Starting phenix.real_space_refine on Thu Dec 26 03:25:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyh_37928/12_2024/8wyh_37928_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4448 atoms to isotropic. 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 195 5.16 5 C 24889 2.51 5 N 6443 2.21 5 O 7325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 38852 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8083 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8076 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8083 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "X" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "Z" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 21.53, per 1000 atoms: 0.55 Number of scatterers: 38852 At special positions: 0 Unit cell: (171, 161.595, 241.965, 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 195 16.00 O 7325 8.00 N 6443 7.00 C 24889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.04 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 670 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 524 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 589 " distance=2.06 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.04 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 524 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.00 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS T 133 " - pdb=" SG CYS T 141 " distance=2.03 Simple disulfide: pdb=" SG CYS T 344 " - pdb=" SG CYS T 361 " distance=2.04 Simple disulfide: pdb=" SG CYS T 530 " - pdb=" SG CYS T 542 " distance=2.04 Simple disulfide: pdb=" SG CYS X 133 " - pdb=" SG CYS X 141 " distance=2.03 Simple disulfide: pdb=" SG CYS X 344 " - pdb=" SG CYS X 361 " distance=2.04 Simple disulfide: pdb=" SG CYS X 530 " - pdb=" SG CYS X 542 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 133 " - pdb=" SG CYS Z 141 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 344 " - pdb=" SG CYS Z 361 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 530 " - pdb=" SG CYS Z 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 4.7 seconds 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9184 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 54 sheets defined 32.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.842A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.935A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 780 removed outlier: 3.609A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 869 through 878 removed outlier: 3.732A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 947 through 964 removed outlier: 4.106A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1000 removed outlier: 4.050A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1032 removed outlier: 3.696A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1145 removed outlier: 3.756A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.516A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 753 through 757 Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.572A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 removed outlier: 3.687A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 869 through 882 removed outlier: 3.585A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.515A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.724A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.679A pdb=" N HIS B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.632A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 990 removed outlier: 3.613A pdb=" N ALA B 989 " --> pdb=" O PRO B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1032 removed outlier: 3.532A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1145 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 750 through 754 removed outlier: 3.523A pdb=" N LEU C 754 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.744A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.833A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.584A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.573A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 961 removed outlier: 3.758A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 990 through 1032 removed outlier: 4.435A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing helix chain 'T' and resid 25 through 36 removed outlier: 3.599A pdb=" N ASP T 30 " --> pdb=" O LYS T 26 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS T 34 " --> pdb=" O ASP T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 53 removed outlier: 4.706A pdb=" N ALA T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER T 47 " --> pdb=" O SER T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 79 removed outlier: 4.198A pdb=" N ALA T 65 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER T 70 " --> pdb=" O GLY T 66 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE T 72 " --> pdb=" O LYS T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 88 Processing helix chain 'T' and resid 90 through 102 removed outlier: 4.283A pdb=" N LEU T 100 " --> pdb=" O GLN T 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN T 102 " --> pdb=" O GLN T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 130 removed outlier: 3.886A pdb=" N ASN T 121 " --> pdb=" O ASN T 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR T 122 " --> pdb=" O THR T 118 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET T 123 " --> pdb=" O ILE T 119 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER T 128 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR T 129 " --> pdb=" O THR T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 153 Processing helix chain 'T' and resid 159 through 167 Processing helix chain 'T' and resid 173 through 175 No H-bonds generated for 'chain 'T' and resid 173 through 175' Processing helix chain 'T' and resid 176 through 194 removed outlier: 4.238A pdb=" N VAL T 185 " --> pdb=" O GLU T 181 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU T 186 " --> pdb=" O GLU T 182 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN T 188 " --> pdb=" O VAL T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 198 through 204 Processing helix chain 'T' and resid 220 through 234 removed outlier: 3.706A pdb=" N GLU T 224 " --> pdb=" O GLY T 220 " (cutoff:3.500A) Processing helix chain 'T' and resid 234 through 251 removed outlier: 3.574A pdb=" N HIS T 239 " --> pdb=" O PRO T 235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA T 246 " --> pdb=" O ALA T 242 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET T 249 " --> pdb=" O ARG T 245 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA T 251 " --> pdb=" O LYS T 247 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 301 Processing helix chain 'T' and resid 303 through 318 removed outlier: 3.789A pdb=" N ILE T 307 " --> pdb=" O ASP T 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE T 308 " --> pdb=" O ALA T 304 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 309 " --> pdb=" O GLN T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 368 through 382 removed outlier: 3.711A pdb=" N HIS T 373 " --> pdb=" O PHE T 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY T 377 " --> pdb=" O HIS T 373 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS T 378 " --> pdb=" O HIS T 374 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE T 379 " --> pdb=" O GLU T 375 " (cutoff:3.500A) Processing helix chain 'T' and resid 384 through 388 removed outlier: 3.656A pdb=" N ALA T 387 " --> pdb=" O ALA T 384 " (cutoff:3.500A) Processing helix chain 'T' and resid 389 through 393 removed outlier: 3.631A pdb=" N ARG T 393 " --> pdb=" O PHE T 390 " (cutoff:3.500A) Processing helix chain 'T' and resid 399 through 404 removed outlier: 3.750A pdb=" N ALA T 403 " --> pdb=" O GLY T 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL T 404 " --> pdb=" O PHE T 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 399 through 404' Processing helix chain 'T' and resid 407 through 412 Processing helix chain 'T' and resid 414 through 421 Processing helix chain 'T' and resid 431 through 443 removed outlier: 3.713A pdb=" N GLU T 435 " --> pdb=" O ASP T 431 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN T 437 " --> pdb=" O GLU T 433 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU T 440 " --> pdb=" O ILE T 436 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS T 441 " --> pdb=" O ASN T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 449 through 466 removed outlier: 3.967A pdb=" N MET T 455 " --> pdb=" O PRO T 451 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU T 456 " --> pdb=" O PHE T 452 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU T 457 " --> pdb=" O THR T 453 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS T 465 " --> pdb=" O TRP T 461 " (cutoff:3.500A) Processing helix chain 'T' and resid 472 through 483 Processing helix chain 'T' and resid 504 through 508 Processing helix chain 'T' and resid 521 through 527 Processing helix chain 'T' and resid 530 through 534 Processing helix chain 'T' and resid 538 through 542 Processing helix chain 'T' and resid 548 through 559 removed outlier: 3.562A pdb=" N PHE T 555 " --> pdb=" O GLY T 551 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET T 557 " --> pdb=" O LYS T 553 " (cutoff:3.500A) Processing helix chain 'T' and resid 565 through 573 removed outlier: 3.901A pdb=" N GLU T 571 " --> pdb=" O THR T 567 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL T 573 " --> pdb=" O ALA T 569 " (cutoff:3.500A) Processing helix chain 'T' and resid 580 through 588 removed outlier: 4.661A pdb=" N LEU T 584 " --> pdb=" O ASN T 580 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR T 587 " --> pdb=" O PRO T 583 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE T 588 " --> pdb=" O LEU T 584 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 598 Processing helix chain 'X' and resid 25 through 36 removed outlier: 3.599A pdb=" N ASP X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS X 34 " --> pdb=" O ASP X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 53 removed outlier: 4.708A pdb=" N ALA X 46 " --> pdb=" O GLN X 42 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER X 47 " --> pdb=" O SER X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 79 removed outlier: 4.198A pdb=" N ALA X 65 " --> pdb=" O ASN X 61 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER X 70 " --> pdb=" O GLY X 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA X 71 " --> pdb=" O ASP X 67 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE X 72 " --> pdb=" O LYS X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'X' and resid 90 through 102 removed outlier: 4.284A pdb=" N LEU X 100 " --> pdb=" O GLN X 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN X 102 " --> pdb=" O GLN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 130 removed outlier: 3.886A pdb=" N ASN X 121 " --> pdb=" O ASN X 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 122 " --> pdb=" O THR X 118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET X 123 " --> pdb=" O ILE X 119 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER X 128 " --> pdb=" O SER X 124 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR X 129 " --> pdb=" O THR X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 153 Processing helix chain 'X' and resid 159 through 167 Processing helix chain 'X' and resid 173 through 175 No H-bonds generated for 'chain 'X' and resid 173 through 175' Processing helix chain 'X' and resid 176 through 194 removed outlier: 4.238A pdb=" N VAL X 185 " --> pdb=" O GLU X 181 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU X 186 " --> pdb=" O GLU X 182 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN X 188 " --> pdb=" O VAL X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 198 through 204 Processing helix chain 'X' and resid 220 through 234 removed outlier: 3.706A pdb=" N GLU X 224 " --> pdb=" O GLY X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 251 removed outlier: 3.574A pdb=" N HIS X 239 " --> pdb=" O PRO X 235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA X 246 " --> pdb=" O ALA X 242 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET X 249 " --> pdb=" O ARG X 245 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 293 through 301 Processing helix chain 'X' and resid 303 through 318 removed outlier: 3.788A pdb=" N ILE X 307 " --> pdb=" O ASP X 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE X 308 " --> pdb=" O ALA X 304 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS X 309 " --> pdb=" O GLN X 305 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 382 removed outlier: 3.710A pdb=" N HIS X 373 " --> pdb=" O PHE X 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY X 377 " --> pdb=" O HIS X 373 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS X 378 " --> pdb=" O HIS X 374 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE X 379 " --> pdb=" O GLU X 375 " (cutoff:3.500A) Processing helix chain 'X' and resid 384 through 388 removed outlier: 3.656A pdb=" N ALA X 387 " --> pdb=" O ALA X 384 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 393 removed outlier: 3.630A pdb=" N ARG X 393 " --> pdb=" O PHE X 390 " (cutoff:3.500A) Processing helix chain 'X' and resid 399 through 404 removed outlier: 3.749A pdb=" N ALA X 403 " --> pdb=" O