Starting phenix.real_space_refine on Sat Jun 21 19:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp9_32679/06_2025/7wp9_32679_neut.cif" } resolution = 2.56 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16028 2.51 5 N 4136 2.21 5 O 4802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25077 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8224 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 55, 'TRANS': 991} Chain breaks: 9 Chain: "B" Number of atoms: 8175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8175 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 54, 'TRANS': 984} Chain breaks: 13 Chain: "C" Number of atoms: 8286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8286 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 56, 'TRANS': 998} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.74, per 1000 atoms: 0.67 Number of scatterers: 25077 At special positions: 0 Unit cell: (126.072, 136.784, 175.512, 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 111 16.00 O 4802 8.00 N 4136 7.00 C 16028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 613 " " NAG A1303 " - " ASN A 706 " " NAG A1304 " - " ASN A1131 " " NAG B1301 " - " ASN B 279 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B1131 " " NAG B1304 " - " ASN B 706 " " NAG B1305 " - " ASN B 328 " " NAG C1301 " - " ASN C 279 " " NAG C1302 " - " ASN C 613 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 706 " " NAG C1305 " - " ASN C1131 " " NAG D 1 " - " ASN A 328 " " NAG E 1 " - " ASN A 798 " " NAG F 1 " - " ASN A1095 " " NAG G 1 " - " ASN B 798 " " NAG H 1 " - " ASN B1095 " " NAG I 1 " - " ASN C 798 " " NAG J 1 " - " ASN C1095 " Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 3.6 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 49 sheets defined 22.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.677A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 743 through 750 removed outlier: 3.659A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 754 removed outlier: 3.882A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.809A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.579A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.765A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 852 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.656A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.906A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 905 " --> pdb=" O TYR A 901 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.666A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.606A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.054A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.624A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 removed outlier: 3.883A pdb=" N VAL A 988 " --> pdb=" O GLU A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 989 through 1030 removed outlier: 3.654A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 3.545A pdb=" N SER A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.928A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.916A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.171A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.119A pdb=" N SER B 747 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 748 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 750 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 751 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 752 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 779 removed outlier: 3.655A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 821 removed outlier: 3.541A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.826A pdb=" N ALA B 849 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 850 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.523A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.586A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 937 removed outlier: 3.559A pdb=" N GLY B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.700A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 951 " --> pdb=" O ASP B 947 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.532A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 985 through 1030 removed outlier: 4.421A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE B 994 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B1015 " --> pdb=" O ARG B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.851A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.984A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 368' Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.700A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 386' Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.825A pdb=" N CYS C 740 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 753 removed outlier: 3.709A pdb=" N GLN C 752 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.502A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.660A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.642A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.542A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 removed outlier: 4.024A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.673A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.529A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 removed outlier: 3.644A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.664A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 979 " --> pdb=" O ASN C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.692A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1143 removed outlier: 3.563A pdb=" N ASP C1143 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.604A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.466A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.564A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 118 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 