlier: 6.839A pdb=" N GLY B 132 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU B 119 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 130 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TRP B 121 " --> pdb=" O TRP B 128 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N TRP B 128 " --> pdb=" O TRP B 121 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER B 141 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 140 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN B 183 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.576A pdb=" N LEU B 208 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B 221 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE B 210 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 228 through 232 removed outlier: 4.698A pdb=" N GLY B 229 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 243 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.542A pdb=" N LEU B 286 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL B 273 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 284 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TRP B 275 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU B 282 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 327 through 330 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 360 Processing sheet with id=AB9, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.782A pdb=" N CYS B 415 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 403 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 413 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 421 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B 437 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 423 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 445 through 450 removed outlier: 7.328A pdb=" N CYS B 462 " --> pdb=" O TRP B 446 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL B 448 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA B 460 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP B 450 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 458 " --> pdb=" O TRP B 450 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 459 " --> pdb=" O TRP B 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 471 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 492 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU B 472 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS B 490 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 503 through 506 removed outlier: 3.827A pdb=" N ASP B 503 " --> pdb=" O CYS B 518 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 524 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 543 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 526 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 550 through 555 removed outlier: 3.857A pdb=" N CYS B 552 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 582 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR B 599 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 584 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 595 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 593 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 609 through 612 removed outlier: 4.029A pdb=" N ASP B 609 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 630 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN B 658 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 632 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 666 through 671 removed outlier: 7.053A pdb=" N SER B 681 " --> pdb=" O TRP B 667 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 669 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 679 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 682 " --> pdb=" O CYS B 686 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 686 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 689 " --> pdb=" O GLY B 702 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS B 691 " --> pdb=" O CYS B 700 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N CYS B 700 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1103 through 1107 Processing sheet with id=AC7, first strand: chain 'B' and resid 1196 through 1197 Processing sheet with id=AC8, first strand: chain 'C' and resid 342 through 345 removed outlier: 4.453A pdb=" N LEU C 397 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 412 " --> pdb=" O GLU C 401 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 424 through 429 removed outlier: 3.870A pdb=" N ASP C 426 " --> pdb=" O CYS C 439 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 439 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 445 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER C 461 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 447 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 469 through 474 removed outlier: 7.042A pdb=" N CYS C 486 " --> pdb=" O TRP C 470 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 472 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 484 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP C 474 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL C 482 " --> pdb=" O TRP C 474 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 492 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR C 517 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 494 " --> pdb=" O ARG C 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 525 through 530 removed outlier: 3.938A pdb=" N ASP C 527 " --> pdb=" O CYS C 542 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 542 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 548 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU C 