GLY X 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL X 404 " --> pdb=" O PHE X 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 399 through 404' Processing helix chain 'X' and resid 407 through 412 Processing helix chain 'X' and resid 414 through 421 Processing helix chain 'X' and resid 431 through 443 removed outlier: 3.962A pdb=" N GLU X 435 " --> pdb=" O ASP X 431 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN X 437 " --> pdb=" O GLU X 433 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU X 440 " --> pdb=" O ILE X 436 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS X 441 " --> pdb=" O ASN X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 466 removed outlier: 3.967A pdb=" N MET X 455 " --> pdb=" O PRO X 451 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU X 456 " --> pdb=" O PHE X 452 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU X 457 " --> pdb=" O THR X 453 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS X 465 " --> pdb=" O TRP X 461 " (cutoff:3.500A) Processing helix chain 'X' and resid 472 through 483 Processing helix chain 'X' and resid 504 through 508 Processing helix chain 'X' and resid 521 through 527 Processing helix chain 'X' and resid 530 through 534 Processing helix chain 'X' and resid 538 through 542 Processing helix chain 'X' and resid 548 through 559 removed outlier: 3.563A pdb=" N PHE X 555 " --> pdb=" O GLY X 551 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET X 557 " --> pdb=" O LYS X 553 " (cutoff:3.500A) Processing helix chain 'X' and resid 565 through 573 removed outlier: 3.899A pdb=" N GLU X 571 " --> pdb=" O THR X 567 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL X 573 " --> pdb=" O ALA X 569 " (cutoff:3.500A) Processing helix chain 'X' and resid 580 through 588 removed outlier: 4.661A pdb=" N LEU X 584 " --> pdb=" O ASN X 580 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR X 587 " --> pdb=" O PRO X 583 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE X 588 " --> pdb=" O LEU X 584 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 598 Processing helix chain 'Z' and resid 25 through 36 removed outlier: 3.599A pdb=" N ASP Z 30 " --> pdb=" O LYS Z 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS Z 34 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 53 removed outlier: 4.707A pdb=" N ALA Z 46 " --> pdb=" O GLN Z 42 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER Z 47 " --> pdb=" O SER Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 79 removed outlier: 4.198A pdb=" N ALA Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER Z 70 " --> pdb=" O GLY Z 66 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA Z 71 " --> pdb=" O ASP Z 67 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE Z 72 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 88 Processing helix chain 'Z' and resid 90 through 102 removed outlier: 4.284A pdb=" N LEU Z 100 " --> pdb=" O GLN Z 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN Z 102 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 109 through 130 removed outlier: 3.886A pdb=" N ASN Z 121 " --> pdb=" O ASN Z 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR Z 122 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET Z 123 " --> pdb=" O ILE Z 119 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER Z 128 " --> pdb=" O SER Z 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR Z 129 " --> pdb=" O THR Z 125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 153 Processing helix chain 'Z' and resid 159 through 167 Processing helix chain 'Z' and resid 173 through 175 No H-bonds generated for 'chain 'Z' and resid 173 through 175' Processing helix chain 'Z' and resid 176 through 194 removed outlier: 4.238A pdb=" N VAL Z 185 " --> pdb=" O GLU Z 181 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU Z 186 " --> pdb=" O GLU Z 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN Z 188 " --> pdb=" O VAL Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 198 through 204 Processing helix chain 'Z' and resid 220 through 234 removed outlier: 3.706A pdb=" N GLU Z 224 " --> pdb=" O GLY Z 220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 251 removed outlier: 3.574A pdb=" N HIS Z 239 " --> pdb=" O PRO Z 235 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Z 246 " --> pdb=" O ALA Z 242 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET Z 249 " --> pdb=" O ARG Z 245 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 293 through 301 Processing helix chain 'Z' and resid 303 through 318 removed outlier: 3.789A pdb=" N ILE Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS Z 309 " --> pdb=" O GLN Z 305 " (cutoff:3.500A) Processing helix chain 'Z' and resid 368 through 382 removed outlier: 3.711A pdb=" N HIS Z 373 " --> pdb=" O PHE Z 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY Z 377 " --> pdb=" O HIS Z 373 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS Z 378 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE Z 379 " --> pdb=" O GLU Z 375 " (cutoff:3.500A) Processing helix chain 'Z' and resid 384 through 388 removed outlier: 3.656A pdb=" N ALA Z 387 " --> pdb=" O ALA Z 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 393 removed outlier: 3.631A pdb=" N ARG Z 393 " --> pdb=" O PHE Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 399 through 404 removed outlier: 3.750A pdb=" N ALA Z 403 " --> pdb=" O GLY Z 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL Z 404 " --> pdb=" O PHE Z 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 399 through 404' Processing helix chain 'Z' and resid 407 through 412 Processing helix chain 'Z' and resid 414 through 421 Processing helix chain 'Z' and resid 431 through 443 removed outlier: 3.577A pdb=" N GLU Z 435 " --> pdb=" O ASP Z 431 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN Z 437 " --> pdb=" O GLU Z 433 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU Z 440 " --> pdb=" O ILE Z 436 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS Z 441 " --> pdb=" O ASN Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 449 through 466 removed outlier: 3.967A pdb=" N MET Z 455 " --> pdb=" O PRO Z 451 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU Z 456 " --> pdb=" O PHE Z 452 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU Z 457 " --> pdb=" O THR Z 453 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS Z 465 " --> pdb=" O TRP Z 461 " (cutoff:3.500A) Processing helix chain 'Z' and resid 472 through 483 Processing helix chain 'Z' and resid 504 through 508 Processing helix chain 'Z' and resid 521 through 527 Processing helix chain 'Z' and resid 530 through 534 Processing helix chain 'Z' and resid 538 through 542 Processing helix chain 'Z' and resid 548 through 559 removed outlier: 3.563A pdb=" N PHE Z 555 " --> pdb=" O GLY Z 551 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET Z 557 " --> pdb=" O LYS Z 553 " (cutoff:3.500A) Processing helix chain 'Z' and resid 565 through 573 removed outlier: 3.901A pdb=" N GLU Z 571 " --> pdb=" O THR Z 567 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Z 573 " --> pdb=" O ALA Z 569 " (cutoff:3.500A) Processing helix chain 'Z' and resid 580 through 588 removed outlier: 4.661A pdb=" N LEU Z 584 " --> pdb=" O ASN Z 580 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR Z 587 " --> pdb=" O PRO Z 583 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE Z 588 " --> pdb=" O LEU Z 584 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.601A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 4.215A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.867A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 205 removed outlier: 7.134A pdb=" N ILE A 203 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.518A pdb=" N GLY A 592 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.811A pdb=" N VAL A 538 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 545 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.538A pdb=" N LEU A 512 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 574 through 576 Processing sheet with id=AB5, first strand: chain 'A' and resid 653 through 654 removed outlier: 5.975A pdb=" N GLU A 653 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR A 696 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 691 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.431A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.780A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.780A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.957A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.675A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 203 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.701A pdb=" N VAL B 594 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN B 317 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 592 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B 593 " --> pdb=" O GLN B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.538A pdb=" N LEU B 512 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.531A pdb=" N VAL B 538 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 653 through 654 removed outlier: 6.679A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.496A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.555A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.437A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.941A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.862A pdb=" N VAL C 594 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN C 317 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 592 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AE4, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 540 removed outlier: 3.522A pdb=" N GLY C 547 " --> pdb=" O PHE C 540 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 576 Processing sheet with id=AE8, first strand: chain 'C' and resid 653 through 654 removed outlier: 6.103A pdb=" N GLU C 653 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR C 696 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 669 " --> pdb=" O ILE C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.616A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.689A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.745A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'T' and resid 131 through 134 removed outlier: 6.121A pdb=" N GLU T 140 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 348 through 349 removed outlier: 3.539A pdb=" N ARG T 357 " --> pdb=" O TRP T 349 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 131 through 134 removed outlier: 6.121A pdb=" N GLU X 140 " --> pdb=" O ASN X 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 348 through 349 removed outlier: 3.539A pdb=" N ARG X 357 " --> pdb=" O TRP X 349 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 131 through 134 removed outlier: 6.122A pdb=" N GLU Z 140 " --> pdb=" O ASN Z 134 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 348 through 349 removed outlier: 3.539A pdb=" N ARG Z 357 " --> pdb=" O TRP Z 349 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 2994 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: 17.90 Time building geometry restraints manager: 12.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6425 1.28 - 1.42: 10554 1.42 - 1.55: 22583 1.55 - 1.69: 0 1.69 - 1.82: 282 Bond restraints: 39844 Sorted by residual: bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.149 0.084 1.24e-02 6.50e+03 4.56e+01 bond pdb=" CA SER A 316 " pdb=" CB SER A 316 " ideal model delta sigma weight residual 1.542 1.485 0.058 8.90e-03 1.26e+04 4.19e+01 bond pdb=" C PRO B 715 " pdb=" O PRO B 715 " ideal model delta sigma weight residual 1.234 1.162 0.071 1.14e-02 7.69e+03 3.90e+01 bond pdb=" C PRO C 897 " pdb=" O PRO C 897 " ideal model delta sigma weight residual 1.233 1.159 0.073 1.24e-02 6.50e+03 3.51e+01 bond pdb=" CA SER A 884 " pdb=" CB SER A 884 " ideal model delta sigma weight residual 1.536 1.451 0.085 1.46e-02 4.69e+03 3.42e+01 ... (remaining 39839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 49082 3.09 - 6.18: 4799 6.18 - 9.27: 265 9.27 - 12.36: 29 12.36 - 15.45: 4 Bond angle restraints: 54179 Sorted by residual: angle pdb=" N LEU X 444 " pdb=" CA LEU X 444 " pdb=" C LEU X 444 " ideal model delta sigma weight residual 114.64 100.86 13.78 1.52e+00 4.33e-01 8.22e+01 angle pdb=" N LEU T 444 " pdb=" CA LEU T 444 " pdb=" C LEU T 444 " ideal model delta sigma weight residual 114.64 100.90 13.74 1.52e+00 4.33e-01 8.17e+01 angle pdb=" N LEU Z 444 " pdb=" CA LEU Z 444 " pdb=" C LEU Z 444 " ideal model delta sigma weight residual 114.64 100.90 13.74 1.52e+00 4.33e-01 8.17e+01 angle pdb=" N PHE A 540 " pdb=" CA PHE A 540 " pdb=" C PHE A 540 " ideal model delta sigma weight residual 108.13 123.58 -15.45 1.72e+00 3.38e-01 8.06e+01 angle pdb=" N THR X 434 " pdb=" CA THR X 434 " pdb=" C THR X 434 " ideal model delta sigma weight residual 112.72 101.29 11.43 1.28e+00 6.10e-01 7.98e+01 ... (remaining 54174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18625 17.99 - 35.99: 2659 35.99 - 53.98: 1661 53.98 - 71.98: 521 71.98 - 89.97: 169 Dihedral angle restraints: 23635 sinusoidal: 9380 harmonic: 14255 Sorted by residual: dihedral pdb=" CD ARG C 236 " pdb=" NE ARG C 236 " pdb=" CZ ARG C 236 " pdb=" NH1 ARG C 236 " ideal model delta sinusoidal sigma weight residual 0.00 -89.97 