125 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 124 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 165 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 126 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 163 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 128 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS A 161 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN A 132 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 157 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.547A pdb=" N THR A 312 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.183A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 508 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 428 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 573 removed outlier: 7.004A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.111A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 701 removed outlier: 5.911A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 725 removed outlier: 7.059A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 725 removed outlier: 7.059A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.619A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.486A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.791A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.751A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.794A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.273A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 7.621A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.511A pdb=" N ILE B 355 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.511A pdb=" N ILE B 355 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 397 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 570 through 573 Processing sheet with id=AC8, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.874A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 698 through 700 removed outlier: 6.398A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.445A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.445A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.394A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 6.071A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.052A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.794A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.794A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.720A pdb=" N LEU C 82 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 235 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 105 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 116 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 127 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.751A pdb=" N TYR C 195 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 316 removed outlier: 3.524A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 645 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.863A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.863A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 396 through 399 Processing sheet with id=AE5, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AE6, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE8, first strand: chain 'C' and resid 535 through 540 removed outlier: 3.606A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 545 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 543 " --> pdb=" O PHE C 540 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 582 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.045A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 710 through 725 removed outlier: 6.853A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C1067 " --> pdb=" O ASN C 714 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.469A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1073 through 1075 removed outlier: 3.652A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 795 hydrogen bonds defined for protein. 2166 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: 11.05 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4180 1.32 - 1.45: 7114 1.45 - 1.57: 14208 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25640 Sorted by residual: bond pdb=" C ALA C 369 " pdb=" N PRO C 370 " ideal model delta sigma weight residual 1.335 1.387 -0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C PRO B 983 " pdb=" O PRO B 983 " ideal model delta sigma weight residual 1.240 1.199 0.042 1.12e-02 7.97e+03 1.38e+01 bond pdb=" C PRO A 983 " pdb=" O PRO A 983 " ideal model delta sigma weight residual 1.240 1.203 0.037 1.12e-02 7.97e+03 1.09e+01 bond pdb=" N ASP C 982 " pdb=" CA ASP C 982 " ideal model delta sigma weight residual 1.453 1.480 -0.027 8.30e-03 1.45e+04 1.08e+01 bond pdb=" N LEU B 981 " pdb=" CA LEU B 981 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.27e-02 6.20e+03 7.87e+00 ... (remaining 25635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 34179 2.39 - 4.78: 594 4.78 - 7.17: 71 7.17 - 9.56: 15 9.56 - 11.95: 3 Bond angle restraints: 34862 Sorted by residual: angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 121.54 -10.84 1.22e+00 6.72e-01 7.90e+01 angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 119.24 -8.54 1.22e+00 6.72e-01 4.90e+01 angle pdb=" N ILE B 831 " pdb=" CA ILE B 831 " pdb=" C ILE B 831 " ideal model delta sigma weight residual 113.53 106.82 6.71 9.80e-01 1.04e+00 4.69e+01 angle pdb=" N GLU A 985 " pdb=" CA GLU A 985 " pdb=" C GLU A 985 " ideal model delta sigma weight residual 114.39 105.62 8.77 1.45e+00 4.76e-01 3.65e+01 angle pdb=" C ILE B 192 " pdb=" N ASP B 193 " pdb=" CA ASP B 193 " ideal model delta sigma weight residual 122.46 130.68 -8.22 1.41e+00 5.03e-01 3.40e+01 ... (remaining 34857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 14043 17.65 - 35.30: 1269 35.30 - 52.95: 278 52.95 - 70.59: 67 70.59 - 88.24: 20 Dihedral angle restraints: 15677 sinusoidal: 