567 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 550 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 576 through 579 removed outlier: 4.086A pdb=" N CYS C 576 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 606 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR C 623 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 617 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.728A pdb=" N ASP C 633 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 654 " --> pdb=" O GLN C 682 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN C 682 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE C 656 " --> pdb=" O VAL C 680 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 690 through 695 removed outlier: 3.773A pdb=" N ARG C 692 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 706 " --> pdb=" O CYS C 710 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 711 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 727 " --> pdb=" O VAL C 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 713 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.520A pdb=" N GLY D 541 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 672 through 677 removed outlier: 4.072A pdb=" N ASP D 674 " --> pdb=" O CYS D 687 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 684 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 695 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP D 697 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU D 705 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 716 through 721 removed outlier: 6.884A pdb=" N CYS D 733 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D 719 " --> pdb=" O ALA D 731 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA D 731 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TRP D 721 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE D 729 " --> pdb=" O TRP D 721 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 740 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 739 " --> pdb=" O GLU D 754 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 754 " --> pdb=" O VAL D 739 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 741 " --> pdb=" O SER D 752 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU D 745 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 762 through 767 removed outlier: 3.901A pdb=" N SER D 764 " --> pdb=" O GLY D 779 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 814 removed outlier: 6.687A pdb=" N GLY D 841 " --> pdb=" O ASN D 810 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL D 812 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA D 839 " --> pdb=" O VAL D 812 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP D 814 " --> pdb=" O ARG D 837 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG D 837 " --> pdb=" O TRP D 814 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 847 " --> pdb=" O LYS D 863 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS D 863 " --> pdb=" O ILE D 847 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 849 " --> pdb=" O GLU D 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 871 through 875 removed outlier: 3.978A pdb=" N ASP D 873 " --> pdb=" O CYS D 890 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG D 895 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL D 896 " --> pdb=" O LEU D 914 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 921 through 925 removed outlier: 3.604A pdb=" N HIS D 923 " --> pdb=" O SER D 936 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 337 through 338 removed outlier: 6.518A pdb=" N PHE E 337 " --> pdb=" O ARG E 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 7 through 10 removed outlier: 6.667A pdb=" N LEU F 25 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE F 56 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 27 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 65 through 68 removed outlier: 4.115A pdb=" N CYS F 65 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 116 through 121 removed outlier: 6.749A pdb=" N GLY F 132 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU F 119 " --> pdb=" O ALA F 130 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA F 130 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP F 121 " --> pdb=" O TRP F 128 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TRP F 128 " --> pdb=" O TRP F 121 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER F 141 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY F 153 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 158 through 163 removed outlier: 3.707A pdb=" N SER F 160 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 199 through 203 removed outlier: 4.266A pdb=" N VAL F 201 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA F 212 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL F 203 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ARG F 210 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 232 " --> pdb=" O ILE F 221 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 241 through 246 removed outlier: 6.721A pdb=" N LEU F 257 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL F 244 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA F 255 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP F 246 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU F 253 " --> pdb=" O TRP F 246 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 285 " --> pdb=" O ASP F 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 298 through 301 removed outlier: 3.742A pdb=" N SER F 298 " --> pdb=" O VAL F 312 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 332 through 335 removed outlier: 4.304A