89.97 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG X 177 " pdb=" NE ARG X 177 " pdb=" CZ ARG X 177 " pdb=" NH1 ARG X 177 " ideal model delta sinusoidal sigma weight residual 0.00 -89.41 89.41 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CD ARG Z 177 " pdb=" NE ARG Z 177 " pdb=" CZ ARG Z 177 " pdb=" NH1 ARG Z 177 " ideal model delta sinusoidal sigma weight residual 0.00 -89.34 89.34 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 23632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2376 0.073 - 0.146: 2337 0.146 - 0.219: 1005 0.219 - 0.292: 212 0.292 - 0.364: 23 Chirality restraints: 5953 Sorted by residual: chirality pdb=" CA LEU Z 444 " pdb=" N LEU Z 444 " pdb=" C LEU Z 444 " pdb=" CB LEU Z 444 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA LEU T 444 " pdb=" N LEU T 444 " pdb=" C LEU T 444 " pdb=" CB LEU T 444 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA LEU X 444 " pdb=" N LEU X 444 " pdb=" C LEU X 444 " pdb=" CB LEU X 444 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 5950 not shown) Planarity restraints: 7000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 357 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 357 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 357 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 357 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 357 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 161 " -1.102 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG X 161 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG X 161 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG X 161 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG X 161 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 161 " -1.102 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG Z 161 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG Z 161 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 161 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 161 " -0.017 2.00e-02 2.50e+03 ... (remaining 6997 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6780 2.74 - 3.28: 40082 3.28 - 3.82: 62624 3.82 - 4.36: 86121 4.36 - 4.90: 131365 Nonbonded interactions: 326972 Sorted by model distance: nonbonded pdb=" NH2 ARG C 357 " pdb=" O ILE C 358 " model vdw 2.200 3.120 nonbonded pdb=" O GLU X 22 " pdb=" N GLN X 24 " model vdw 2.238 3.120 nonbonded pdb=" O GLU T 22 " pdb=" N GLN T 24 " model vdw 2.238 3.120 nonbonded pdb=" O GLU Z 22 " pdb=" N GLN Z 24 " model vdw 2.238 3.120 nonbonded pdb=" O GLN B 321 " pdb=" N THR B 323 " model vdw 2.267 3.120 ... (remaining 326967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 319 or resid 321 through 1147)) selection = chain 'B' selection = (chain 'C' and (resid 20 through 319 or resid 321 through 1147)) } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.060 Extract box with map and model: 1.530 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 88.600 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:15.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 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 : 0.013 0.085 39844 Z= 0.835 Angle : 1.859 15.446 54179 Z= 1.318 Chirality : 0.114 0.364 5953 Planarity : 0.049 0.494 7000 Dihedral : 24.313 89.969 14328 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 41.88 Ramachandran Plot: Outliers : 12.54 % Allowed : 24.62 % Favored : 62.85 % Rotamer: Outliers : 35.11 % Allowed : 18.14 % Favored : 46.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.18 (0.08), residues: 4818 helix: -5.08 (0.05), residues: 1574 sheet: -2.80 (0.20), residues: 494 loop : -5.22 (0.08), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 566 HIS 0.010 0.002 HIS B1048 PHE 0.038 0.003 PHE A1121 TYR 0.043 0.003 TYR B 37 ARG 0.009 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2049 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1506 poor density : 543 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 66 HIS cc_start: 0.4494 (OUTLIER) cc_final: 0.4155 (t-90) REVERT: A 102 ARG cc_start: 0.4558 (OUTLIER) cc_final: 0.4230 (mmt-90) REVERT: A 129 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6397 (ttmm) REVERT: A 141 LEU cc_start: 0.3473 (OUTLIER) cc_final: 0.2630 (tt) REVERT: A 213 ARG cc_start: 0.2740 (OUTLIER) cc_final: -0.0406 (mtm180) REVERT: A 317 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (m-40) REVERT: A 355 ARG cc_start: 0.2096 (OUTLIER) cc_final: 0.1599 (mmt180) REVERT: A 428 ASP cc_start: 0.4591 (OUTLIER) cc_final: 0.4373 (m-30) REVERT: A 468 ILE cc_start: 0.1465 (OUTLIER) cc_final: 0.1135 (tt) REVERT: A 740 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (ttm) REVERT: A 776 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: A 780 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 790 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7919 (mtpt) REVERT: A 811 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7033 (ptpt) REVERT: A 849 LEU cc_start: 0.3458 (OUTLIER) cc_final: 0.3100 (tt) REVERT: A 942 PRO cc_start: 0.7020 (OUTLIER) cc_final: 0.6434 (Cg_exo) REVERT: A 947 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (mtpt) REVERT: A 1111 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: B 21 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 32 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: B 80 ASP cc_start: 0.4389 (OUTLIER) cc_final: 0.4076 (m-30) REVERT: B 81 ASN cc_start: 0.6284 (OUTLIER) cc_final: 0.6021 (m110) REVERT: B 96 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.4687 (tm-30) REVERT: B 110 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6120 (tt) REVERT: B 116 SER cc_start: 0.6374 (OUTLIER) cc_final: 0.6139 (m) REVERT: B 125 ASN cc_start: 0.6418 (OUTLIER) cc_final: 0.6167 (m110) REVERT: B 187 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5468 (tptm) REVERT: B 213 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5071 (tpt170) REVERT: B 217 GLN cc_start: 0.3696 (OUTLIER) cc_final: 0.3488 (mp10) REVERT: B 238 GLN cc_start: 0.8125 (tt0) cc_final: 0.7809 (tt0) REVERT: B 329 PHE cc_start: 0.2642 (OUTLIER) cc_final: 0.1672 (t80) REVERT: B 354 ASN cc_start: 0.1742 (OUTLIER) cc_final: 0.1485 (m-40) REVERT: B 388 ASN cc_start: 0.2043 (OUTLIER) cc_final: 0.1745 (t0) REVERT: B 462 LYS cc_start: 0.3624 (OUTLIER) cc_final: 0.2213 (pptt) REVERT: B 466 ARG cc_start: 0.0305 (OUTLIER) cc_final: -0.0843 (ttt180) REVERT: B 471 GLU cc_start: 0.2226 (OUTLIER) cc_final: 0.1765 (tm-30) REVERT: B 481 LYS cc_start: 0.3428 (OUTLIER) cc_final: 0.2193 (pttt) REVERT: B 483 LYS cc_start: 0.3887 (OUTLIER) cc_final: 0.2880 (mptt) REVERT: B 530 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (m) REVERT: B 579 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6044 (mt0) REVERT: B 750 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (t) REVERT: B 895 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: B 984 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7112 (tp) REVERT: B 1028 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8903 (mtpp) REVERT: B 1092 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6979 (tm-30) REVERT: B 1136 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 1141 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 132 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: C 191 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: C 202 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7595 (mmtm) REVERT: C 278 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7924 (ttpt) REVERT: C 314 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7681 (tm130) REVERT: C 328 ARG cc_start: 0.5171 (OUTLIER) cc_final: 0.4828 (ptm160) REVERT: C 392 PHE cc_start: 0.1149 (OUTLIER) cc_final: 0.0866 (p90) REVERT: C 457 ARG cc_start: 0.0763 (OUTLIER) cc_final: 0.0514 (mmm-85) REVERT: C 474 GLN cc_start: 0.1185 (OUTLIER) cc_final: 0.0829 (pt0) REVERT: C 481 LYS cc_start: 0.4009 (OUTLIER) cc_final: 0.2991 (mmtt) REVERT: C 582 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: C 583 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7068 (mm) REVERT: C 584 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7220 (mt) REVERT: C 709 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8380 (m-40) REVERT: C 752 LEU cc_start: 0.8562 (tp) cc_final: 0.8319 (mt) REVERT: C 810 SER cc_start: 0.7613 (OUTLIER) cc_final: 0.7348 (m) REVERT: C 830 ASP cc_start: 0.1494 (OUTLIER) cc_final: 0.1163 (m-30) REVERT: C 847 ARG cc_start: 0.2651 (OUTLIER) cc_final: 0.0482 (tpt170) REVERT: C 853 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: C 854 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6433 (ttpp) REVERT: C 990 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: T 30 ASP cc_start: 0.5617 (OUTLIER) cc_final: 0.4714 (t0) REVERT: T 107 VAL cc_start: 0.1655 (OUTLIER) cc_final: 0.1150 (p) REVERT: T 108 LEU cc_start: -0.1816 (OUTLIER) cc_final: -0.2037 (tt) REVERT: T 174 LYS cc_start: 0.0493 (OUTLIER) cc_final: -0.0013 (tptt) REVERT: T 183 TYR cc_start: -0.0535 (OUTLIER) cc_final: -0.1653 (t80) REVERT: T 295 ASP cc_start: 0.3833 (OUTLIER) cc_final: 0.2702 (m-30) REVERT: T 300 GLN cc_start: -0.0855 (OUTLIER) cc_final: -0.1804 (tp40) REVERT: T 430 GLU cc_start: -0.0435 (OUTLIER) cc_final: -0.0847 (tp30) REVERT: T 438 PHE cc_start: 0.1089 (OUTLIER) cc_final: 0.0816 (t80) REVERT: T 445 THR cc_start: 0.4991 (OUTLIER) cc_final: 0.4686 (p) REVERT: T 465 LYS cc_start: 0.2574 (OUTLIER) cc_final: 0.1778 (ptmm) REVERT: T 509 ASP cc_start: 0.2551 (OUTLIER) cc_final: 0.0909 (m-30) REVERT: T 567 THR cc_start: 0.2859 (OUTLIER) cc_final: 0.2610 (p) REVERT: T 600 LYS cc_start: 0.1129 (OUTLIER) cc_final: 0.0267 (tttm) REVERT: X 23 GLU cc_start: 0.3016 (OUTLIER) cc_final: 0.2295 (tp30) REVERT: X 62 MET cc_start: 0.0637 (OUTLIER) cc_final: -0.0355 (tmt) REVERT: X 98 GLN cc_start: 0.1111 (OUTLIER) cc_final: 0.0332 (tm-30) REVERT: X 136 ASP cc_start: -0.1897 (OUTLIER) cc_final: -0.2231 (m-30) REVERT: X 171 GLU cc_start: 0.3062 (tt0) cc_final: 0.2304 (tm-30) REVERT: X 232 GLU cc_start: 0.2111 (OUTLIER) cc_final: 0.1823 (mm-30) REVERT: X 249 MET cc_start: -0.0242 (mtp) cc_final: -0.0464 (ttm) REVERT: X 274 PHE cc_start: 0.4262 (m-80) cc_final: 0.3951 (m-10) REVERT: X 379 ILE cc_start: -0.1144 (OUTLIER) cc_final: -0.1403 (mm) REVERT: X 398 GLU cc_start: 0.2769 (OUTLIER) cc_final: 0.2322 (mt-10) REVERT: X 438 PHE cc_start: 0.1002 (OUTLIER) cc_final: 0.0424 (t80) REVERT: X 527 GLU cc_start: 0.2440 (OUTLIER) cc_final: 0.1699 (tp30) REVERT: X 536 GLU cc_start: 0.2156 (pm20) cc_final: 0.1614 (pt0) REVERT: X 539 LEU cc_start: -0.2690 (OUTLIER) cc_final: -0.3007 (pt) REVERT: X 577 LYS cc_start: 0.2287 (OUTLIER) cc_final: 0.2023 (ptpp) REVERT: X 590 PRO cc_start: -0.3512 (OUTLIER) cc_final: -0.3874 (Cg_endo) REVERT: X 597 ASP cc_start: 0.2715 (OUTLIER) cc_final: 0.2192 (m-30) REVERT: X 601 ASN cc_start: 0.1914 (OUTLIER) cc_final: 0.1577 (t0) REVERT: Z 86 GLN cc_start: 0.1649 (OUTLIER) cc_final: 0.0709 (mp10) REVERT: Z 117 ASN cc_start: 0.3563 (OUTLIER) cc_final: 0.3308 (t0) REVERT: Z 151 ILE cc_start: 0.2664 (OUTLIER) cc_final: 0.2032 (mp) REVERT: Z 219 ARG cc_start: -0.0600 (OUTLIER) cc_final: -0.1203 (ppt170) REVERT: Z 270 MET cc_start: -0.0676 (tpp) cc_final: -0.1233 (mmm) REVERT: Z 305 GLN cc_start: 0.3047 (OUTLIER) cc_final: 0.1935 (pp30) REVERT: Z 329 GLU cc_start: 0.3712 (OUTLIER) cc_final: 0.3098 (tt0) REVERT: Z 344 CYS cc_start: 0.1550 (OUTLIER) cc_final: 0.1140 (t) REVERT: Z 431 ASP cc_start: 0.2154 (OUTLIER) cc_final: 0.1202 (p0) REVERT: Z 474 MET cc_start: 0.1038 (OUTLIER) cc_final: 0.0317 (ttp) REVERT: Z 495 GLU cc_start: 0.2992 (OUTLIER) cc_final: 0.1216 (tt0) REVERT: Z 557 MET cc_start: 0.2641 (tmm) cc_final: 0.2366 (ttp) REVERT: Z 560 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.2242 (mt) REVERT: Z 577 LYS cc_start: 0.1370 (OUTLIER) cc_final: 0.1016 (mtpt) outliers start: 1506 outliers final: 318 residues processed: 1813 average time/residue: 1.3345 time to fit residues: 3001.4155 Evaluate side-chains 748 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 421 poor density : 327 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 463 PRO Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 942 PRO Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 463 PRO Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 585 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 630 PRO Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 463 PRO Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 536 LYS Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 553 LYS Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 564 PHE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 151 ILE Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 266 LEU Chi-restraints excluded: chain T residue 284 PRO Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 306 ARG Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 430 GLU Chi-restraints excluded: chain T residue 436 ILE Chi-restraints excluded: chain T residue 438 PHE Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 465 LYS Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain T residue 496 THR Chi-restraints excluded: chain T residue 502 SER Chi-restraints excluded: chain T residue 503 LEU Chi-restraints excluded: chain T residue 509 ASP Chi-restraints excluded: chain T residue 567 THR Chi-restraints excluded: chain T residue 600 