6507 harmonic: 9170 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -169.71 83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 429 " pdb=" CB CYS A 429 " ideal model delta sinusoidal sigma weight residual -86.00 -139.37 53.37 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A 535 " pdb=" SG CYS A 535 " pdb=" SG CYS A 587 " pdb=" CB CYS A 587 " ideal model delta sinusoidal sigma weight residual -86.00 -35.21 -50.79 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 15674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3972 0.131 - 0.261: 64 0.261 - 0.392: 3 0.392 - 0.523: 1 0.523 - 0.653: 1 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CA PRO B 983 " pdb=" N PRO B 983 " pdb=" C PRO B 983 " pdb=" CB PRO B 983 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PRO C 983 " pdb=" N PRO C 983 " pdb=" C PRO C 983 " pdb=" CB PRO C 983 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" C PRO A 983 " pdb=" CB PRO A 983 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4038 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 983 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PRO A 983 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO A 983 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 984 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " -0.053 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO A 984 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 209 " 0.048 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO C 210 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " 0.040 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 7241 2.82 - 3.34: 19606 3.34 - 3.86: 41003 3.86 - 4.38: 45139 4.38 - 4.90: 79393 Nonbonded interactions: 192382 Sorted by model distance: nonbonded pdb=" OE1 GLU A 295 " pdb=" OH TYR A 633 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.319 3.040 nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.323 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.336 3.040 nonbonded pdb=" O ALA B 876 " pdb=" OG1 THR B 880 " model vdw 2.343 3.040 ... (remaining 192377 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 17 through 23 or resid 25 through 401 or resid 403 through \ 407 or resid 414 through 415 or resid 417 through 419 or resid 421 through 464 \ or resid 468 through 495 or resid 503 through 1144 or resid 1301 through 1304)) selection = (chain 'B' and (resid 17 through 368 or resid 374 through 1144 or resid 1301 thr \ ough 1304)) selection = (chain 'C' and (resid 17 through 23 or resid 25 through 368 or resid 374 through \ 401 or resid 403 through 407 or resid 414 through 415 or resid 417 through 419 \ or resid 421 through 464 or resid 468 through 495 or resid 503 through 1144 or r \ esid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 61.950 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25698 Z= 0.220 Angle : 0.797 25.216 35006 Z= 0.466 Chirality : 0.052 0.653 4041 Planarity : 0.006 0.077 4467 Dihedral : 14.320 88.243 9663 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 0.40 % Allowed : 6.56 % Favored : 93.05 % Cbeta Deviations : 0.03 % 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: -4.01 (0.12), residues: 3077 helix: -2.77 (0.15), residues: 589 sheet: -1.72 (0.20), residues: 593 loop : -3.11 (0.11), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 433 HIS 0.002 0.000 HIS C 516 PHE 0.022 0.001 PHE A 138 TYR 0.024 0.001 TYR B 366 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 21) link_NAG-ASN : angle 4.28357 ( 63) link_BETA1-4 : bond 0.00549 ( 7) link_BETA1-4 : angle 1.27525 ( 21) hydrogen bonds : bond 0.24995 ( 766) hydrogen bonds : angle 9.88153 ( 2166) SS BOND : bond 0.00196 ( 30) SS BOND : angle 0.89279 ( 60) covalent geometry : bond 0.00384 (25640) covalent geometry : angle 0.77620 (34862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 486 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6732 (mt-10) REVERT: A 405 ARG cc_start: 0.2760 (OUTLIER) cc_final: 0.2384 (pmt170) REVERT: A 753 TYR cc_start: 0.7373 (m-80) cc_final: 0.6680 (m-80) REVERT: A 866 MET cc_start: 0.8678 (mtt) cc_final: 0.8440 (mtt) REVERT: A 901 TYR cc_start: 0.7796 (m-10) cc_final: 0.7463 (m-10) REVERT: B 115 LEU cc_start: 0.7363 (tt) cc_final: 0.7096 (mp) REVERT: B 978 PHE cc_start: 0.7526 (m-80) cc_final: 0.6934 (m-10) REVERT: B 981 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7187 (tt) REVERT: B 1135 TYR cc_start: 0.7820 (t80) cc_final: 0.7615 (t80) REVERT: C 63 THR cc_start: 0.7960 (m) cc_final: 0.7556 (p) REVERT: C 902 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7654 (mtt-85) outliers start: 11 outliers final: 3 residues processed: 495 average time/residue: 1.3215 time to fit residues: 757.4799 Evaluate side-chains 362 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 357 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain B residue 981 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 202 HIS A 268 GLN A 318 GLN A 411 GLN A 419 ASN A 445 ASN A 529 ASN A 553 ASN A 641 GLN A 672 GLN A 687 GLN A 774 ASN A 850 GLN A1002 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 49 HIS B 700 ASN B 707 ASN B 759 GLN B 771 GLN B 781 GLN B 898 GLN B 932 GLN B 952 ASN B 954 GLN B1098 HIS C 183 ASN C 311 GLN C 318 GLN C 367 ASN C 560 GLN C 672 GLN C 687 GLN C 898 GLN C 952 ASN C 975 ASN C1020 ASN C1045 HIS C1051 GLN C1071 ASN C1110 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.200885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153491 restraints weight = 33531.350| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.60 r_work: 0.3672 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25698 Z= 0.240 Angle : 0.667 20.751 35006 Z= 0.342 Chirality : 0.048 0.392 4041 Planarity : 0.005 0.077 4467 Dihedral : 6.742 59.971 3960 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.32 % Allowed : 13.94 % Favored : 83.74 % 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: -2.76 (0.14), residues: 3077 helix: -0.78 (0.20), residues: 578 sheet: -1.11 (0.20), residues: 630 loop : -2.57 (0.12), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 433 HIS 0.006 0.001 HIS B1045 PHE 0.032 0.002 PHE C 903 TYR 0.026 0.002 TYR B 263 ARG 0.009 0.001 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 21) link_NAG-ASN : angle 3.99903 ( 63) link_BETA1-4 : bond 0.00429 ( 7) link_BETA1-4 : angle 1.09009 ( 21) hydrogen bonds : bond 0.04789 ( 766) hydrogen bonds : angle 6.38773 ( 2166) SS BOND : bond 0.00856 ( 30) SS BOND : angle 1.66729 ( 60) covalent geometry : bond 0.00565 (25640) covalent geometry : angle 0.64181 (34862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 411 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7151 (mmm-85) REVERT: A 294 SER cc_start: 0.8712 (m) cc_final: 0.8415 (p) REVERT: A 316 ARG cc_start: 0.7357 (ttm110) cc_final: 0.7024 (ttm-80) REVERT: A 600 ASN cc_start: 0.8002 (t0) cc_final: 0.7768 (t0) REVERT: B 172 MET cc_start: 0.6450 (ttp) cc_final: 0.6111 (ttp) REVERT: B 571 ASP cc_start: 0.7341 (t0) cc_final: 0.7069 (t0) REVERT: B 722 GLU cc_start: 0.8458 (tt0) cc_final: 0.8191 (tt0) REVERT: B 752 GLN cc_start: 0.7955 (mp10) cc_final: 0.7716 (mp10) REVERT: B 897 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: B 981 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7433 (tt) REVERT: B 1028 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7993 (mt-10) REVERT: B 1115 ASP cc_start: 0.7825 (m-30) cc_final: 0.7590 (m-30) REVERT: B 1124 ASP cc_start: 0.7529 (m-30) cc_final: 0.7252 (m-30) REVERT: C 58 PHE cc_start: 0.8157 (m-10) cc_final: 0.7808 (m-10) REVERT: C 301 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7828 (mmtm) REVERT: C 947 ASP cc_start: 0.7697 (m-30) cc_final: 0.7421 (m-30) REVERT: C 989 GLN cc_start: 0.8489 (mt0) cc_final: 0.8152 (mt0) outliers start: 64 outliers final: 28 residues processed: 453 average time/residue: 1.3440 time to fit residues: 705.3622 Evaluate side-chains 418 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 388 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 215 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 271 optimal weight: 0.0970 chunk 157 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 529 ASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 687 GLN A 952 ASN A 962 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN A1132 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 436 ASN B 672 GLN B 700 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 916 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.199608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151560 restraints weight = 33265.099| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.67 r_work: 0.3663 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25698 Z= 0.201 Angle : 0.607 21.141 35006 Z= 0.310 Chirality : 0.046 0.397 4041 Planarity : 0.004 0.086 4467 Dihedral : 6.096 59.553 3950 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.08 % Allowed : 15.94 % Favored : 80.99 % 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: -2.31 (0.14), residues: 3077 helix: -0.10 (0.21), residues: 600 sheet: -0.92 (0.20), residues: 632 loop : -2.37 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 433 HIS 0.004 0.001 HIS C1061 PHE 0.024 0.002 PHE C 967 TYR 0.023 0.001 TYR B 263 ARG 0.008 0.000 ARG C 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 21) link_NAG-ASN : angle 3.90052 ( 63) link_BETA1-4 : bond 0.00243 ( 7) link_BETA1-4 : angle 0.97283 ( 21) hydrogen bonds : bond 0.04502 ( 766) hydrogen bonds : angle 5.92657 ( 2166) SS BOND : bond 0.00415 ( 30) SS BOND : angle 1.60924 ( 60) covalent geometry : bond 0.00474 (25640) covalent geometry : angle 0.58082 (34862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 409 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9140 (m-10) cc_final: 0.8765 (m-80) REVERT: A 100 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7169 (mmm-85) REVERT: A 301 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8269 (mtpp) REVERT: A 316 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7232 (ttm-80) REVERT: A 550 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7694 (t) REVERT: A 553 ASN cc_start: 0.8200 (t0) cc_final: 0.7908 (t0) REVERT: A 564 ARG cc_start: 0.7351 (mmt90) cc_final: 0.6933 (mtt180) REVERT: A 600 ASN cc_start: 0.8014 (t0) cc_final: 0.7794 (t0) REVERT: A 752 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 987 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 1069 GLU cc_start: 0.8457 (pm20) cc_final: 0.8054 (pm20) REVERT: B 571 ASP cc_start: 0.7342 (t0) cc_final: 0.6953 (t0) REVERT: B 752 GLN cc_start: 0.8129 (mp10) cc_final: 0.7814 (mp10) REVERT: B 981 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7448 (tt) REVERT: C 34 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7864 (mpt180) REVERT: C 128 VAL cc_start: 0.4814 (OUTLIER) cc_final: 0.4541 (p) REVERT: C 206 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6786 (mm) REVERT: C 319 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: C 947 ASP cc_start: 0.7781 (m-30) cc_final: 0.7505 (m-30) REVERT: C 989 GLN cc_start: 0.8474 (mt0) cc_final: 0.8043 (mt0) outliers start: 85 outliers final: 36 residues processed: 458 average time/residue: 1.4076 time to fit residues: 746.6147 Evaluate side-chains 441 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 295 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN B 79 ASN B 97 ASN B 202 HIS B 236 GLN B 314 ASN B 700 ASN B 707 ASN B 776 GLN B 962 GLN C 340 ASN C 603 ASN C 801 GLN C 957 ASN C 975 ASN C1071 ASN C1116 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.199446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150331 restraints weight = 33430.962| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.65 r_work: 0.3641 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25698 Z= 0.194 Angle : 0.596 20.311 35006 Z= 0.304 Chirality : 0.046 0.437 4041 Planarity : 0.004 0.084 4467 Dihedral : 5.819 59.875 3950 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 16.77 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.14), residues: 3077 helix: 0.21 (0.21), residues: 607 sheet: -0.86 (0.19), residues: 646 loop : -2.17 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 433 HIS 0.004 0.001 HIS B 951 PHE 0.024 0.002 PHE C 967 TYR 0.023 0.001 TYR B 165 ARG 0.008 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 21) link_NAG-ASN : angle 3.79796 ( 63) link_BETA1-4 : bond 0.00341 ( 7) link_BETA1-4 : angle 0.99587 ( 21) hydrogen bonds : bond 0.04156 ( 766) hydrogen bonds : angle 5.70562 ( 2166) SS BOND : bond 0.00348 ( 30) SS BOND : angle 1.56724 ( 60) covalent geometry : bond 0.00460 (25640) covalent geometry : angle 0.57095 (34862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 407 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9064 (m-10) cc_final: 0.8840 (m-80) REVERT: A 100 ARG cc_start: 0.7382 (mmt90) cc_final: 0.7054 (mmm160) REVERT: A 316 ARG cc_start: 0.6982 (ttm110) cc_final: 0.6733 (ttm-80) REVERT: A 465 ILE cc_start: -0.0872 (OUTLIER) cc_final: -0.1130 (mt) REVERT: A 529 ASN cc_start: 0.8196 (t0) cc_final: 0.7961 (t0) REVERT: A 550 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7452 (t) REVERT: A 553 ASN cc_start: 0.8143 (t0) cc_final: 0.7811 (t0) REVERT: A 600 ASN cc_start: 0.7711 (t0) cc_final: 0.7499 (t0) REVERT: A 987 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: A 1069 GLU cc_start: 0.8152 (pm20) cc_final: 0.7733 (pm20) REVERT: B 571 ASP cc_start: 0.6859 (t0) cc_final: 0.6511 (t0) REVERT: B 752 GLN cc_start: 0.7917 (mp10) cc_final: 0.7603 (mp10) REVERT: B 851 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8312 (ttmm) REVERT: B 897 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: B 928 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8545 (tp) REVERT: B 981 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7367 (tt) REVERT: C 128 VAL cc_start: 0.4768 (OUTLIER) cc_final: 0.4471 (p) REVERT: C 206 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6796 (mm) REVERT: C 301 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7445 (mmtm) REVERT: C 319 PRO cc_start: 0.8423 (Cg_endo) cc_final: 0.8213 (Cg_exo) REVERT: C 638 ASN cc_start: 0.7289 (m110) cc_final: 0.7080 (m-40) REVERT: C 918 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7925 (tttp) REVERT: C 989 GLN cc_start: 0.8386 (mt0) cc_final: 0.8068 (mt0) outliers start: 90 outliers final: 45 residues processed: 457 average time/residue: 1.4806 time to fit residues: 796.1915 Evaluate side-chains 455 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 401 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1116 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 chunk 193 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 270 optimal weight: 0.0970 chunk 181 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 30 ASN B 314 ASN B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN B 954 GLN C 603 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1071 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.199920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152381 restraints weight = 33487.872| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.62 r_work: 0.3667 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25698 Z= 0.140 Angle : 0.570 20.157 35006 Z= 0.290 Chirality : 0.045 0.427 4041 Planarity : 0.004 0.072 4467 Dihedral : 5.599 59.021 3950 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.83 % Allowed : 17.75 % Favored : 79.43 % 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: -1.79 (0.14), residues: 3077 helix: 0.59 (0.21), residues: 606 sheet: -0.78 (0.19), residues: 636 loop : -2.06 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 433 HIS 0.005 0.001 HIS B 951 PHE 0.025 0.001 PHE C 32 TYR 0.017 0.001 TYR B 366 ARG 0.009 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 21) link_NAG-ASN : angle 3.71669 ( 63) link_BETA1-4 : bond 0.00356 ( 7) link_BETA1-4 : angle 0.97401 ( 21) hydrogen bonds : bond 0.03761 ( 766) hydrogen bonds : angle 5.56653 ( 2166) SS BOND : bond 0.00379 ( 30) SS BOND : angle 1.70652 ( 60) covalent geometry : bond 0.00329 (25640) covalent geometry : angle 0.54367 (34862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7170 (mmm160) REVERT: A 316 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7159 (ttm-80) REVERT: A 529 ASN cc_start: 0.8385 (t0) cc_final: 0.8135 (t0) REVERT: A 550 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7675 (t) REVERT: A 553 ASN cc_start: 0.8158 (t0) cc_final: 0.7757 (t0) REVERT: A 600 ASN cc_start: 0.8016 (t0) cc_final: 0.7791 (t0) REVERT: A 987 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 1069 GLU cc_start: 0.8396 (pm20) cc_final: 0.7976 (pm20) REVERT: B 58 PHE cc_start: 0.8541 (m-10) cc_final: 0.8297 (m-10) REVERT: B 185 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: B 571 ASP cc_start: 0.7234 (t0) cc_final: 0.6821 (t0) REVERT: B 752 GLN cc_start: 0.8141 (mp10) cc_final: 0.7757 (mp10) REVERT: B 816 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 851 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8352 (ttmm) REVERT: B 897 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8392 (mtm) REVERT: B 909 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8301 (p) REVERT: B 978 PHE cc_start: 0.8307 (m-10) cc_final: 0.7205 (m-10) REVERT: B 981 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7457 (tt) REVERT: B 1124 ASP cc_start: 0.7897 (m-30) cc_final: 0.7645 (m-30) REVERT: C 128 VAL cc_start: 0.4838 (OUTLIER) cc_final: 0.4566 (p) REVERT: C 206 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6717 (mm) REVERT: C 301 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7644 (mmtm) REVERT: C 319 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8180 (Cg_exo) REVERT: C 638 ASN cc_start: 0.7445 (m110) cc_final: 