pdb=" N SER F 633 " --> pdb=" O SER F 629 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE F 624 " --> pdb=" O ARG F 617 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG F 617 " --> pdb=" O PHE F 624 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 342 through 345 removed outlier: 7.984A pdb=" N PHE F 360 " --> pdb=" O ASN F 375 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN F 375 " --> pdb=" O PHE F 360 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE F 362 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 388 through 393 removed outlier: 6.507A pdb=" N ALA F 404 " --> pdb=" O ALA F 389 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL F 391 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA F 402 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP F 393 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU F 400 " --> pdb=" O TRP F 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 411 " --> pdb=" O THR F 403 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 410 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU F 426 " --> pdb=" O VAL F 410 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 412 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 434 through 438 removed outlier: 6.958A pdb=" N GLY F 450 " --> pdb=" O ASN F 435 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL F 437 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU F 448 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F 451 " --> pdb=" O PHE F 455 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE F 455 " --> pdb=" O SER F 451 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER F 468 " --> pdb=" O CYS F 458 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP F 460 " --> pdb=" O SER F 466 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER F 466 " --> pdb=" O ASP F 460 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 477 through 482 removed outlier: 6.671A pdb=" N THR F 493 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL F 480 " --> pdb=" O ALA F 491 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA F 491 " --> pdb=" O VAL F 480 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE F 482 " --> pdb=" O THR F 489 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR F 489 " --> pdb=" O PHE F 482 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN F 498 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 512 " --> pdb=" O LEU F 501 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 521 through 526 removed outlier: 3.557A pdb=" N CYS F 523 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET F 542 " --> pdb=" O GLY F 538 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 543 " --> pdb=" O CYS F 558 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 545 " --> pdb=" O MET F 556 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 565 through 570 removed outlier: 6.812A pdb=" N CYS F 581 " --> pdb=" O ALA F 566 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 568 " --> pdb=" O ALA F 579 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA F 579 " --> pdb=" O VAL F 568 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TRP F 570 " --> pdb=" O HIS F 577 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N HIS F 577 " --> pdb=" O TRP F 570 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 591 " --> pdb=" O ALA F 602 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 602 " --> pdb=" O VAL F 591 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 671 through 672 removed outlier: 3.525A pdb=" N CYS F 672 " --> pdb=" O LYS F 676 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 2961 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: 7.96 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10182 1.35 - 1.47: 7971 1.47 - 1.60: 12767 1.60 - 1.72: 0 1.72 - 1.84: 300 Bond restraints: 31220 Sorted by residual: bond pdb=" CB CYS F 685 " pdb=" SG CYS F 685 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" C CYS F 675 " pdb=" N LYS F 676 " ideal model delta sigma weight residual 1.325 1.334 -0.009 1.14e-02 7.69e+03 6.77e-01 bond pdb=" N GLY E 383 " pdb=" CA GLY E 383 " ideal model delta sigma weight residual 1.449 1.461 -0.011 1.45e-02 4.76e+03 6.08e-01 bond pdb=" CB PRO F 110 " pdb=" CG PRO F 110 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.97e-01 bond pdb=" C VAL B 876 " pdb=" O VAL B 876 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.87e-01 ... (remaining 31215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 42178 1.83 - 3.67: 351 3.67 - 5.50: 17 5.50 - 7.34: 1 7.34 - 9.17: 2 Bond angle restraints: 42549 Sorted by residual: angle pdb=" C LYS F 676 " pdb=" CA LYS F 676 " pdb=" CB LYS F 676 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" CA VAL B 876 " pdb=" C VAL B 876 " pdb=" N ASP B 877 " ideal model delta sigma weight residual 116.60 120.35 -3.75 1.45e+00 4.76e-01 6.70e+00 angle pdb=" CA LEU D 823 " pdb=" CB LEU D 823 " pdb=" CG LEU D 823 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.49e+00 angle pdb=" CA TRP D 922 " pdb=" CB TRP D 922 " pdb=" CG TRP D 922 " ideal model delta sigma weight residual 113.60 118.19 -4.59 1.90e+00 2.77e-01 5.84e+00 angle pdb=" CA CYS B1200 " pdb=" CB CYS B1200 " pdb=" SG CYS B1200 " ideal model delta sigma weight residual 114.40 119.79 -5.39 2.30e+00 1.89e-01 5.50e+00 ... (remaining 42544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 17467 17.11 - 34.22: 686 34.22 - 51.33: 122 51.33 - 68.44: 34 68.44 - 85.55: 7 Dihedral angle restraints: 18316 sinusoidal: 6414 harmonic: 11902 Sorted by residual: dihedral pdb=" CB CYS F 663 " pdb=" SG CYS F 663 " pdb=" SG CYS F 672 " pdb=" CB CYS F 672 " ideal model delta