LYS Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain T residue 611 SER Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 23 GLU Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 62 MET Chi-restraints excluded: chain X residue 87 GLU Chi-restraints excluded: chain X residue 98 GLN Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 131 LYS Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 232 GLU Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 379 ILE Chi-restraints excluded: chain X residue 398 GLU Chi-restraints excluded: chain X residue 414 THR Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 493 HIS Chi-restraints excluded: chain X residue 494 ASP Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 509 ASP Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 539 LEU Chi-restraints excluded: chain X residue 545 SER Chi-restraints excluded: chain X residue 567 THR Chi-restraints excluded: chain X residue 577 LYS Chi-restraints excluded: chain X residue 590 PRO Chi-restraints excluded: chain X residue 597 ASP Chi-restraints excluded: chain X residue 601 ASN Chi-restraints excluded: chain X residue 611 SER Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 24 GLN Chi-restraints excluded: chain Z residue 86 GLN Chi-restraints excluded: chain Z residue 117 ASN Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 151 ILE Chi-restraints excluded: chain Z residue 219 ARG Chi-restraints excluded: chain Z residue 245 ARG Chi-restraints excluded: chain Z residue 255 TYR Chi-restraints excluded: chain Z residue 265 HIS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 282 THR Chi-restraints excluded: chain Z residue 284 PRO Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 324 THR Chi-restraints excluded: chain Z residue 329 GLU Chi-restraints excluded: chain Z residue 344 CYS Chi-restraints excluded: chain Z residue 385 TYR Chi-restraints excluded: chain Z residue 414 THR Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 474 MET Chi-restraints excluded: chain Z residue 495 GLU Chi-restraints excluded: chain Z residue 496 THR Chi-restraints excluded: chain Z residue 503 LEU Chi-restraints excluded: chain Z residue 560 LEU Chi-restraints excluded: chain Z residue 577 LYS Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 409 optimal weight: 6.9990 chunk 367 optimal weight: 7.9990 chunk 203 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 321 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 414 GLN A 422 ASN A 486 ASN A 531 ASN A 562 GLN A 612 GLN A 640 ASN A 751 ASN A 779 GLN A 955 ASN A 957 GLN A1142 GLN B 238 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 474 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 640 ASN B 774 GLN B 784 GLN B 856 ASN B 907 ASN B 919 ASN B 935 GLN B 965 GLN B1002 GLN C 115 GLN C 121 ASN C 165 ASN C 196 ASN C 217 GLN C 321 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 437 ASN C 474 GLN C 563 GLN C 606 GLN C 657 ASN C 804 GLN C 853 GLN C 856 ASN C 872 GLN C 901 GLN C 913 GLN C 926 GLN C 949 GLN C 960 ASN C1005 GLN C1023 ASN C1048 HIS C1074 ASN C1106 GLN C1135 ASN T 58 ASN T 64 ASN ** T 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 102 GLN T 149 ASN T 194 ASN T 250 ASN T 300 GLN T 305 GLN T 374 HIS T 442 GLN T 505 HIS ** T 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 586 ASN X 34 HIS X 76 GLN ** X 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN X 103 ASN X 149 ASN X 175 GLN ** X 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 ASN ** X 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN ** X 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 442 GLN X 508 ASN X 535 HIS ** X 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 49 ASN Z 89 GLN Z 149 ASN Z 194 ASN Z 250 ASN Z 340 GLN ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 374 HIS Z 472 GLN Z 505 HIS Z 586 ASN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 39844 Z= 0.309 Angle : 0.944 12.787 54179 Z= 0.487 Chirality : 0.051 0.402 5953 Planarity : 0.008 0.127 7000 Dihedral : 13.667 89.279 6093 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 1.25 % Allowed : 15.40 % Favored : 83.35 % Rotamer: Outliers : 12.85 % Allowed : 29.28 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.09), residues: 4818 helix: -3.84 (0.08), residues: 1619 sheet: -2.39 (0.19), residues: 598 loop : -4.16 (0.09), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.013 0.001 HIS Z 345 PHE 0.032 0.003 PHE C 833 TYR 0.029 0.002 TYR B 396 ARG 0.016 0.001 ARG T 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 551 poor density : 340 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7712 (m-10) cc_final: 0.7429 (m-10) REVERT: A 66 HIS cc_start: 0.4238 (OUTLIER) cc_final: 0.3865 (t-90) REVERT: A 141 LEU cc_start: 0.3400 (OUTLIER) cc_final: 0.2899 (tp) REVERT: A 213 ARG cc_start: 0.2486 (OUTLIER) cc_final: -0.0638 (mtm180) REVERT: A 223 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6320 (mm-30) REVERT: A 236 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7501 (mmt90) REVERT: A 468 ILE cc_start: 0.1962 (OUTLIER) cc_final: 0.1429 (tt) REVERT: A 878 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8940 (tt) REVERT: A 990 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 993 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 1111 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: B 24 THR cc_start: 0.3298 (OUTLIER) cc_final: 0.2905 (m) REVERT: B 26 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.5022 (mt0) REVERT: B 110 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6332 (tt) REVERT: B 129 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6065 (tppp) REVERT: B 202 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8198 (mtmm) REVERT: B 213 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.4977 (tpt170) REVERT: B 238 GLN cc_start: 0.7774 (tt0) cc_final: 0.7425 (tt0) REVERT: B 273 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6790 (mmp-170) REVERT: B 329 PHE cc_start: 0.2699 (OUTLIER) cc_final: 0.1503 (t80) REVERT: B 474 GLN cc_start: 0.1698 (OUTLIER) cc_final: 0.0791 (tm-30) REVERT: B 483 LYS cc_start: 0.3761 (OUTLIER) cc_final: 0.3110 (mttp) REVERT: B 559 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7642 (mp) REVERT: B 579 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6305 (mp10) REVERT: B 585 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: B 645 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7333 (ttp80) REVERT: B 750 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7982 (t) REVERT: B 773 GLU cc_start: 0.7856 (tt0) cc_final: 0.7633 (tt0) REVERT: B 849 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4584 (tt) REVERT: B 984 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7184 (tt) REVERT: B 1136 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 25 THR cc_start: 0.5322 (OUTLIER) cc_final: 0.5002 (m) REVERT: C 52 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: C 190 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5867 (mtt-85) REVERT: C 271 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: C 304 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8644 (mttm) REVERT: C 309 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: C 314 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7538 (tm130) REVERT: C 326 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7195 (mt) REVERT: C 374 PHE cc_start: 0.1471 (OUTLIER) cc_final: 0.0239 (m-10) REVERT: C 481 LYS cc_start: 0.3706 (OUTLIER) cc_final: 0.2831 (mmmt) REVERT: C 488 TYR cc_start: -0.0657 (OUTLIER) cc_final: -0.1129 (t80) REVERT: C 794 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8275 (tp) REVERT: C 804 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8501 (mm-40) REVERT: C 847 ARG cc_start: 0.1888 (OUTLIER) cc_final: 0.0427 (tpt170) REVERT: C 947 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8257 (mtmm) REVERT: T 108 LEU cc_start: -0.0990 (OUTLIER) cc_final: -0.1194 (tt) REVERT: T 152 MET cc_start: -0.2509 (OUTLIER) cc_final: -0.2947 (tpt) REVERT: T 158 TYR cc_start: 0.0781 (t80) cc_final: 0.0005 (t80) REVERT: T 174 LYS cc_start: 0.1398 (OUTLIER) cc_final: 0.0647 (tptt) REVERT: T 183 TYR cc_start: -0.0947 (OUTLIER) cc_final: -0.2146 (t80) REVERT: T 223 ILE cc_start: 0.2983 (OUTLIER) cc_final: 0.2317 (tt) REVERT: T 287 GLN cc_start: 0.2467 (OUTLIER) cc_final: 0.1795 (pp30) REVERT: T 295 ASP cc_start: 0.3186 (OUTLIER) cc_final: 0.2348 (m-30) REVERT: T 455 MET cc_start: 0.3390 (ttm) cc_final: 0.3124 (ttm) REVERT: T 465 LYS cc_start: 0.2061 (OUTLIER) cc_final: 0.0969 (ptmm) REVERT: T 519 THR cc_start: 0.3175 (m) cc_final: 0.2961 (p) REVERT: T 559 ARG cc_start: 0.3245 (ptt90) cc_final: 0.2460 (mtp180) REVERT: T 579 MET cc_start: -0.0854 (OUTLIER) cc_final: -0.1175 (ptt) REVERT: T 585 LEU cc_start: 0.3335 (OUTLIER) cc_final: 0.3031 (tm) REVERT: X 62 MET cc_start: 0.0162 (OUTLIER) cc_final: -0.0675 (tmt) REVERT: X 249 MET cc_start: -0.0287 (mtp) cc_final: -0.0566 (ttm) REVERT: X 306 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.1634 (mmm160) REVERT: X 376 MET cc_start: 0.0739 (mtm) cc_final: 0.0103 (mmm) REVERT: X 383 MET cc_start: -0.1248 (mtt) cc_final: -0.1660 (tmt) REVERT: X 438 PHE cc_start: 0.1996 (OUTLIER) cc_final: 0.0275 (t80) REVERT: X 503 LEU cc_start: 0.1627 (OUTLIER) cc_final: 0.1062 (tp) REVERT: X 534 LYS cc_start: 0.3253 (OUTLIER) cc_final: 0.2377 (tmtm) REVERT: X 567 THR cc_start: 0.2603 (OUTLIER) cc_final: 0.2349 (p) REVERT: Z 22 GLU cc_start: 0.2624 (OUTLIER) cc_final: 0.1578 (tt0) REVERT: Z 57 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.3218 (pm20) REVERT: Z 151 ILE cc_start: 0.2347 (OUTLIER) cc_final: 0.1845 (mp) REVERT: Z 160 GLU cc_start: 0.0584 (OUTLIER) cc_final: -0.0528 (mm-30) REVERT: Z 269 ASP cc_start: 0.0878 (OUTLIER) cc_final: -0.0192 (p0) REVERT: Z 323 MET cc_start: -0.2142 (mmp) cc_final: -0.2376 (mtm) REVERT: Z 340 GLN cc_start: 0.0764 (OUTLIER) cc_final: -0.0130 (tp40) REVERT: Z 366 MET cc_start: -0.1024 (mmm) cc_final: -0.1628 (mmm) REVERT: Z 431 ASP cc_start: 0.2554 (OUTLIER) cc_final: 0.1569 (p0) REVERT: Z 480 MET cc_start: 0.2251 (tpp) cc_final: 0.0583 (pp-130) REVERT: Z 495 GLU cc_start: 0.2269 (OUTLIER) cc_final: 0.0752 (tt0) REVERT: Z 577 LYS cc_start: 0.1757 (OUTLIER) cc_final: 0.1084 (mttt) outliers start: 551 outliers final: 185 residues processed: 829 average time/residue: 1.2691 time to fit residues: 1326.8534 Evaluate side-chains 500 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 249 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 585 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 136 ASP Chi-restraints excluded: chain T residue 152 MET Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 364 VAL Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 371 THR Chi-restraints excluded: chain T residue 465 LYS Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 502 SER Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain X residue 62 MET Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 306 ARG Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain X residue 567 THR Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 22 GLU Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 151 ILE Chi-restraints excluded: chain Z residue 160 GLU Chi-restraints excluded: chain Z residue 255 TYR Chi-restraints excluded: chain Z residue 265 HIS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 288 LYS Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 340 GLN Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 394 ASN Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 491 VAL Chi-restraints excluded: chain Z residue 495 GLU Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 577 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 244 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 366 optimal weight: 30.0000 chunk 299 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 441 optimal weight: 6.9990 chunk 476 optimal weight: 30.0000 chunk 392 optimal weight: 8.9990 chunk 437 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 353 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 957 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B1002 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 856 ASN C1011 GLN T 61 ASN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN T 96 GLN T 442 GLN T 599 ASN X 33 ASN ** X 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 102 GLN ** X 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 401 HIS X 535 HIS ** X 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 96 GLN Z 340 GLN ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 39844 Z= 0.420 Angle : 0.864 16.477 54179 Z= 0.441 Chirality : 0.050 0.311 5953 Planarity : 0.007 0.089 7000 Dihedral : 10.217 87.616 5534 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.98 % Allowed : 13.51 % Favored : 85.51 % Rotamer: Outliers : 9.77 % Allowed : 30.40 % Favored : 59.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.10), residues: 4818 helix: -2.58 (0.10), residues: 1673 sheet: -2.01 (0.20), residues: 580 loop : -3.64 (0.10), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 566 HIS 0.014 0.002 HIS C 207 PHE 0.036 0.003 PHE X 438 TYR 0.025 0.002 TYR C 279 ARG 0.009 0.001 ARG T 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 419 poor density : 286 time to evaluate : 4.