0.7188 (m-40) REVERT: C 918 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8066 (tttp) REVERT: C 947 ASP cc_start: 0.7846 (m-30) cc_final: 0.7535 (m-30) REVERT: C 989 GLN cc_start: 0.8481 (mt0) cc_final: 0.8151 (mt0) outliers start: 78 outliers final: 46 residues processed: 451 average time/residue: 1.7967 time to fit residues: 944.2784 Evaluate side-chains 447 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 393 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 961 LYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1129 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 144 optimal weight: 50.0000 chunk 185 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1071 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 975 ASN C1071 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.198150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150246 restraints weight = 33192.836| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.54 r_work: 0.3647 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 25698 Z= 0.268 Angle : 0.637 20.342 35006 Z= 0.324 Chirality : 0.048 0.455 4041 Planarity : 0.004 0.072 4467 Dihedral : 5.724 54.017 3950 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.15 % Allowed : 18.18 % Favored : 78.67 % 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: -1.81 (0.14), residues: 3077 helix: 0.41 (0.21), residues: 609 sheet: -0.81 (0.20), residues: 613 loop : -1.99 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 883 HIS 0.005 0.001 HIS A1061 PHE 0.033 0.002 PHE C 967 TYR 0.024 0.002 TYR B 165 ARG 0.005 0.000 ARG C 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 21) link_NAG-ASN : angle 3.92412 ( 63) link_BETA1-4 : bond 0.00306 ( 7) link_BETA1-4 : angle 1.08136 ( 21) hydrogen bonds : bond 0.04565 ( 766) hydrogen bonds : angle 5.70019 ( 2166) SS BOND : bond 0.00437 ( 30) SS BOND : angle 2.09137 ( 60) covalent geometry : bond 0.00641 (25640) covalent geometry : angle 0.60920 (34862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 401 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.7508 (ttm110) cc_final: 0.7259 (ttm-80) REVERT: A 465 ILE cc_start: -0.0850 (OUTLIER) cc_final: -0.1124 (mt) REVERT: A 529 ASN cc_start: 0.8403 (t0) cc_final: 0.8155 (t0) REVERT: A 550 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7655 (t) REVERT: A 553 ASN cc_start: 0.8158 (t0) cc_final: 0.7765 (t0) REVERT: A 600 ASN cc_start: 0.8019 (t0) cc_final: 0.7802 (t0) REVERT: A 756 PHE cc_start: 0.7735 (t80) cc_final: 0.7515 (t80) REVERT: A 987 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 1069 GLU cc_start: 0.8394 (pm20) cc_final: 0.7990 (pm20) REVERT: B 571 ASP cc_start: 0.7343 (t0) cc_final: 0.6922 (t0) REVERT: B 742 ASP cc_start: 0.4994 (OUTLIER) cc_final: 0.4684 (m-30) REVERT: B 752 GLN cc_start: 0.8182 (mp10) cc_final: 0.7818 (mp10) REVERT: B 897 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8450 (mtm) REVERT: B 973 VAL cc_start: 0.8841 (t) cc_final: 0.8455 (m) REVERT: B 976 ASP cc_start: 0.7711 (m-30) cc_final: 0.7269 (m-30) REVERT: B 981 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7792 (tt) REVERT: C 58 PHE cc_start: 0.8126 (m-10) cc_final: 0.7899 (m-80) REVERT: C 206 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6757 (mm) REVERT: C 301 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7686 (mmtm) REVERT: C 319 PRO cc_start: 0.8441 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: C 737 MET cc_start: 0.8219 (tpp) cc_final: 0.7956 (tmm) REVERT: C 918 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8095 (tttp) REVERT: C 982 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7699 (t0) REVERT: C 989 GLN cc_start: 0.8491 (mt0) cc_final: 0.8111 (mt0) outliers start: 87 outliers final: 55 residues processed: 454 average time/residue: 1.2832 time to fit residues: 679.5399 Evaluate side-chains 457 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 393 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 918 LYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 0.3980 chunk 229 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 122 optimal weight: 0.0040 chunk 75 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN A1116 ASN B 17 ASN B 30 ASN B 314 ASN B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 516 HIS C 975 ASN C1071 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.199894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151233 restraints weight = 33361.617| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.58 r_work: 0.3662 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25698 Z= 0.130 Angle : 0.586 19.772 35006 Z= 0.294 Chirality : 0.045 0.426 4041 Planarity : 0.004 0.065 4467 Dihedral : 5.433 55.050 3950 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.79 % Allowed : 19.41 % Favored : 77.80 % 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: -1.59 (0.14), residues: 3077 helix: 0.80 (0.21), residues: 612 sheet: -0.72 (0.20), residues: 620 loop : -1.92 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 433 HIS 0.006 0.001 HIS B 951 PHE 0.023 0.001 PHE C 538 TYR 0.016 0.001 TYR B 366 ARG 0.008 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 21) link_NAG-ASN : angle 3.98912 ( 63) link_BETA1-4 : bond 0.00392 ( 7) link_BETA1-4 : angle 0.98849 ( 21) hydrogen bonds : bond 0.03604 ( 766) hydrogen bonds : angle 5.48701 ( 2166) SS BOND : bond 0.00353 ( 30) SS BOND : angle 1.58651 ( 60) covalent geometry : bond 0.00302 (25640) covalent geometry : angle 0.55769 (34862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 395 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7684 (mmt90) cc_final: 0.7250 (mmm160) REVERT: A 316 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7175 (ttm-80) REVERT: A 465 ILE cc_start: -0.0836 (OUTLIER) cc_final: -0.1125 (mt) REVERT: A 529 ASN cc_start: 0.8388 (t0) cc_final: 0.8164 (t0) REVERT: A 553 ASN cc_start: 0.8132 (t0) cc_final: 0.7756 (t0) REVERT: A 