sinusoidal sigma weight residual -86.00 -162.81 76.81 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS F 663 " pdb=" SG CYS F 663 " pdb=" SG CYS F 675 " pdb=" CB CYS F 675 " ideal model delta sinusoidal sigma weight residual -86.00 -17.18 -68.82 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 672 " pdb=" SG CYS F 672 " pdb=" SG CYS F 675 " pdb=" CB CYS F 675 " ideal model delta sinusoidal sigma weight residual 93.00 149.54 -56.54 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 18313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2677 0.028 - 0.055: 1348 0.055 - 0.083: 406 0.083 - 0.110: 286 0.110 - 0.138: 87 Chirality restraints: 4804 Sorted by residual: chirality pdb=" CA VAL F 244 " pdb=" N VAL F 244 " pdb=" C VAL F 244 " pdb=" CB VAL F 244 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE D 847 " pdb=" N ILE D 847 " pdb=" C ILE D 847 " pdb=" CB ILE D 847 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE C 727 " pdb=" N ILE C 727 " pdb=" C ILE C 727 " pdb=" CB ILE C 727 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 4801 not shown) Planarity restraints: 5469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 361 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 362 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 723 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 724 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 724 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 724 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 882 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 883 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 883 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 883 " 0.022 5.00e-02 4.00e+02 ... (remaining 5466 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 892 2.72 - 3.26: 27873 3.26 - 3.81: 42810 3.81 - 4.35: 52827 4.35 - 4.90: 93928 Nonbonded interactions: 218330 Sorted by model distance: nonbonded pdb=" OG SER D 734 " pdb=" OD1 ASP D 736 " model vdw 2.171 3.040 nonbonded pdb=" OG SER A 995 " pdb=" OE1 GLN A 998 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASP B 465 " pdb=" OG1 THR B 467 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR F 313 " pdb=" OG1 THR F 317 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP B1041 " pdb=" OG1 THR B1044 " model vdw 2.261 3.040 ... (remaining 218325 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.040 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31229 Z= 0.114 Angle : 0.443 9.173 42567 Z= 0.239 Chirality : 0.042 0.138 4804 Planarity : 0.003 0.053 5469 Dihedral : 9.830 85.552 10553 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.54 % Allowed : 4.27 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -1.12 (0.13), residues: 4043 helix: -0.46 (0.17), residues: 845 sheet: 0.39 (0.16), residues: 1050 loop : -1.47 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 986 TYR 0.014 0.001 TYR F 659 PHE 0.013 0.001 PHE E 337 TRP 0.015 0.001 TRP D 922 HIS 0.004 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (31220) covalent geometry : angle 0.43797 / 0.24 (42549) SS BOND : bond 0.00521 / 0.24 ( 9) SS BOND : angle 3.22133 / 1.84 ( 18) hydrogen bonds : bond 0.32990 / 22.44 ( 1060) hydrogen bonds : angle 7.38782 / 5.23 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 168 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 836 MET cc_start: 0.3001 (tpp) cc_final: 0.2134 (ttt) REVERT: D 561 ARG cc_start: 0.1786 (OUTLIER) cc_final: 0.0869 (mmp80) REVERT: F 95 ASP cc_start: -0.2423 (OUTLIER) cc_final: -0.2828 (p0) outliers start: 76 outliers final: 20 residues processed: 239 average time/residue: 0.2086 time to fit residues: 80.5143 Evaluate side-chains 143 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1060 THR Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 overall best weight: 1.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 ASN A 909 GLN A1230 GLN B 792 GLN C 465 HIS C 509 GLN C1022 GLN ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 HIS D1102 GLN E 203 HIS E 368 GLN F 96 HIS F 701 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.075170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.054877 restraints weight = 190267.141| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 6.72 r_work: 0.3156 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31229 Z= 0.127 Angle : 0.546 11.610 42567 Z= 0.295 Chirality : 0.044 0.169 4804 Planarity : 0.004 0.046 5469 Dihedral : 4.711 57.702 4387 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.77 % Allowed : 6.38 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.52 (0.13), residues: 4043 helix: 0.87 (0.17), residues: 894 sheet: 0.60 (0.16), residues: 1040 loop : -1.42 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 498 TYR 0.016 0.001 TYR E 127 PHE 0.023 0.001 PHE A 989 TRP 0.023 0.001 TRP C1102 HIS 0.012 0.001 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (31220) covalent geometry : angle 0.53783 / 0.29 (42549) SS BOND : bond 0.01590 / 1.12 ( 9) SS BOND : angle 4.72650 / 2.49 ( 18) hydrogen bonds : bond 0.05819 / 3.85 ( 1060) hydrogen bonds : angle 4.89307 / 3.46 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8224 (ppp) cc_final: 0.7864 (ppp) REVERT: A 533 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: B 1032 MET cc_start: 0.9327 (mmm) cc_final: 0.8919 (mmm) REVERT: B 1186 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8122 (mmtp) REVERT: C 603 MET cc_start: 0.8949 (mtm) cc_final: 0.8673 (mtm) REVERT: C 1113 MET cc_start: 0.8469 (tpp) cc_final: 0.8176 (tpt) REVERT: D 561 ARG cc_start: 0.3941 (OUTLIER) cc_final: 0.3096 (mmp80) REVERT: E 83 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8573 (ptm) REVERT: E 198 LEU cc_start: 0.9421 (mt) cc_final: 0.9202 (pp) REVERT: F 396 MET cc_start: 0.7837 (mmt) cc_final: 0.7630 (mpp) outliers start: 53 outliers final: 28 residues processed: 169 average time/residue: 0.1854 time to fit residues: 53.2879 Evaluate side-chains 145 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 249 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 333 optimal weight: 5.9990 chunk 271 optimal weight: 0.0770 chunk 402 optimal weight: 20.0000 chunk 302 optimal weight: 0.0970 chunk 122 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 314 optimal weight: 20.0000 chunk 110 optimal weight: 50.0000 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS B1043 GLN B1205 HIS ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS ** E 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 701 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.073900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.052598 restraints weight = 194206.198| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 6.98 r_work: 0.3067 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31229 Z= 0.131 Angle : 0.492 8.982 42567 Z= 0.264 Chirality : 0.043 0.385 4804 Planarity : 0.003 0.044 5469 Dihedral : 4.514 57.788 4381 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.84 % Allowed : 6.54 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.28 (0.13), residues: 4043 helix: 1.24 (0.17), residues: 917 sheet: 0.66 (0.16), residues: 1061 loop : -1.36 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.012 0.001 TYR F 590 PHE 0.017 0.001 PHE A1194 TRP 0.027 0.001 TRP E 394 HIS 0.007 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (31220) covalent geometry : angle 0.48842 / 0.26 (42549) SS BOND : bond 0.00489 / 0.25 ( 9) SS BOND : angle 2.94267 / 1.52 ( 18) hydrogen bonds : bond 0.04835 / 3.24 ( 1060) hydrogen bonds : angle 4.38302 / 3.09 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 MET cc_start: 0.9050 (ttm) cc_final: 0.8683 (tpt) REVERT: B 514 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7098 (tpp) REVERT: B 792 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: C 603 MET cc_start: 0.9000 (mtm) cc_final: 0.8731 (mtm) REVERT: D 561 ARG cc_start: 0.3761 (OUTLIER) cc_final: 0.2917 (mmp80) REVERT: E 138 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9101 (tm-30) REVERT: E 198 LEU cc_start: 0.9428 (mt) cc_final: 0.9213 (pp) outliers start: 55 outliers final: 30 residues processed: 161 average time/residue: 0.1742 time to fit residues: 48.6177 Evaluate side-chains 145 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 104 optimal weight: 8.9990 chunk 250 optimal weight: 0.0870 chunk 308 optimal weight: 40.0000 chunk 122 optimal weight: 2.9990 chunk 170 optimal weight: 0.0370 chunk 144 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 397 optimal weight: 40.0000 chunk 98 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 overall best weight: 4.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 ASN B 542 HIS ** B 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS E 196 GLN E 441 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.071972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.049588 restraints weight = 188794.229| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 6.46 r_work: 0.2961 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31229 Z= 0.199 Angle : 0.567 8.902 42567 Z= 0.302 Chirality : 0.045 0.207 4804 Planarity : 0.004 0.055 5469 Dihedral : 4.635 59.391 4374 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.07 % Allowed : 7.08 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.37 (0.13), residues: 4043 helix: 1.26 (0.17), residues: 913 sheet: 0.59 (0.16), residues: 1049 loop : -1.44 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 813 TYR 0.016 0.002 TYR A1065 PHE 0.018 0.002 PHE C 783 TRP 0.024 0.002 TRP B 368 HIS 0.012 0.001 HIS F 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (31220) covalent geometry : angle 0.56476 / 0.30 (42549) SS BOND : bond 0.00520 / 0.27 ( 9) SS BOND : angle 2.28995 / 1.25 ( 18) hydrogen bonds : bond 0.05089 / 3.42 ( 1060) hydrogen bonds : angle 4.34242 / 3.05 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 108 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 MET cc_start: 0.8840 (tpp) cc_final: 0.8629 (tpp) REVERT: B 514 MET cc_start: 0.7276 (tpp) cc_final: 0.6875 (tpp) REVERT: B 792 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 1049 MET cc_start: 0.8503 (mpp) cc_final: 0.8215 (mpp) REVERT: B 1186 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7863 (tppp) REVERT: C 603 MET cc_start: 0.9038 (mtm) cc_final: 0.8725 (mtm) REVERT: C 662 VAL cc_start: 0.9598 (OUTLIER) cc_final: 0.9381 (m) REVERT: D 561 ARG cc_start: 0.3496 (OUTLIER) cc_final: 0.2634 (mmp80) REVERT: F 269 MET cc_start: 0.7070 (mpp) cc_final: 0.6844 (mpp) REVERT: F 456 MET cc_start: 0.8808 (ptp) cc_final: 0.8512 (ptt) outliers start: 62 outliers final: 37 residues processed: 163 average time/residue: 0.1720 time to fit residues: 48.1954 Evaluate side-chains 148 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 332 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 387 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 302 optimal weight: 30.0000 chunk 324 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS A 909 GLN A1069 ASN ** A1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS ** B 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 HIS ** D 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** E 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.069892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.046817 restraints weight = 