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4179 (OUTLIER) cc_final: 0.3735 (t-90) REVERT: A 141 LEU cc_start: 0.3649 (OUTLIER) cc_final: 0.3044 (tp) REVERT: A 213 ARG cc_start: 0.2686 (OUTLIER) cc_final: -0.0302 (mtp85) REVERT: A 225 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 236 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7508 (mmt90) REVERT: A 304 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: A 468 ILE cc_start: 0.2353 (OUTLIER) cc_final: 0.1636 (tt) REVERT: A 528 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4778 (ptpt) REVERT: A 869 MET cc_start: 0.8867 (mtt) cc_final: 0.8528 (mtt) REVERT: A 990 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 993 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 1111 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: B 24 THR cc_start: 0.3541 (OUTLIER) cc_final: 0.3234 (m) REVERT: B 32 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: B 110 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6380 (tt) REVERT: B 213 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.4907 (tpt170) REVERT: B 238 GLN cc_start: 0.7779 (tt0) cc_final: 0.7443 (tt0) REVERT: B 273 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6928 (mmp-170) REVERT: B 458 LYS cc_start: 0.1067 (OUTLIER) cc_final: -0.0148 (ptmm) REVERT: B 474 GLN cc_start: 0.1888 (OUTLIER) cc_final: 0.0980 (tm-30) REVERT: B 483 LYS cc_start: 0.3652 (OUTLIER) cc_final: 0.3029 (mptt) REVERT: B 559 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 645 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7302 (ttp80) REVERT: B 750 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8159 (t) REVERT: B 849 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4850 (tt) REVERT: B 984 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7323 (tp) REVERT: B 1092 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: B 1136 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8458 (p) REVERT: C 52 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: C 304 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8651 (mttm) REVERT: C 314 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7518 (tm130) REVERT: C 326 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7481 (mt) REVERT: C 462 LYS cc_start: 0.1993 (OUTLIER) cc_final: 0.1413 (mttp) REVERT: C 481 LYS cc_start: 0.3797 (OUTLIER) cc_final: 0.3178 (mmtt) REVERT: C 488 TYR cc_start: -0.0617 (OUTLIER) cc_final: -0.1098 (t80) REVERT: C 918 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: C 947 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8569 (mtmm) REVERT: T 101 GLN cc_start: 0.1869 (OUTLIER) cc_final: 0.0785 (mp10) REVERT: T 152 MET cc_start: -0.2636 (OUTLIER) cc_final: -0.3106 (tpt) REVERT: T 181 GLU cc_start: 0.2144 (mt-10) cc_final: 0.1789 (tm-30) REVERT: T 183 TYR cc_start: -0.0770 (OUTLIER) cc_final: -0.1988 (t80) REVERT: T 223 ILE cc_start: 0.2926 (OUTLIER) cc_final: 0.2173 (tt) REVERT: T 249 MET cc_start: 0.1124 (OUTLIER) cc_final: 0.0643 (ttm) REVERT: T 287 GLN cc_start: 0.2832 (OUTLIER) cc_final: 0.2014 (pp30) REVERT: T 295 ASP cc_start: 0.3567 (OUTLIER) cc_final: 0.2649 (m-30) REVERT: T 455 MET cc_start: 0.3508 (ttm) cc_final: 0.3240 (ttm) REVERT: T 559 ARG cc_start: 0.3050 (ptt90) cc_final: 0.2479 (mtp180) REVERT: T 579 MET cc_start: -0.1014 (ptt) cc_final: -0.2475 (tmm) REVERT: X 62 MET cc_start: -0.0169 (OUTLIER) cc_final: -0.0487 (tmt) REVERT: X 82 MET cc_start: 0.2692 (ttm) cc_final: 0.1486 (tpt) REVERT: X 114 LYS cc_start: 0.5145 (mmtp) cc_final: 0.4638 (pttt) REVERT: X 171 GLU cc_start: 0.1893 (OUTLIER) cc_final: 0.0885 (tt0) REVERT: X 227 GLU cc_start: 0.1619 (OUTLIER) cc_final: 0.0998 (mp0) REVERT: X 249 MET cc_start: -0.0151 (mtp) cc_final: -0.0496 (ttm) REVERT: X 376 MET cc_start: 0.0255 (mtm) cc_final: -0.0037 (mmm) REVERT: X 400 PHE cc_start: 0.1892 (OUTLIER) cc_final: 0.1225 (t80) REVERT: X 438 PHE cc_start: 0.1959 (OUTLIER) cc_final: 0.0471 (t80) REVERT: X 474 MET cc_start: 0.3515 (tpt) cc_final: 0.3057 (mtp) REVERT: X 511 SER cc_start: 0.0447 (OUTLIER) cc_final: -0.0758 (p) REVERT: Z 22 GLU cc_start: 0.2677 (OUTLIER) cc_final: 0.1502 (tp30) REVERT: Z 82 MET cc_start: 0.2262 (OUTLIER) cc_final: 0.1690 (ttp) REVERT: Z 151 ILE cc_start: 0.2908 (OUTLIER) cc_final: 0.2427 (mp) REVERT: Z 269 ASP cc_start: 0.0734 (OUTLIER) cc_final: 0.0059 (p0) REVERT: Z 305 GLN cc_start: 0.2323 (OUTLIER) cc_final: 0.1767 (pp30) REVERT: Z 323 MET cc_start: -0.1981 (mmp) cc_final: -0.2245 (mtm) REVERT: Z 340 GLN cc_start: 0.0912 (OUTLIER) cc_final: -0.0012 (tp40) REVERT: Z 366 MET cc_start: -0.0996 (mmm) cc_final: -0.1657 (mmm) REVERT: Z 408 MET cc_start: 0.2914 (OUTLIER) cc_final: 0.2638 (mmp) REVERT: Z 431 ASP cc_start: 0.2620 (OUTLIER) cc_final: 0.1628 (p0) REVERT: Z 480 MET cc_start: 0.2370 (tpp) cc_final: 0.0670 (pp-130) REVERT: Z 577 LYS cc_start: 0.2389 (OUTLIER) cc_final: 0.1469 (mtmt) outliers start: 419 outliers final: 198 residues processed: 665 average time/residue: 1.1729 time to fit residues: 1002.5255 Evaluate side-chains 500 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 247 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 101 GLN Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 136 ASP Chi-restraints excluded: chain T residue 152 MET Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain T residue 249 MET Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 371 THR Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 62 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 227 GLU Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain X residue 446 ILE Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 596 LYS Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 22 GLU Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 151 ILE Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 288 LYS Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 340 GLN Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 408 MET Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 491 VAL Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 577 LYS Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 435 optimal weight: 5.9990 chunk 331 optimal weight: 40.0000 chunk 228 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 296 optimal weight: 0.5980 chunk 442 optimal weight: 30.0000 chunk 468 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 360 ASN A 531 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 474 GLN B 555 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 762 GLN C 207 HIS ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 804 GLN C 856 ASN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 96 GLN X 290 ASN ** X 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 442 GLN X 535 HIS Z 58 ASN ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39844 Z= 0.238 Angle : 0.750 13.508 54179 Z= 0.377 Chirality : 0.045 0.278 5953 Planarity : 0.006 0.071 7000 Dihedral : 9.020 81.160 5452 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.42 % Favored : 88.77 % Rotamer: Outliers : 7.81 % Allowed : 30.89 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.11), residues: 4818 helix: -1.67 (0.11), residues: 1701 sheet: -1.67 (0.21), residues: 570 loop : -3.28 (0.11), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 48 HIS 0.012 0.001 HIS X 505 PHE 0.034 0.002 PHE B 855 TYR 0.024 0.001 TYR Z 252 ARG 0.012 0.001 ARG X 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 269 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4088 (OUTLIER) cc_final: 0.3647 (t70) REVERT: A 213 ARG cc_start: 0.2918 (OUTLIER) cc_final: -0.0063 (mtp85) REVERT: A 223 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: A 225 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7632 (mp) REVERT: A 236 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7398 (mmt90) REVERT: A 304 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8389 (mtmm) REVERT: A 990 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 993 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 1111 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: B 24 THR cc_start: 0.3357 (OUTLIER) cc_final: 0.3090 (m) REVERT: B 32 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: B 105 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7544 (pt) REVERT: B 110 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6351 (tt) REVERT: B 213 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.4877 (tpt170) REVERT: B 215 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5929 (t80) REVERT: B 238 GLN cc_start: 0.7690 (tt0) cc_final: 0.7406 (tt0) REVERT: B 314 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: B 458 LYS cc_start: 0.1089 (OUTLIER) cc_final: -0.0073 (ptmm) REVERT: B 483 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3331 (mttp) REVERT: B 557 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7958 (mppt) REVERT: B 750 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.7984 (t) REVERT: B 773 GLU cc_start: 0.7876 (tt0) cc_final: 0.7636 (tt0) REVERT: B 984 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7354 (tp) REVERT: B 1092 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: B 1136 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8497 (p) REVERT: C 52 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: C 172 SER cc_start: 0.5659 (OUTLIER) cc_final: 0.5395 (p) REVERT: C 309 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: C 314 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7424 (tm130) REVERT: C 326 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7371 (mt) REVERT: C 462 LYS cc_start: 0.1747 (OUTLIER) cc_final: 0.1337 (mttp) REVERT: C 481 LYS cc_start: 0.3593 (OUTLIER) cc_final: 0.3180 (mmtt) REVERT: C 488 TYR cc_start: -0.0348 (OUTLIER) cc_final: -0.0924 (t80) REVERT: C 709 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: C 918 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: T 39 LEU cc_start: 0.1087 (OUTLIER) cc_final: 0.0741 (tp) REVERT: T 62 MET cc_start: 0.3323 (tpp) cc_final: 0.3015 (mtp) REVERT: T 152 MET cc_start: -0.2593 (OUTLIER) cc_final: -0.2965 (tpt) REVERT: T 174 LYS cc_start: 0.1214 (OUTLIER) cc_final: 0.0488 (tppt) REVERT: T 181 GLU cc_start: 0.2268 (mt-10) cc_final: 0.1877 (tm-30) REVERT: T 183 TYR cc_start: -0.0879 (OUTLIER) cc_final: -0.1920 (t80) REVERT: T 190 MET cc_start: 0.1372 (tmt) cc_final: 0.0910 (tpt) REVERT: T 223 ILE cc_start: 0.2878 (OUTLIER) cc_final: 0.2131 (tt) REVERT: T 287 GLN cc_start: 0.2819 (OUTLIER) cc_final: 0.2195 (pp30) REVERT: T 295 ASP cc_start: 0.3504 (OUTLIER) cc_final: 0.2818 (m-30) REVERT: T 455 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3429 (ttm) REVERT: T 462 MET cc_start: 0.3383 (mpm) cc_final: 0.1852 (mtt) REVERT: T 509 ASP cc_start: 0.2174 (OUTLIER) cc_final: 0.0950 (m-30) REVERT: T 557 MET cc_start: 0.3366 (tpt) cc_final: 0.3013 (tpp) REVERT: T 559 ARG cc_start: 0.2877 (ptt90) cc_final: 0.2390 (mtp180) REVERT: T 579 MET cc_start: -0.1055 (ptt) cc_final: -0.3049 (mmm) REVERT: X 20 THR cc_start: -0.1217 (OUTLIER) cc_final: -0.1906 (p) REVERT: X 62 MET cc_start: -0.0324 (OUTLIER) cc_final: -0.0553 (tmt) REVERT: X 82 MET cc_start: 0.2611 (ttm) cc_final: 0.1524 (tpt) REVERT: X 114 LYS cc_start: 0.5111 (mmtp) cc_final: 0.4805 (pttt) REVERT: X 216 ASP cc_start: 0.0531 (OUTLIER) cc_final: 0.0089 (t0) REVERT: X 249 MET cc_start: -0.0143 (mtp) cc_final: -0.0533 (ttm) REVERT: X 383 MET cc_start: -0.0701 (mtt) cc_final: -0.1120 (tmt) REVERT: X 400 PHE cc_start: 0.2004 (OUTLIER) cc_final: 0.1355 (t80) REVERT: X 438 PHE cc_start: 0.2167 (OUTLIER) cc_final: 0.0698 (t80) REVERT: X 442 GLN cc_start: -0.1088 (OUTLIER) cc_final: -0.1758 (tt0) REVERT: X 475 LYS cc_start: 0.3708 (OUTLIER) cc_final: 0.2648 (mmtp) REVERT: X 480 MET cc_start: 0.1500 (mtt) cc_final: -0.0364 (ttt) REVERT: X 534 LYS cc_start: 0.3184 (OUTLIER) cc_final: 0.2449 (ptpt) REVERT: X 596 LYS cc_start: 0.0975 (OUTLIER) cc_final: 0.0465 (mppt) REVERT: Z 22 GLU cc_start: 0.2224 (OUTLIER) cc_final: 0.1185 (tt0) REVERT: Z 82 MET cc_start: 0.2211 (OUTLIER) cc_final: 0.1767 (ttp) REVERT: Z 150 GLU cc_start: 0.1751 (tp30) cc_final: 0.0294 (mt-10) REVERT: Z 151 ILE cc_start: 0.3069 (OUTLIER) cc_final: 0.2735 (mp) REVERT: Z 152 MET cc_start: 0.0743 (tpp) cc_final: -0.0510 (mtt) REVERT: Z 221 GLN cc_start: 0.3671 (tt0) cc_final: 0.2972 (tp-100) REVERT: Z 269 ASP cc_start: 0.0599 (OUTLIER) cc_final: 0.0093 (p0) REVERT: Z 305 GLN cc_start: 0.2304 (OUTLIER) cc_final: 0.1682 (pp30) REVERT: Z 323 MET cc_start: -0.2076 (mmp) cc_final: -0.2351 (mtm) REVERT: Z 408 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.2547 (mmp) REVERT: Z 475 LYS cc_start: 0.4691 (mmmt) cc_final: 0.4113 (mmtp) outliers start: 335 outliers final: 150 residues processed: 576 average time/residue: 1.2154 time to fit residues: 893.1452 Evaluate side-chains 448 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 242 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 152 MET Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 341 LYS Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 455 MET Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 509 ASP Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 62 MET Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain X residue 446 ILE Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain X residue 596 LYS Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 22 GLU Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 151 ILE Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 