600 ASN cc_start: 0.8044 (t0) cc_final: 0.7830 (t0) REVERT: A 756 PHE cc_start: 0.7681 (t80) cc_final: 0.7471 (t80) REVERT: A 987 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 1069 GLU cc_start: 0.8346 (pm20) cc_final: 0.7994 (pm20) REVERT: B 185 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7784 (ttm-80) REVERT: B 530 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7594 (tt) REVERT: B 571 ASP cc_start: 0.7247 (t0) cc_final: 0.6809 (t0) REVERT: B 752 GLN cc_start: 0.8144 (mp10) cc_final: 0.7755 (mp10) REVERT: B 816 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 909 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 973 VAL cc_start: 0.8864 (t) cc_final: 0.8593 (m) REVERT: C 58 PHE cc_start: 0.8122 (m-10) cc_final: 0.7880 (m-10) REVERT: C 128 VAL cc_start: 0.4972 (OUTLIER) cc_final: 0.4702 (p) REVERT: C 206 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6724 (mm) REVERT: C 301 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7671 (mmtm) REVERT: C 737 MET cc_start: 0.8050 (tpp) cc_final: 0.7807 (tmm) REVERT: C 892 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: C 989 GLN cc_start: 0.8448 (mt0) cc_final: 0.8161 (mt0) outliers start: 77 outliers final: 48 residues processed: 433 average time/residue: 1.7008 time to fit residues: 857.5346 Evaluate side-chains 442 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 304 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 285 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 17 ASN B 541 ASN B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.199478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150410 restraints weight = 33278.197| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.61 r_work: 0.3655 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25698 Z= 0.151 Angle : 0.588 19.776 35006 Z= 0.298 Chirality : 0.045 0.435 4041 Planarity : 0.004 0.056 4467 Dihedral : 5.301 54.778 3948 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.83 % Allowed : 19.45 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.51 (0.14), residues: 3077 helix: 0.91 (0.21), residues: 612 sheet: -0.65 (0.20), residues: 618 loop : -1.89 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 433 HIS 0.007 0.001 HIS B 951 PHE 0.025 0.001 PHE C 538 TYR 0.024 0.001 TYR B 165 ARG 0.005 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 21) link_NAG-ASN : angle 4.05379 ( 63) link_BETA1-4 : bond 0.00324 ( 7) link_BETA1-4 : angle 1.00323 ( 21) hydrogen bonds : bond 0.03741 ( 766) hydrogen bonds : angle 5.44456 ( 2166) SS BOND : bond 0.00349 ( 30) SS BOND : angle 1.79949 ( 60) covalent geometry : bond 0.00359 (25640) covalent geometry : angle 0.55770 (34862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 389 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7240 (t70) REVERT: A 100 ARG cc_start: 0.7681 (mmt90) cc_final: 0.7236 (mmm160) REVERT: A 465 ILE cc_start: -0.0824 (OUTLIER) cc_final: -0.1112 (mt) REVERT: A 529 ASN cc_start: 0.8376 (t0) cc_final: 0.8154 (t0) REVERT: A 553 ASN cc_start: 0.8116 (t0) cc_final: 0.7755 (t0) REVERT: A 600 ASN cc_start: 0.8058 (t0) cc_final: 0.7843 (t0) REVERT: A 987 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 1069 GLU cc_start: 0.8360 (pm20) cc_final: 0.8002 (pm20) REVERT: B 185 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7807 (ttm-80) REVERT: B 530 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7457 (tt) REVERT: B 571 ASP cc_start: 0.7374 (t0) cc_final: 0.6913 (t0) REVERT: B 742 ASP cc_start: 0.4992 (OUTLIER) cc_final: 0.4659 (m-30) REVERT: B 752 GLN cc_start: 0.8138 (mp10) cc_final: 0.7772 (mp10) REVERT: B 909 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8306 (p) REVERT: B 973 VAL cc_start: 0.8856 (t) cc_final: 0.8569 (m) REVERT: B 981 LEU cc_start: 0.8000 (tp) cc_final: 0.7773 (tt) REVERT: B 1088 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7910 (mtt180) REVERT: C 58 PHE cc_start: 0.8112 (m-10) cc_final: 0.7858 (m-10) REVERT: C 128 VAL cc_start: 0.5009 (OUTLIER) cc_final: 0.4740 (p) REVERT: C 206 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6711 (mm) REVERT: C 301 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7690 (mmtm) REVERT: C 525 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5557 (mtmm) REVERT: C 892 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: C 918 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8038 (tttp) REVERT: C 967 PHE cc_start: 0.7795 (m-10) cc_final: 0.7548 (m-80) REVERT: C 989 GLN cc_start: 0.8439 (mt0) cc_final: 0.8139 (mt0) outliers start: 78 outliers final: 52 residues processed: 439 average time/residue: 1.3206 time to fit residues: 673.0215 Evaluate side-chains 445 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 961 LYS Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 107 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 276 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 17 ASN B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN B 954 GLN C 603 ASN C 975 ASN C1071 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.198742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.150433 restraints weight = 33292.616| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.61 r_work: 0.3649 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25698 Z= 0.192 Angle : 0.612 19.832 35006 Z= 0.310 Chirality : 0.046 0.445 4041 Planarity : 0.004 0.057 4467 Dihedral : 5.356 54.565 3948 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.61 % Allowed : 20.32 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.51 (0.15), residues: 3077 helix: 0.94 (0.21), residues: 607 sheet: -0.62 (0.20), residues: 619 loop : -1.91 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 883 HIS 0.008 0.001 HIS B 951 PHE 0.026 0.001 PHE C 538 TYR 0.022 0.001 TYR C1135 ARG 0.005 0.000 ARG A 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 21) link_NAG-ASN : angle 4.11276 ( 63) link_BETA1-4 : bond 0.00332 ( 