187350.346| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 6.41 r_work: 0.2856 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 31229 Z= 0.410 Angle : 0.807 11.481 42567 Z= 0.422 Chirality : 0.051 0.244 4804 Planarity : 0.006 0.096 5469 Dihedral : 5.535 59.194 4373 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.40 % Allowed : 8.08 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -1.14 (0.13), residues: 4043 helix: 0.16 (0.16), residues: 911 sheet: 0.17 (0.16), residues: 1057 loop : -1.72 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 561 TYR 0.027 0.003 TYR D1214 PHE 0.036 0.003 PHE A 405 TRP 0.035 0.003 TRP D 876 HIS 0.021 0.002 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.41 (31220) covalent geometry : angle 0.80489 / 0.42 (42549) SS BOND : bond 0.00647 / 0.32 ( 9) SS BOND : angle 2.76042 / 1.52 ( 18) hydrogen bonds : bond 0.07002 / 4.67 ( 1060) hydrogen bonds : angle 5.13392 / 3.60 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 110 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8902 (ptt) cc_final: 0.8434 (ptt) REVERT: A 810 MET cc_start: 0.8739 (tpp) cc_final: 0.8459 (tpp) REVERT: A 1226 CYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 514 MET cc_start: 0.7127 (tpp) cc_final: 0.6866 (tpp) REVERT: B 556 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6520 (p0) REVERT: B 1049 MET cc_start: 0.8453 (mpp) cc_final: 0.8183 (mpp) REVERT: B 1196 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8183 (t-100) REVERT: C 603 MET cc_start: 0.9142 (mtm) cc_final: 0.8814 (mtm) REVERT: C 662 VAL cc_start: 0.9689 (OUTLIER) cc_final: 0.9455 (m) REVERT: C 1113 MET cc_start: 0.8939 (tpt) cc_final: 0.8650 (tmm) REVERT: D 561 ARG cc_start: 0.3439 (OUTLIER) cc_final: 0.2711 (mmp80) REVERT: D 1069 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8605 (ttt180) REVERT: F 73 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8113 (t0) REVERT: F 603 MET cc_start: 0.7608 (mmm) cc_final: 0.7339 (mmm) outliers start: 72 outliers final: 48 residues processed: 173 average time/residue: 0.1726 time to fit residues: 51.0531 Evaluate side-chains 165 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1160 ILE Chi-restraints excluded: chain B residue 1196 TRP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1122 LYS Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1069 ARG Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 542 MET Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 663 CYS Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 363 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 230 optimal weight: 0.0670 chunk 177 optimal weight: 1.9990 chunk 348 optimal weight: 50.0000 chunk 386 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN A1069 ASN A1208 HIS B 801 HIS B1208 HIS D 668 HIS F 290 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.071439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.048598 restraints weight = 187840.561| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.48 r_work: 0.2975 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31229 Z= 0.100 Angle : 0.494 9.116 42567 Z= 0.262 Chirality : 0.042 0.141 4804 Planarity : 0.003 0.069 5469 Dihedral : 4.620 59.457 4369 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.60 % Allowed : 8.98 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.41 (0.13), residues: 4043 helix: 1.34 (0.17), residues: 894 sheet: 0.45 (0.16), residues: 1044 loop : -1.42 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 893 TYR 0.012 0.001 TYR B 806 PHE 0.022 0.001 PHE D1095 TRP 0.015 0.001 TRP B 432 HIS 0.005 0.001 HIS B1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (31220) covalent geometry : angle 0.49196 / 0.26 (42549) SS BOND : bond 0.00250 / 0.12 ( 9) SS BOND : angle 2.14143 / 1.24 ( 18) hydrogen bonds : bond 0.04142 / 2.77 ( 1060) hydrogen bonds : angle 4.23294 / 2.97 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8908 (ptt) cc_final: 0.8478 (ptt) REVERT: A 810 MET cc_start: 0.8804 (tpp) cc_final: 0.8564 (tpp) REVERT: A 1100 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8259 (tt) REVERT: B 514 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6962 (tpp) REVERT: B 1196 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7988 (t-100) REVERT: C 557 MET cc_start: 0.9227 (mmt) cc_final: 0.9008 (mmt) REVERT: C 603 MET cc_start: 0.9019 (mtm) cc_final: 0.8707 (mtm) REVERT: C 662 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9455 (m) REVERT: C 780 MET cc_start: 0.7988 (mmp) cc_final: 0.7781 (mmp) REVERT: D 561 ARG cc_start: 0.3649 (OUTLIER) cc_final: 0.2809 (mmp80) REVERT: E 464 MET cc_start: 0.8367 (ttm) cc_final: 0.8077 (tpt) REVERT: F 73 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8058 (t0) REVERT: F 456 MET cc_start: 0.8772 (ptp) cc_final: 0.8409 (ptt) REVERT: F 461 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5828 (tp) REVERT: F 542 MET cc_start: 0.7159 (mmm) cc_final: 0.6882 (mmm) REVERT: F 603 MET cc_start: 0.7670 (mmm) cc_final: 0.7468 (mmm) outliers start: 48 outliers final: 31 residues processed: 152 average time/residue: 0.1723 time to fit residues: 45.7605 Evaluate side-chains 145 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1162 MET Chi-restraints excluded: chain B residue 1196 TRP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 247 optimal weight: 20.0000 chunk 133 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 212 optimal weight: 0.3980 chunk 198 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 339 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 393 optimal weight: 20.