288 LYS Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 394 ASN Chi-restraints excluded: chain Z residue 408 MET Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 390 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 400 optimal weight: 30.0000 chunk 324 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 chunk 420 optimal weight: 30.0000 chunk 118 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 957 GLN B 314 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN B 615 ASN B 762 GLN C 612 GLN C 804 GLN T 51 ASN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN T 442 GLN X 51 ASN ** X 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 305 GLN Z 345 HIS ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 39844 Z= 0.367 Angle : 0.766 13.407 54179 Z= 0.388 Chirality : 0.048 0.328 5953 Planarity : 0.006 0.078 7000 Dihedral : 8.480 81.309 5408 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.77 % Allowed : 11.46 % Favored : 87.78 % Rotamer: Outliers : 8.18 % Allowed : 29.77 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.11), residues: 4818 helix: -1.24 (0.12), residues: 1720 sheet: -1.64 (0.21), residues: 576 loop : -3.21 (0.11), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 473 HIS 0.007 0.001 HIS T 34 PHE 0.035 0.002 PHE Z 438 TYR 0.022 0.002 TYR C 279 ARG 0.007 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 263 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4273 (OUTLIER) cc_final: 0.3677 (t70) REVERT: A 213 ARG cc_start: 0.3201 (OUTLIER) cc_final: 0.0014 (mpt-90) REVERT: A 225 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7585 (mp) REVERT: A 236 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7074 (mmm-85) REVERT: A 304 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: A 354 ASN cc_start: 0.1025 (OUTLIER) cc_final: 0.0820 (t0) REVERT: A 696 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8876 (m) REVERT: A 990 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 993 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 1111 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: B 24 THR cc_start: 0.3385 (OUTLIER) cc_final: 0.3124 (m) REVERT: B 32 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: B 105 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7566 (pt) REVERT: B 213 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4937 (tpt170) REVERT: B 215 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.6004 (t80) REVERT: B 217 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.4314 (mm110) REVERT: B 238 GLN cc_start: 0.7766 (tt0) cc_final: 0.7510 (tt0) REVERT: B 458 LYS cc_start: 0.1079 (OUTLIER) cc_final: -0.0065 (ptmm) REVERT: B 483 LYS cc_start: 0.3746 (OUTLIER) cc_final: 0.3144 (mptt) REVERT: B 557 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8006 (mppt) REVERT: B 559 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 750 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (t) REVERT: B 984 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7429 (tp) REVERT: B 1092 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: B 1136 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 52 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: C 314 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7466 (tm130) REVERT: C 326 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7329 (mt) REVERT: C 462 LYS cc_start: 0.1917 (OUTLIER) cc_final: 0.1413 (mttp) REVERT: C 481 LYS cc_start: 0.3551 (OUTLIER) cc_final: 0.3307 (mmtt) REVERT: C 488 TYR cc_start: -0.0409 (OUTLIER) cc_final: -0.1191 (t80) REVERT: C 709 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8207 (m-40) REVERT: C 761 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (t) REVERT: C 847 ARG cc_start: 0.1883 (OUTLIER) cc_final: 0.0482 (tpt170) REVERT: C 918 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: T 39 LEU cc_start: 0.0987 (OUTLIER) cc_final: 0.0657 (tp) REVERT: T 82 MET cc_start: 0.3406 (mpm) cc_final: 0.2059 (ptp) REVERT: T 174 LYS cc_start: 0.1208 (OUTLIER) cc_final: 0.0648 (tptt) REVERT: T 181 GLU cc_start: 0.2521 (mt-10) cc_final: 0.2295 (mm-30) REVERT: T 183 TYR cc_start: -0.0856 (OUTLIER) cc_final: -0.1860 (t80) REVERT: T 190 MET cc_start: 0.1466 (tmt) cc_final: 0.0837 (tpt) REVERT: T 287 GLN cc_start: 0.2902 (OUTLIER) cc_final: 0.2287 (pp30) REVERT: T 295 ASP cc_start: 0.3428 (OUTLIER) cc_final: 0.2867 (m-30) REVERT: T 428 PHE cc_start: -0.1757 (t80) cc_final: -0.2611 (m-80) REVERT: T 442 GLN cc_start: 0.3092 (OUTLIER) cc_final: 0.2236 (pt0) REVERT: T 462 MET cc_start: 0.4059 (mpm) cc_final: 0.2838 (mtt) REVERT: T 509 ASP cc_start: 0.2015 (OUTLIER) cc_final: 0.0650 (m-30) REVERT: T 559 ARG cc_start: 0.2834 (ptt90) cc_final: 0.2330 (mtp180) REVERT: T 579 MET cc_start: -0.1090 (OUTLIER) cc_final: -0.2522 (tmm) REVERT: X 20 THR cc_start: -0.1189 (OUTLIER) cc_final: -0.1790 (p) REVERT: X 82 MET cc_start: 0.2726 (ttm) cc_final: 0.1620 (tpt) REVERT: X 162 LEU cc_start: 0.0482 (OUTLIER) cc_final: 0.0094 (pp) REVERT: X 216 ASP cc_start: 0.0656 (OUTLIER) cc_final: 0.0189 (t0) REVERT: X 249 MET cc_start: 0.0054 (mtp) cc_final: -0.0320 (ttt) REVERT: X 383 MET cc_start: -0.0629 (mtt) cc_final: -0.1118 (tmt) REVERT: X 400 PHE cc_start: 0.2072 (OUTLIER) cc_final: 0.1367 (t80) REVERT: X 438 PHE cc_start: 0.2538 (OUTLIER) cc_final: 0.1243 (t80) REVERT: X 475 LYS cc_start: 0.3602 (OUTLIER) cc_final: 0.2676 (mmtt) REVERT: X 511 SER cc_start: -0.0018 (OUTLIER) cc_final: -0.0589 (p) REVERT: X 527 GLU cc_start: 0.2858 (OUTLIER) cc_final: 0.1970 (tp30) REVERT: X 534 LYS cc_start: 0.3226 (OUTLIER) cc_final: 0.2417 (ptpt) REVERT: Z 82 MET cc_start: 0.2361 (OUTLIER) cc_final: 0.1882 (ttp) REVERT: Z 151 ILE cc_start: 0.3449 (OUTLIER) cc_final: 0.3225 (mp) REVERT: Z 152 MET cc_start: 0.0832 (tpp) cc_final: -0.0378 (mtt) REVERT: Z 221 GLN cc_start: 0.3709 (tt0) cc_final: 0.3012 (tp40) REVERT: Z 269 ASP cc_start: 0.0367 (OUTLIER) cc_final: -0.0202 (p0) REVERT: Z 306 ARG cc_start: 0.2897 (OUTLIER) cc_final: 0.1717 (tpp-160) REVERT: Z 323 MET cc_start: -0.2041 (mmp) cc_final: -0.2406 (mtm) REVERT: Z 366 MET cc_start: -0.1468 (OUTLIER) cc_final: -0.3237 (mpm) REVERT: Z 408 MET cc_start: 0.2913 (OUTLIER) cc_final: 0.2666 (mmp) outliers start: 351 outliers final: 178 residues processed: 581 average time/residue: 1.2247 time to fit residues: 910.0094 Evaluate side-chains 466 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 232 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 371 THR Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 463 VAL Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 509 ASP Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 20 THR Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 151 ILE Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 276 THR Chi-restraints excluded: chain Z residue 288 LYS Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 366 MET Chi-restraints excluded: chain Z residue 394 ASN Chi-restraints excluded: chain Z residue 408 MET Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 157 optimal weight: 4.9990 chunk 422 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 469 optimal weight: 30.0000 chunk 389 optimal weight: 40.0000 chunk 217 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 155 optimal weight: 0.9980 chunk 246 optimal weight: 40.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 207 HIS ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 30 ASN C 804 GLN C1054 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 305 GLN ** T 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 442 GLN X 601 ASN Z 89 GLN Z 305 GLN ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 39844 Z= 0.303 Angle : 0.727 12.935 54179 Z= 0.365 Chirality : 0.046 0.321 5953 Planarity : 0.006 0.078 7000 Dihedral : 8.078 80.658 5391 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.63 % Favored : 88.75 % Rotamer: Outliers : 7.67 % Allowed : 30.36 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.11), residues: 4818 helix: -0.98 (0.12), residues: 1725 sheet: -1.48 (0.21), residues: 588 loop : -3.07 (0.11), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 594 HIS 0.007 0.001 HIS T 34 PHE 0.032 0.002 PHE B 855 TYR 0.020 0.002 TYR A 266 ARG 0.007 0.001 ARG Z 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 329 poor density : 244 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4119 (OUTLIER) cc_final: 0.3765 (t-90) REVERT: A 213 ARG cc_start: 0.3274 (OUTLIER) cc_final: 0.0278 (mpt-90) REVERT: A 223 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6412 (mm-30) REVERT: A 225 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 236 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7474 (mmt90) REVERT: A 304 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8375 (mtmm) REVERT: A 354 ASN cc_start: 0.1215 (OUTLIER) cc_final: 0.1005 (t0) REVERT: A 869 MET cc_start: 0.8883 (mtt) cc_final: 0.8407 (mtt) REVERT: A 990 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 993 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7572 (mp) REVERT: A 1045 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (tttt) REVERT: A 1111 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7104 (pp20) REVERT: B 24 THR cc_start: 0.3345 (OUTLIER) cc_final: 0.3112 (m) REVERT: B 32 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: B 105 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7518 (pt) REVERT: B 213 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.4916 (tpt90) REVERT: B 215 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.6052 (t80) REVERT: B 238 GLN cc_start: 0.7770 (tt0) cc_final: 0.7308 (tt0) REVERT: B 265 TYR cc_start: 0.6317 (t80) cc_final: 0.5877 (t80) REVERT: B 273 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7000 (mmp-170) REVERT: B 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: B 458 LYS cc_start: 0.0847 (OUTLIER) cc_final: -0.0164 (ptmm) REVERT: B 483 LYS cc_start: 0.3517 (OUTLIER) cc_final: 0.2960 (mptt) REVERT: B 984 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7446 (tp) REVERT: B 1092 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: C 52 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: C 238 GLN cc_start: 0.7084 (pp30) cc_final: 0.6802 (pp30) REVERT: C 314 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7449 (tm130) REVERT: C 326 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7246 (mt) REVERT: C 462 LYS cc_start: 0.1841 (OUTLIER) cc_final: 0.1348 (mttp) REVERT: C 481 LYS cc_start: 0.3452 (OUTLIER) cc_final: 0.3064 (mtmt) REVERT: C 709 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: C 761 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8457 (t) REVERT: C 847 ARG cc_start: 0.1786 (OUTLIER) cc_final: 0.0406 (tpt170) REVERT: T 62 MET cc_start: 0.2285 (OUTLIER) cc_final: 0.2082 (tpt) REVERT: T 82 MET cc_start: 0.3426 (mpm) cc_final: 0.2074 (ptp) REVERT: T 91 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3598 (pp) REVERT: T 152 MET cc_start: -0.2668 (OUTLIER) cc_final: -0.2957 (tpt) REVERT: T 174 LYS cc_start: 0.1348 (OUTLIER) cc_final: 0.0675 (tptt) REVERT: T 183 TYR cc_start: -0.0904 (OUTLIER) cc_final: -0.1866 (t80) REVERT: T 190 MET cc_start: 0.1482 (tmt) cc_final: 0.0808 (tpt) REVERT: T 252 TYR cc_start: 0.0610 (OUTLIER) cc_final: 0.0198 (t80) REVERT: T 287 GLN cc_start: 0.2954 (OUTLIER) cc_final: 0.2306 (pp30) REVERT: T 295 ASP cc_start: 0.3275 (OUTLIER) cc_final: 0.2781 (m-30) REVERT: T 428 PHE cc_start: -0.1635 (t80) cc_final: -0.2460 (m-80) REVERT: T 442 GLN cc_start: 0.3496 (OUTLIER) cc_final: 0.2685 (pt0) REVERT: T 462 MET cc_start: 0.4067 (mpm) cc_final: 0.3063 (mtt) REVERT: T 509 ASP cc_start: 0.2045 (OUTLIER) cc_final: 0.0631 (m-30) REVERT: T 559 ARG cc_start: 0.2844 (ptt90) cc_final: 0.2370 (mtp180) REVERT: T 579 MET cc_start: -0.0991 (OUTLIER) cc_final: -0.2497 (tmm) REVERT: T 606 TRP cc_start: 0.0943 (OUTLIER) cc_final: 0.0630 (m-90) REVERT: X 20 THR cc_start: -0.1255 (OUTLIER) cc_final: -0.1768 (p) REVERT: X 82 MET cc_start: 0.2811 (ttm) cc_final: 0.1640 (tpt) REVERT: X 110 GLU cc_start: 0.1674 (OUTLIER) cc_final: 0.0536 (pt0) REVERT: X 152 MET cc_start: 0.0773 (pp-130) cc_final: -0.1597 (tpp) REVERT: X 162 LEU cc_start: 0.0364 (OUTLIER) cc_final: 0.0079 (pp) REVERT: X 216 ASP cc_start: 0.0482 (OUTLIER) cc_final: 0.0050 (t0) REVERT: X 249 MET cc_start: 0.0141 (mtp) cc_final: -0.0245 (ttt) REVERT: X 376 MET cc_start: -0.0531 (mtp) cc_final: -0.0996 (mmm) REVERT: X 383 MET cc_start: -0.0467 (mtt) cc_final: -0.1053 (tmt) REVERT: X 400 PHE cc_start: 0.2098 (OUTLIER) cc_final: 0.1358 (t80) REVERT: X 438 PHE cc_start: 0.2469 (OUTLIER) cc_final: 0.1258 (t80) REVERT: X 475 LYS cc_start: 0.3795 (OUTLIER) cc_final: 0.2813 (mmtt) REVERT: X 511 SER cc_start: -0.0052 (OUTLIER) cc_final: -0.0512 (p) REVERT: X 527 GLU cc_start: 0.3044 (OUTLIER) cc_final: 0.2157 (tp30) REVERT: X 534 LYS cc_start: 0.3310 (OUTLIER) cc_final: 0.2561 (ptpt) REVERT: Z 82 MET cc_start: 0.2325 (ttm) cc_final: 0.1920 (ttp) REVERT: Z 150 GLU cc_start: 0.1851 (tp30) cc_final: 0.0661 (mt-10) REVERT: Z 152 MET cc_start: 0.0818 (tpp) cc_final: -0.0395 (mtt) REVERT: Z 221 GLN cc_start: 0.3699 (tt0) cc_final: 0.2943 (tp40) REVERT: Z 269 ASP cc_start: 0.0274 (OUTLIER) cc_final: -0.0033 (p0) REVERT: Z 323 MET cc_start: -0.2166 (mmp) cc_final: -0.2469 (mtm) REVERT: Z 366 MET cc_start: -0.1698 (OUTLIER) cc_final: -0.3110 (mmm) REVERT: Z 408 MET cc_start: 0.2811 (OUTLIER) cc_final: 0.2581 (mmp) REVERT: Z 431 ASP cc_start: 0.2507 (OUTLIER) cc_final: 0.1798 (p0) outliers start: 329 outliers final: 161 residues processed: 540 average time/residue: 1.2497 time to fit residues: 868.7896 Evaluate side-chains 441 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 225 time to evaluate : 4.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 152 MET Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 252 TYR Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 463 VAL Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 509 ASP Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain T residue 606 TRP Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 265 HIS Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 440 LEU Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 203 TRP Chi-restraints excluded: chain Z residue 269 ASP Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 366 MET Chi-restraints excluded: chain Z residue 394 ASN Chi-restraints excluded: chain Z residue 408 MET Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 540 HIS Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 452 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 342 optimal weight: 30.0000 chunk 265 optimal weight: 0.7980 chunk 395 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 467 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 531 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 370 ASN C 804 GLN C 856 ASN T 81 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 442 GLN X 442 GLN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 305 GLN Z 493 HIS ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39844 Z= 0.199 Angle : 0.685 16.383 54179 Z= 0.340 Chirality : 0.044 0.313 5953 Planarity : 0.005 0.075 7000 Dihedral : 7.283 61.546 5367 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.88 % Favored : 89.54 % Rotamer: Outliers : 5.99 % Allowed : 31.52 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 4818 helix: -0.75 (0.13), residues: 1747 sheet: -1.43 (0.20), residues: 617 loop : -2.83 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP T 473 HIS 0.006 0.001 HIS X 505 PHE 0.033 0.002 PHE B 855 TYR 0.021 0.001 TYR A 266 ARG 0.012 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 246 time to evaluate : 4.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7438 (ttpp) REVERT: A 213 ARG cc_start: 0.3613 (OUTLIER) cc_final: 0.0406 (mpt-90) REVERT: A 304 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: A 990 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 1111 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: B 32 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: B 105 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7471 (pt) REVERT: B 110 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6195 (tp) REVERT: B 213 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.4924 (tpt90) REVERT: B 215 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.6023 (t80) REVERT: B 238 GLN cc_start: 0.7719 (tt0) cc_final: 0.7234 (tt0) REVERT: B 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: B 458 LYS cc_start: 0.0519 (OUTLIER) cc_final: -0.0298 (ptmm) REVERT: B 474 GLN cc_start: 0.2129 (OUTLIER) cc_final: 0.1891 (tt0) REVERT: B 773 GLU cc_start: 0.7890 (tt0) cc_final: 0.7647 (tt0) REVERT: B 984 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7377 (tp) REVERT: B 1092 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: C 88 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7132 (p0) REVERT: C 172 SER cc_start: 0.5747 (OUTLIER) cc_final: 0.5460 (p) REVERT: C 461 LEU cc_start: 0.0448 (OUTLIER) cc_final: -0.0475 (tt) REVERT: C 462 LYS cc_start: 0.1778 (OUTLIER) cc_final: 0.1210 (mttp) REVERT: C 558 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 709 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: T 62 MET cc_start: 0.2059 (OUTLIER) cc_final: 0.1833 (tpt) REVERT: T 82 MET cc_start: 0.3189 (mpm) cc_final: 0.2094 (mtm) REVERT: T 152 MET cc_start: -0.2652 (OUTLIER) cc_final: -0.2887 (tpt) REVERT: T 174 LYS cc_start: 0.1361 (OUTLIER) cc_final: 0.0937 (tmtt) REVERT: T 183 TYR cc_start: -0.0823 (OUTLIER) cc_final: -0.1679 (t80) REVERT: T 190 MET cc_start: 0.1431 (tmt) cc_final: 0.0777 (tpt) REVERT: T 223 ILE cc_start: 0.3035 (OUTLIER) cc_final: 0.2166 (tt) REVERT: T 252 TYR cc_start: 0.0495 (OUTLIER) cc_final: 0.0122 (t80) REVERT: T 287 GLN cc_start: 0.2951 (OUTLIER) cc_final: 0.2290 (pp30) REVERT: T 295 ASP cc_start: 0.3342 (OUTLIER) cc_final: 0.3047 (m-30) REVERT: T 332 MET cc_start: 0.1593 (tmt) cc_final: -0.0743 (mtm) REVERT: T 366 MET cc_start: 0.2292 (mmm) cc_final: 0.0909 (mmm) REVERT: T 369 PHE cc_start: 0.0931 (OUTLIER) cc_final: -0.0290 (p90) REVERT: T 428 PHE cc_start: -0.1606 (t80) cc_final: -0.2390 (t80) REVERT: T 442 GLN cc_start: 0.3380 (OUTLIER) cc_final: 0.2628 (pt0) REVERT: T 462 MET cc_start: 0.4332 (mpm) cc_final: 0.3409 (mtt) REVERT: T 559 ARG cc_start: 0.2859 (ptt90) cc_final: 0.2412 (mtp180) REVERT: T 579 MET cc_start: -0.1062 (OUTLIER) cc_final: -0.2514 (tmm) REVERT: X 20 THR cc_start: -0.1288 (OUTLIER) cc_final: -0.1725 (p) REVERT: X 82 MET cc_start: 0.2514 (ttm) cc_final: 0.1505 (tpt) REVERT: X 110 GLU cc_start: 0.1429 (OUTLIER) cc_final: 0.0328 (pt0) REVERT: X 216 ASP cc_start: 0.0409 (OUTLIER) cc_final: 0.0012 (t0) REVERT: X 249 MET cc_start: 0.0165 (mtp) cc_final: -0.0324 (ttt) REVERT: X 376 MET cc_start: -0.0513 (mtp) cc_final: -0.1067 (mmm) REVERT: X 383 MET cc_start: -0.0627 (mtt) cc_final: -0.1233 (tmt) REVERT: X 400 PHE cc_start: 0.2160 (OUTLIER) cc_final: 0.1416 (t80) REVERT: X 438 PHE cc_start: 0.2567 (OUTLIER) cc_final: 0.1534 (t80) REVERT: X 475 LYS cc_start: 0.3709 (OUTLIER) cc_final: 0.2683 (mmtp) REVERT: X 480 MET cc_start: 0.1013 (mtt) cc_final: -0.0871 (ttp) REVERT: X 511 SER cc_start: -0.0130 (OUTLIER) cc_final: -0.0445 (p) REVERT: X 527 GLU cc_start: 0.3170 (OUTLIER) cc_final: 0.1978 (tp30) REVERT: X 534 LYS cc_start: 0.3322 (OUTLIER) cc_final: 0.2618 (ptpt) REVERT: Z 82 MET cc_start: 0.2439 (OUTLIER) cc_final: 0.2088 (ttp) REVERT: Z 150 GLU cc_start: 0.1956 (tp30) cc_final: 0.0776 (mt-10) REVERT: Z 152 MET cc_start: 0.0817 (tpp) cc_final: -0.0467 (mtt) REVERT: Z 221 GLN cc_start: 0.3734 (tt0) cc_final: 0.3030 (tp40) REVERT: Z 305 GLN cc_start: 0.2181 (OUTLIER) cc_final: 0.1965 (pm20) REVERT: Z 306 ARG cc_start: 0.2844 (OUTLIER) cc_final: 0.1743 (tpp-160) REVERT: Z 323 MET cc_start: -0.2207 (mmp) cc_final: -0.2444 (mtm) REVERT: Z 402 GLU cc_start: 0.2978 (OUTLIER) cc_final: 0.2172 (tp30) REVERT: Z 475 LYS cc_start: 0.4498 (mmmt) cc_final: 0.3932 (mmtp) outliers start: 257 outliers final: 127 residues processed: 480 average time/residue: 1.1957 time to fit residues: 735.6731 Evaluate side-chains 391 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 219 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 152 MET Chi-restraints excluded: chain T residue 174 LYS Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 252 TYR Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 369 PHE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 463 VAL Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 365 THR Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 440 LEU Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 305 GLN Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain Z residue 324 THR Chi-restraints excluded: chain Z residue 358 ILE Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 402 GLU Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 289 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 0.0470 chunk 140 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 297 optimal weight: 0.0970 chunk 318 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 367 optimal weight: 30.0000 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 856 ASN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 378 HIS ** T 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 442 GLN ** X 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 305 GLN Z 340 GLN ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 572 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39844 Z= 0.210 Angle : 0.686 15.721 54179 Z= 0.339 Chirality : 0.044 0.308 5953 Planarity : 0.005 0.073 7000 Dihedral : 6.802 59.739 5335 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.78 % Favored : 89.71 % Rotamer: Outliers : 5.29 % Allowed : 32.36 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.12), residues: 4818 helix: -0.59 (0.13), residues: 1738 sheet: -1.29 (0.20), residues: 650 loop : -2.73 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 473 HIS 0.010 0.001 HIS X 265 PHE 0.030 0.002 PHE B 855 TYR 0.022 0.001 TYR A 266 ARG 0.009 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 233 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.5794 (OUTLIER) cc_final: 0.5428 (tm-30) REVERT: A 90 VAL cc_start: 0.8138 (p) cc_final: 0.7891 (t) REVERT: A 213 ARG cc_start: 0.3916 (OUTLIER) cc_final: 0.0617 (mpt-90) REVERT: A 304 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8392 (mtmm) REVERT: A 990 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: B 213 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.4933 (tpt170) REVERT: B 215 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.6020 (t80) REVERT: B 238 GLN cc_start: 0.7764 (tt0) cc_final: 0.7238 (tt0) REVERT: B 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: B 458 LYS cc_start: 0.0323 (OUTLIER) cc_final: -0.0370 (ptmm) REVERT: B 474 GLN cc_start: 0.2095 (OUTLIER) cc_final: 0.0739 (mt0) REVERT: B 984 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 1092 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: C 52 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 88 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7167 (p0) REVERT: C 236 ARG cc_start: 0.7388 (mpp80) cc_final: 0.7130 (mpp80) REVERT: C 314 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 461 LEU cc_start: 0.0652 (OUTLIER) cc_final: -0.0486 (tt) REVERT: C 462 LYS cc_start: 0.1823 (OUTLIER) cc_final: 0.1252 (mttp) REVERT: C 1142 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: T 39 LEU cc_start: 0.1642 (OUTLIER) cc_final: 0.1345 (tm) REVERT: T 62 MET cc_start: 0.2113 (OUTLIER) cc_final: 0.1902 (tpt) REVERT: T 82 MET cc_start: 0.3095 (mpm) cc_final: 0.2214 (mtm) REVERT: T 183 TYR cc_start: -0.0821 (OUTLIER) cc_final: -0.1602 (t80) REVERT: T 190 MET cc_start: 0.1499 (tmt) cc_final: 0.0746 (tpt) REVERT: T 223 ILE cc_start: 0.3092 (OUTLIER) cc_final: 0.2227 (tt) REVERT: T 252 TYR cc_start: 0.0417 (OUTLIER) cc_final: 0.0083 (t80) REVERT: T 287 GLN cc_start: 0.2721 (OUTLIER) cc_final: 0.2332 (pp30) REVERT: T 295 ASP cc_start: 0.3614 (OUTLIER) cc_final: 0.3322 (m-30) REVERT: T 366 MET cc_start: 0.2284 (mmm) cc_final: 0.1830 (mmt) REVERT: T 428 PHE cc_start: -0.1556 (t80) cc_final: -0.2324 (t80) REVERT: T 442 GLN cc_start: 0.3064 (OUTLIER) cc_final: 0.2461 (pt0) REVERT: T 462 MET cc_start: 0.4258 (mpm) cc_final: 0.3375 (mtt) REVERT: T 475 LYS cc_start: 0.5447 (tppt) cc_final: 0.4566 (pptt) REVERT: T 559 ARG cc_start: 0.3010 (ptt90) cc_final: 0.2623 (mtp180) REVERT: T 579 MET cc_start: -0.1072 (OUTLIER) cc_final: -0.2504 (tmm) REVERT: X 20 THR cc_start: -0.1249 (OUTLIER) cc_final: -0.1657 (p) REVERT: X 82 MET cc_start: 0.2400 (ttm) cc_final: 0.1617 (tpt) REVERT: X 110 GLU cc_start: 0.1445 (OUTLIER) cc_final: 0.0395 (pt0) REVERT: X 152 MET cc_start: 0.0532 (pp-130) cc_final: -0.1879 (tpp) REVERT: X 216 ASP cc_start: 0.0367 (OUTLIER) cc_final: -0.0041 (t0) REVERT: X 249 MET cc_start: 0.0101 (mtp) cc_final: -0.0382 (ttt) REVERT: X 376 MET cc_start: -0.0563 (OUTLIER) cc_final: -0.1023 (mmm) REVERT: X 383 MET cc_start: -0.0725 (mtt) cc_final: -0.1290 (tmt) REVERT: X 400 PHE cc_start: 0.2034 (OUTLIER) cc_final: 0.1395 (t80) REVERT: X 438 PHE cc_start: 0.2806 (OUTLIER) cc_final: 0.1654 (t80) REVERT: X 455 MET cc_start: 0.2629 (ptt) cc_final: 0.2199 (tpp) REVERT: X 475 LYS cc_start: 0.3701 (OUTLIER) cc_final: 0.2715 (mmtp) REVERT: X 480 MET cc_start: 0.1063 (mtt) cc_final: 0.0649 (mtt) REVERT: X 511 SER cc_start: -0.0173 (OUTLIER) cc_final: -0.0599 (p) REVERT: X 527 GLU cc_start: 0.3147 (OUTLIER) cc_final: 0.2038 (tp30) REVERT: X 534 LYS cc_start: 0.3317 (OUTLIER) cc_final: 0.2646 (ptpt) REVERT: Z 82 MET cc_start: 0.2384 (OUTLIER) cc_final: 0.2014 (ttp) REVERT: Z 152 MET cc_start: 0.0763 (tpp) cc_final: -0.0525 (mtt) REVERT: Z 221 GLN cc_start: 0.3759 (tt0) cc_final: 0.3068 (tp40) REVERT: Z 325 GLN cc_start: 0.3378 (OUTLIER) cc_final: 0.2862 (pp30) REVERT: Z 402 GLU cc_start: 0.3034 (OUTLIER) cc_final: 0.2017 (tp30) REVERT: Z 475 LYS cc_start: 0.4551 (mmmt) cc_final: 0.4073 (mmtp) outliers start: 227 outliers final: 127 residues processed: 440 average time/residue: 1.1853 time to fit residues: 671.8294 Evaluate side-chains 385 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 219 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 252 TYR Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 463 VAL Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 376 MET Chi-restraints excluded: chain X residue 400 PHE Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 325 GLN Chi-restraints excluded: chain Z residue 362 THR Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 402 GLU Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 425 optimal weight: 50.0000 chunk 447 optimal weight: 7.9990 chunk 408 optimal weight: 30.0000 