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN B 621 HIS C1118 HIS ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.070399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.046969 restraints weight = 185451.803| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.86 r_work: 0.2859 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31229 Z= 0.193 Angle : 0.537 9.942 42567 Z= 0.282 Chirality : 0.043 0.145 4804 Planarity : 0.004 0.069 5469 Dihedral : 4.516 59.482 4367 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.74 % Allowed : 9.08 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.38 (0.13), residues: 4043 helix: 1.31 (0.17), residues: 901 sheet: 0.46 (0.16), residues: 1042 loop : -1.38 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 555 TYR 0.011 0.001 TYR B 806 PHE 0.015 0.001 PHE A1194 TRP 0.014 0.001 TRP D 876 HIS 0.010 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (31220) covalent geometry : angle 0.53525 / 0.28 (42549) SS BOND : bond 0.00386 / 0.22 ( 9) SS BOND : angle 2.30033 / 1.30 ( 18) hydrogen bonds : bond 0.04657 / 3.12 ( 1060) hydrogen bonds : angle 4.28182 / 3.00 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 412 MET cc_start: 0.8970 (ptt) cc_final: 0.8634 (ptt) REVERT: A 810 MET cc_start: 0.8769 (tpp) cc_final: 0.8498 (tpp) REVERT: A 1100 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8096 (tt) REVERT: B 514 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6914 (tpp) REVERT: B 1196 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7889 (t-100) REVERT: C 662 VAL cc_start: 0.9658 (OUTLIER) cc_final: 0.9411 (m) REVERT: D 561 ARG cc_start: 0.3619 (OUTLIER) cc_final: 0.2898 (mmp80) REVERT: E 464 MET cc_start: 0.8263 (ttm) cc_final: 0.8013 (tpt) REVERT: F 456 MET cc_start: 0.8790 (ptp) cc_final: 0.8428 (ptt) REVERT: F 461 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5943 (tp) REVERT: F 603 MET cc_start: 0.7477 (mmm) cc_final: 0.7241 (mmm) outliers start: 52 outliers final: 35 residues processed: 152 average time/residue: 0.1689 time to fit residues: 45.7106 Evaluate side-chains 147 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1162 MET Chi-restraints excluded: chain B residue 1196 TRP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 291 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 399 optimal weight: 0.0980 chunk 26 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.070692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.047455 restraints weight = 186683.588| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 5.80 r_work: 0.2887 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31229 Z= 0.137 Angle : 0.496 11.112 42567 Z= 0.258 Chirality : 0.042 0.140 4804 Planarity : 0.003 0.063 5469 Dihedral : 4.177 59.224 4364 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.47 % Allowed : 9.38 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.17 (0.13), residues: 4043 helix: 1.61 (0.18), residues: 896 sheet: 0.56 (0.16), residues: 1043 loop : -1.28 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 555 TYR 0.010 0.001 TYR B 806 PHE 0.018 0.001 PHE D1095 TRP 0.012 0.001 TRP B 368 HIS 0.007 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (31220) covalent geometry : angle 0.49464 / 0.26 (42549) SS BOND : bond 0.00764 / 0.32 ( 9) SS BOND : angle 1.95294 / 1.07 ( 18) hydrogen bonds : bond 0.03911 / 2.64 ( 1060) hydrogen bonds : angle 4.09111 / 2.86 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 412 MET cc_start: 0.8961 (ptt) cc_final: 0.8456 (ptt) REVERT: A 994 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 1100 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8101 (tt) REVERT: B 412 MET cc_start: 0.9169 (pmm) cc_final: 0.8873 (pmm) REVERT: B 511 MET cc_start: 0.6804 (mtp) cc_final: 0.6069 (ptm) REVERT: B 514 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.5858 (mmt) REVERT: C 557 MET cc_start: 0.9172 (mmt) cc_final: 0.8933 (mmt) REVERT: C 603 MET cc_start: 0.8894 (mtt) cc_final: 0.8442 (mtm) REVERT: C 662 VAL cc_start: 0.9665 (OUTLIER) cc_final: 0.9407 (m) REVERT: D 561 ARG cc_start: 0.3823 (OUTLIER) cc_final: 0.3181 (mmp80) REVERT: F 456 MET cc_start: 0.8811 (ptp) cc_final: 0.8463 (ptt) REVERT: F 461 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5993 (tp) REVERT: F 542 MET cc_start: 0.7227 (mmm) cc_final: 0.6951 (mmm) REVERT: F 603 MET cc_start: 0.7525 (mmm) cc_final: 0.7325 (mmm) outliers start: 44 outliers final: 33 residues processed: 143 average time/residue: 0.1698 time to fit residues: 43.1751 Evaluate side-chains 146 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1162 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 105 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 397 optimal weight: 40.0000 chunk 197 optimal weight: 6.9990 chunk 326 optimal weight: 50.0000 chunk 291 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 400 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 404 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.046643 restraints weight = 185619.956| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 5.72 r_work: 0.2868 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31229 Z= 0.216 Angle : 0.564 10.804 42567 Z= 0.292 Chirality : 0.044 0.145 4804 Planarity : 0.004 0.064 5469 Dihedral : 4.214 35.293 4360 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.57 % Allowed : 9.68 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.28 (0.13), residues: 4043 helix: 1.43 (0.17), residues: 896 sheet: 0.47 (0.16), residues: 1053 loop : -1.30 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1069 TYR 0.013 0.001 TYR E 371 PHE 0.016 0.001 PHE A 405 TRP 0.016 0.001 TRP D 876 HIS 0.011 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (31220) covalent geometry : angle 0.56302 / 0.29 (42549) SS BOND : bond 0.00382 / 0.19 ( 9) SS BOND : angle 1.83500 / 0.98 ( 18) hydrogen bonds : bond 0.04658 / 3.13 ( 1060) hydrogen bonds : angle 4.27953 / 2.99 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 412 MET cc_start: 0.8990 (ptt) cc_final: 0.8483 (ptt) REVERT: A 810 MET cc_start: 0.8721 (tpt) cc_final: 0.8491 (tpp) REVERT: A 961 MET cc_start: 0.8902 (mtp) cc_final: 0.8638 (mtp) REVERT: A 994 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 1100 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8061 (tt) REVERT: B 514 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6109 (mmt) REVERT: B 1196 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7906 (t-100) REVERT: C 557 MET cc_start: 0.9184 (mmt) cc_final: 0.8863 (mmt) REVERT: C 603 MET cc_start: 0.8952 (mtt) cc_final: 0.8487 (mtm) REVERT: C 662 VAL cc_start: 0.9634 (OUTLIER) cc_final: 0.9374 (m) REVERT: D 561 ARG cc_start: 0.3625 (OUTLIER) cc_final: 0.2905 (mmp80) REVERT: F 456 MET cc_start: 0.8894 (ptp) cc_final: 0.8505 (ptt) REVERT: F 461 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5828 (tp) outliers start: 47 outliers final: 33 residues processed: 147 average time/residue: 0.1687 time to fit residues: 43.7704 Evaluate side-chains 146 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1162 MET Chi-restraints excluded: chain B residue 1196 TRP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 268 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 356 optimal weight: 30.0000 chunk 362 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.070380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.048097 restraints weight = 187785.484| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 5.66 r_work: 0.2893 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31229 Z= 0.181 Angle : 0.531 11.363 42567 Z= 0.275 Chirality : 0.043 0.140 4804 Planarity : 0.003 0.065 5469 Dihedral : 4.136 35.406 4360 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.40 % Allowed : 9.98 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: -0.23 (0.13), residues: 4043 helix: 1.49 (0.18), residues: 904 sheet: 0.51 (0.16), residues: 1058 loop : -1.29 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1069 TYR 0.011 0.001 TYR C 718 PHE 0.016 0.001 PHE D1095 TRP 0.013 0.001 TRP E 394 HIS 0.010 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (31220) covalent geometry : angle 0.53000 / 0.27 (42549) SS BOND : bond 0.00311 / 0.16 ( 9) SS BOND : angle 1.86716 / 1.03 ( 18) hydrogen bonds : bond 0.04243 / 2.86 ( 1060) hydrogen bonds : angle 4.17806 / 2.92 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 412 MET cc_start: 0.8953 (ptt) cc_final: 0.8477 (ptt) REVERT: A 810 MET cc_start: 0.8636 (tpt) cc_final: 0.8411 (tpp) REVERT: A 994 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 1100 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8138 (tt) REVERT: B 514 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6105 (mmt) REVERT: B 1196 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7917 (t-100) REVERT: C 557 MET cc_start: 0.9176 (mmt) cc_final: 0.8970 (mmt) REVERT: C 603 MET cc_start: 0.8938 (mtt) cc_final: 0.8501 (mpp) REVERT: C 662 VAL cc_start: 0.9675 (OUTLIER) cc_final: 0.9414 (m) REVERT: D 561 ARG cc_start: 0.3939 (OUTLIER) cc_final: 0.3321 (mmp80) REVERT: E 138 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9246 (tm-30) REVERT: F 456 MET cc_start: 0.8884 (ptp) cc_final: 0.8523 (ptt) REVERT: F 461 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6014 (tp) REVERT: F 542 MET cc_start: 0.7302 (mmm) cc_final: 0.6979 (mmm) outliers start: 42 outliers final: 34 residues processed: 144 average time/residue: 0.1702 time to fit residues: 43.4483 Evaluate side-chains 148 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1048 CYS Chi-restraints excluded: chain B residue 1162 MET Chi-restraints excluded: chain B residue 1196 TRP Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 823 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 72 TYR Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 672 CYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 687 VAL Chi-restraints excluded: chain F residue 699 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 139 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 253 optimal weight: 1.9990 chunk 405 optimal weight: 0.9980 chunk 353 optimal weight: 30.0000 chunk 185 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1069 ASN C1118 HIS ** F 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.070917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.048323 restraints weight = 190661.775| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 6.12 r_work: 0.2905 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31229 Z= 0.103 Angle : 0.484 11.422 42567 Z= 0.248 Chirality : 0.041 0.137 4804 Planarity : 0.003 0.060 5469 Dihedral : 3.846 35.505 4360 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.27 % Allowed : 10.25 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % 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: 0.01 (0.14), residues: 4043 helix: 1.76 (0.18), residues: 905 sheet: 0.63 (0.16), residues: 1049 loop : -1.15 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 411 TYR 0.009 0.001 TYR B 806 PHE 0.020 0.001 PHE A 962 TRP 0.013 0.001 TRP A 368 HIS 0.004 0.001 HIS D1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (31220) covalent geometry : angle 0.48311 / 0.25 (42549) SS BOND : bond 0.00319 / 0.16 ( 9) SS BOND : angle 1.73921 / 0.99 ( 18) hydrogen bonds : bond 0.03398 / 2.29 ( 1060) hydrogen bonds : angle 3.95678 / 2.77 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12381.89 seconds wall clock time: 211 minutes 26.33 seconds (12686.33 seconds total)