chunk 435 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 342 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 393 optimal weight: 3.9990 chunk 412 optimal weight: 6.9990 chunk 434 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A1135 ASN B 49 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 442 GLN X 58 ASN ** X 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 378 HIS ** X 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 340 GLN ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.152 39844 Z= 0.653 Angle : 0.878 16.314 54179 Z= 0.444 Chirality : 0.055 0.350 5953 Planarity : 0.007 0.181 7000 Dihedral : 7.292 57.365 5315 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.69 % Favored : 87.75 % Rotamer: Outliers : 5.69 % Allowed : 31.83 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 4818 helix: -0.95 (0.12), residues: 1717 sheet: -1.46 (0.21), residues: 601 loop : -2.96 (0.11), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 353 HIS 0.012 0.002 HIS X 505 PHE 0.035 0.003 PHE T 230 TYR 0.033 0.003 TYR B 904 ARG 0.011 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 233 time to evaluate : 4.330 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 66 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.3788 (t-90) REVERT: A 213 ARG cc_start: 0.3916 (OUTLIER) cc_final: 0.0744 (mtt-85) REVERT: A 304 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8268 (mtmm) REVERT: A 869 MET cc_start: 0.8905 (mtt) cc_final: 0.8435 (mtt) REVERT: A 990 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: B 213 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5221 (tpt170) REVERT: B 215 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.6282 (t80) REVERT: B 238 GLN cc_start: 0.7857 (tt0) cc_final: 0.7532 (tt0) REVERT: B 458 LYS cc_start: 0.0740 (OUTLIER) cc_final: -0.0296 (ptmm) REVERT: B 474 GLN cc_start: 0.2104 (OUTLIER) cc_final: 0.0675 (mt0) REVERT: B 532 LEU cc_start: 0.7708 (mm) cc_final: 0.7448 (mt) REVERT: B 984 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7473 (tt) REVERT: B 1092 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: C 52 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: C 314 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: C 462 LYS cc_start: 0.2050 (OUTLIER) cc_final: 0.1202 (mptp) REVERT: C 632 TRP cc_start: 0.6005 (OUTLIER) cc_final: 0.5526 (t60) REVERT: C 755 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8120 (mm-40) REVERT: C 847 ARG cc_start: 0.2126 (OUTLIER) cc_final: 0.0621 (tpt170) REVERT: T 39 LEU cc_start: 0.1597 (OUTLIER) cc_final: 0.1276 (tm) REVERT: T 62 MET cc_start: 0.2410 (OUTLIER) cc_final: 0.1924 (tpt) REVERT: T 183 TYR cc_start: -0.0647 (OUTLIER) cc_final: -0.1416 (t80) REVERT: T 190 MET cc_start: 0.2046 (tmt) cc_final: 0.0837 (tpt) REVERT: T 287 GLN cc_start: 0.2996 (OUTLIER) cc_final: 0.2368 (pp30) REVERT: T 295 ASP cc_start: 0.3461 (OUTLIER) cc_final: 0.3043 (m-30) REVERT: T 332 MET cc_start: 0.1488 (tmt) cc_final: -0.0770 (mtm) REVERT: T 366 MET cc_start: 0.2513 (mmm) cc_final: 0.1341 (mmm) REVERT: T 369 PHE cc_start: 0.0890 (OUTLIER) cc_final: -0.0502 (p90) REVERT: T 376 MET cc_start: 0.1802 (tmm) cc_final: 0.1413 (tpp) REVERT: T 428 PHE cc_start: -0.1557 (t80) cc_final: -0.2374 (t80) REVERT: T 442 GLN cc_start: 0.3633 (OUTLIER) cc_final: 0.2913 (pt0) REVERT: T 474 MET cc_start: -0.0250 (ttt) cc_final: -0.0771 (mmm) REVERT: T 557 MET cc_start: 0.2546 (tpt) cc_final: 0.1714 (ptt) REVERT: T 559 ARG cc_start: 0.2985 (ptt90) cc_final: 0.2487 (mtp180) REVERT: T 579 MET cc_start: -0.0795 (OUTLIER) cc_final: -0.2451 (tmm) REVERT: X 20 THR cc_start: -0.1035 (OUTLIER) cc_final: -0.1575 (p) REVERT: X 82 MET cc_start: 0.2796 (ttm) cc_final: 0.1630 (tpt) REVERT: X 110 GLU cc_start: 0.1494 (OUTLIER) cc_final: 0.0350 (pt0) REVERT: X 152 MET cc_start: 0.0426 (pp-130) cc_final: -0.1868 (tpp) REVERT: X 216 ASP cc_start: 0.0355 (OUTLIER) cc_final: -0.0076 (t0) REVERT: X 237 TYR cc_start: 0.1729 (OUTLIER) cc_final: 0.1006 (p90) REVERT: X 249 MET cc_start: 0.0264 (mtp) cc_final: -0.0391 (ttt) REVERT: X 323 MET cc_start: 0.1095 (tpt) cc_final: 0.0576 (tpp) REVERT: X 438 PHE cc_start: 0.2898 (OUTLIER) cc_final: 0.1719 (t80) REVERT: X 455 MET cc_start: 0.2828 (ptt) cc_final: 0.2290 (tpp) REVERT: X 475 LYS cc_start: 0.3582 (OUTLIER) cc_final: 0.2622 (mmtp) REVERT: X 480 MET cc_start: 0.1223 (mtt) cc_final: 0.0880 (mtt) REVERT: X 511 SER cc_start: 0.0086 (OUTLIER) cc_final: -0.0420 (p) REVERT: X 527 GLU cc_start: 0.3320 (OUTLIER) cc_final: 0.2203 (tp30) REVERT: X 534 LYS cc_start: 0.3549 (OUTLIER) cc_final: 0.2649 (ptpt) REVERT: Z 62 MET cc_start: 0.1510 (ttm) cc_final: 0.1003 (tpt) REVERT: Z 82 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.2076 (ttp) REVERT: Z 152 MET cc_start: 0.0754 (tpp) cc_final: -0.0615 (mtt) REVERT: Z 221 GLN cc_start: 0.4049 (tt0) cc_final: 0.3189 (tp40) REVERT: Z 366 MET cc_start: -0.1612 (OUTLIER) cc_final: -0.3033 (mmm) REVERT: Z 431 ASP cc_start: 0.2043 (OUTLIER) cc_final: 0.1314 (p0) outliers start: 244 outliers final: 145 residues processed: 454 average time/residue: 1.1810 time to fit residues: 690.0091 Evaluate side-chains 398 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 217 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 295 ASP Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 369 PHE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 463 VAL Chi-restraints excluded: chain T residue 468 ILE Chi-restraints excluded: chain T residue 473 TRP Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 176 LEU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 237 TYR Chi-restraints excluded: chain X residue 432 ASN Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 505 HIS Chi-restraints excluded: chain X residue 511 SER Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 82 MET Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 324 THR Chi-restraints excluded: chain Z residue 325 GLN Chi-restraints excluded: chain Z residue 358 ILE Chi-restraints excluded: chain Z residue 362 THR Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 366 MET Chi-restraints excluded: chain Z residue 431 ASP Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 286 optimal weight: 0.7980 chunk 460 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 320 optimal weight: 0.0980 chunk 483 optimal weight: 0.3980 chunk 444 optimal weight: 30.0000 chunk 384 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 chunk 235 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 207 HIS A 388 ASN B 49 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 579 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 442 GLN T 493 HIS X 58 ASN X 63 ASN X 96 GLN X 340 GLN X 442 GLN ** X 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 599 ASN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39844 Z= 0.186 Angle : 0.706 15.745 54179 Z= 0.348 Chirality : 0.044 0.305 5953 Planarity : 0.005 0.081 7000 Dihedral : 6.710 59.028 5313 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.78 % Favored : 90.72 % Rotamer: Outliers : 3.50 % Allowed : 34.09 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4818 helix: -0.63 (0.13), residues: 1733 sheet: -1.23 (0.20), residues: 627 loop : -2.67 (0.11), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP T 302 HIS 0.015 0.001 HIS X 505 PHE 0.029 0.002 PHE B 855 TYR 0.030 0.001 TYR A 266 ARG 0.011 0.001 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 224 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.4039 (OUTLIER) cc_final: 0.0790 (mtt-85) REVERT: A 304 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8326 (mtmm) REVERT: A 388 ASN cc_start: 0.2583 (OUTLIER) cc_final: 0.2031 (t0) REVERT: A 990 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 213 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.4909 (tpm170) REVERT: B 215 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 238 GLN cc_start: 0.7717 (tt0) cc_final: 0.7175 (tt0) REVERT: B 458 LYS cc_start: 0.0338 (OUTLIER) cc_final: -0.0392 (ptmm) REVERT: B 474 GLN cc_start: 0.2252 (OUTLIER) cc_final: 0.1007 (mt0) REVERT: B 773 GLU cc_start: 0.7910 (tt0) cc_final: 0.7592 (tt0) REVERT: B 869 MET cc_start: 0.8966 (mtt) cc_final: 0.8670 (mtt) REVERT: B 984 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (tp) REVERT: B 1092 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: C 462 LYS cc_start: 0.1806 (OUTLIER) cc_final: 0.1034 (mptp) REVERT: C 558 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7201 (t80) REVERT: C 859 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8715 (t) REVERT: T 62 MET cc_start: 0.2391 (OUTLIER) cc_final: 0.1977 (tpt) REVERT: T 82 MET cc_start: 0.2941 (mpm) cc_final: 0.1324 (ppp) REVERT: T 123 MET cc_start: 0.0687 (mpp) cc_final: 0.0385 (mpp) REVERT: T 183 TYR cc_start: -0.0875 (OUTLIER) cc_final: -0.1584 (t80) REVERT: T 190 MET cc_start: 0.2002 (tmt) cc_final: 0.0811 (tpt) REVERT: T 287 GLN cc_start: 0.3023 (OUTLIER) cc_final: 0.2369 (pp30) REVERT: T 366 MET cc_start: 0.2153 (mmm) cc_final: 0.1064 (mmm) REVERT: T 369 PHE cc_start: 0.0684 (OUTLIER) cc_final: -0.0734 (p90) REVERT: T 376 MET cc_start: 0.1759 (mmm) cc_final: 0.1452 (tpp) REVERT: T 428 PHE cc_start: -0.1548 (t80) cc_final: -0.2279 (t80) REVERT: T 442 GLN cc_start: 0.3290 (OUTLIER) cc_final: 0.2832 (pt0) REVERT: T 557 MET cc_start: 0.2677 (tpt) cc_final: 0.1811 (ptt) REVERT: T 559 ARG cc_start: 0.2728 (ptt90) cc_final: 0.2492 (ttp-170) REVERT: T 579 MET cc_start: -0.1040 (OUTLIER) cc_final: -0.2483 (tmm) REVERT: X 20 THR cc_start: -0.1010 (OUTLIER) cc_final: -0.1470 (p) REVERT: X 82 MET cc_start: 0.2396 (ttm) cc_final: 0.1650 (tpt) REVERT: X 110 GLU cc_start: 0.1459 (OUTLIER) cc_final: 0.0357 (pt0) REVERT: X 152 MET cc_start: 0.0483 (pp-130) cc_final: -0.1776 (tpp) REVERT: X 216 ASP cc_start: 0.0343 (OUTLIER) cc_final: -0.0038 (t0) REVERT: X 237 TYR cc_start: 0.1618 (OUTLIER) cc_final: 0.0829 (p90) REVERT: X 323 MET cc_start: 0.0996 (tpt) cc_final: 0.0277 (tpp) REVERT: X 383 MET cc_start: -0.0159 (mtt) cc_final: -0.0656 (tpp) REVERT: X 438 PHE cc_start: 0.2796 (OUTLIER) cc_final: 0.1525 (t80) REVERT: X 455 MET cc_start: 0.2917 (ptt) cc_final: 0.2350 (tpp) REVERT: X 475 LYS cc_start: 0.3639 (OUTLIER) cc_final: 0.2568 (mmtp) REVERT: X 480 MET cc_start: 0.1041 (mtt) cc_final: 0.0589 (mtt) REVERT: X 527 GLU cc_start: 0.3356 (OUTLIER) cc_final: 0.1933 (tp30) REVERT: X 534 LYS cc_start: 0.3212 (OUTLIER) cc_final: 0.2488 (ptpt) REVERT: Z 62 MET cc_start: 0.1210 (ttm) cc_final: 0.0844 (tpt) REVERT: Z 82 MET cc_start: 0.2377 (ttm) cc_final: 0.2072 (ttp) REVERT: Z 152 MET cc_start: 0.0730 (tpp) cc_final: -0.0684 (mtt) REVERT: Z 221 GLN cc_start: 0.3812 (tt0) cc_final: 0.2989 (tp40) REVERT: Z 557 MET cc_start: 0.3068 (tmt) cc_final: 0.0312 (ttm) outliers start: 150 outliers final: 99 residues processed: 362 average time/residue: 1.2677 time to fit residues: 589.4808 Evaluate side-chains 339 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 213 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 183 TYR Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 265 HIS Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain T residue 365 THR Chi-restraints excluded: chain T residue 369 PHE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 468 ILE Chi-restraints excluded: chain T residue 473 TRP Chi-restraints excluded: chain T residue 488 VAL Chi-restraints excluded: chain T residue 548 THR Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 573 VAL Chi-restraints excluded: chain T residue 579 MET Chi-restraints excluded: chain T residue 585 LEU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 216 ASP Chi-restraints excluded: chain X residue 237 TYR Chi-restraints excluded: chain X residue 438 PHE Chi-restraints excluded: chain X residue 475 LYS Chi-restraints excluded: chain X residue 527 GLU Chi-restraints excluded: chain X residue 534 LYS Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 498 CYS Chi-restraints excluded: chain Z residue 499 ASP Chi-restraints excluded: chain Z residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 305 optimal weight: 4.9990 chunk 409 optimal weight: 30.0000 chunk 117 optimal weight: 0.0570 chunk 354 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 385 optimal weight: 50.0000 chunk 161 optimal weight: 2.9990 chunk 395 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.0470 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 599 ASN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.236434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.208684 restraints weight = 61263.346| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.08 r_work: 0.4244 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 39844 Z= 0.243 Angle : 0.802 59.197 54179 Z= 0.422 Chirality : 0.044 0.307 5953 Planarity : 0.005 0.123 7000 Dihedral : 6.575 58.972 5301 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.03 % Favored : 90.47 % Rotamer: Outliers : 3.38 % Allowed : 34.09 % Favored : 62.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 4818 helix: -0.62 (0.13), residues: 1733 sheet: -1.24 (0.20), residues: 631 loop : -2.66 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 606 HIS 0.013 0.001 HIS X 505 PHE 0.067 0.002 PHE A 127 TYR 0.018 0.001 TYR X 127 ARG 0.007 0.001 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15702.43 seconds wall clock time: 282 minutes 17.61 seconds (16937.61 seconds total)