7) link_BETA1-4 : angle 1.04122 ( 21) hydrogen bonds : bond 0.04049 ( 766) hydrogen bonds : angle 5.51250 ( 2166) SS BOND : bond 0.00412 ( 30) SS BOND : angle 1.96896 ( 60) covalent geometry : bond 0.00460 (25640) covalent geometry : angle 0.58111 (34862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 386 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7238 (t70) REVERT: A 465 ILE cc_start: -0.0819 (OUTLIER) cc_final: -0.1110 (mt) REVERT: A 529 ASN cc_start: 0.8363 (t0) cc_final: 0.8114 (t0) REVERT: A 553 ASN cc_start: 0.8118 (t0) cc_final: 0.7740 (t0) REVERT: A 600 ASN cc_start: 0.8024 (t0) cc_final: 0.7810 (t0) REVERT: A 987 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 1069 GLU cc_start: 0.8382 (pm20) cc_final: 0.7994 (pm20) REVERT: B 185 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7825 (ttm-80) REVERT: B 571 ASP cc_start: 0.7448 (t0) cc_final: 0.6953 (t0) REVERT: B 752 GLN cc_start: 0.8155 (mp10) cc_final: 0.7740 (mp10) REVERT: B 909 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 973 VAL cc_start: 0.8819 (t) cc_final: 0.8360 (m) REVERT: B 976 ASP cc_start: 0.7695 (m-30) cc_final: 0.7207 (m-30) REVERT: B 1088 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (mtt180) REVERT: C 58 PHE cc_start: 0.8077 (m-10) cc_final: 0.7613 (m-10) REVERT: C 128 VAL cc_start: 0.4989 (OUTLIER) cc_final: 0.4713 (p) REVERT: C 206 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6696 (mm) REVERT: C 301 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7666 (mmtm) REVERT: C 525 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5570 (mtmm) REVERT: C 918 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8039 (tttp) REVERT: C 989 GLN cc_start: 0.8437 (mt0) cc_final: 0.8112 (mt0) outliers start: 72 outliers final: 51 residues processed: 429 average time/residue: 1.9825 time to fit residues: 997.8499 Evaluate side-chains 440 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 762 ARG Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 135 optimal weight: 0.0050 chunk 217 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 177 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 700 ASN B 776 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1071 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.199613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150495 restraints weight = 33134.327| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.62 r_work: 0.3655 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25698 Z= 0.142 Angle : 0.591 19.561 35006 Z= 0.299 Chirality : 0.045 0.427 4041 Planarity : 0.004 0.057 4467 Dihedral : 5.207 55.052 3948 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.35 % Allowed : 20.79 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.43 (0.15), residues: 3077 helix: 1.02 (0.21), residues: 612 sheet: -0.62 (0.20), residues: 629 loop : -1.86 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 433 HIS 0.009 0.001 HIS B 951 PHE 0.023 0.001 PHE C 538 TYR 0.023 0.001 TYR B 165 ARG 0.005 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 21) link_NAG-ASN : angle 4.02484 ( 63) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.00657 ( 21) hydrogen bonds : bond 0.03650 ( 766) hydrogen bonds : angle 5.40115 ( 2166) SS BOND : bond 0.00375 ( 30) SS BOND : angle 1.68092 ( 60) covalent geometry : bond 0.00339 (25640) covalent geometry : angle 0.56252 (34862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7257 (t70) REVERT: A 100 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7474 (mmt90) REVERT: A 465 ILE cc_start: -0.0806 (OUTLIER) cc_final: -0.1101 (mt) REVERT: A 529 ASN cc_start: 0.8368 (t0) cc_final: 0.8093 (t0) REVERT: A 553 ASN cc_start: 0.8100 (t0) cc_final: 0.7752 (t0) REVERT: A 600 ASN cc_start: 0.8031 (t0) cc_final: 0.7822 (t0) REVERT: A 987 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: A 1069 GLU cc_start: 0.8366 (pm20) cc_final: 0.8000 (pm20) REVERT: B 185 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7837 (ttm-80) REVERT: B 571 ASP cc_start: 0.7440 (t0) cc_final: 0.6975 (t0) REVERT: B 752 GLN cc_start: 0.8153 (mp10) cc_final: 0.7770 (mp10) REVERT: B 761 LYS cc_start: 0.8382 (tttm) cc_final: 0.8154 (tttm) REVERT: B 909 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 973 VAL cc_start: 0.8853 (t) cc_final: 0.8544 (m) REVERT: B 1088 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.8000 (mtt180) REVERT: C 58 PHE cc_start: 0.8109 (m-10) cc_final: 0.7761 (m-10) REVERT: C 128 VAL cc_start: 0.5008 (OUTLIER) cc_final: 0.4743 (p) REVERT: C 206 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6690 (mm) REVERT: C 301 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7707 (mmtm) REVERT: C 918 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8042 (tttp) REVERT: C 989 GLN cc_start: 0.8417 (mt0) cc_final: 0.8126 (mt0) outliers start: 65 outliers final: 50 residues processed: 422 average time/residue: 1.3632 time to fit residues: 666.4915 Evaluate side-chains 436 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 378 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 961 LYS Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 88 optimal weight: 0.0870 chunk 81 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 194 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 277 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN B 17 ASN B 700 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 268 GLN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1071 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.200158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151413 restraints weight = 33396.955| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.65 r_work: 0.3683 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25698 Z= 0.122 Angle : 0.579 19.449 35006 Z= 0.292 Chirality : 0.044 0.426 4041 Planarity : 0.004 0.055 4467 Dihedral : 5.085 55.073 3948 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.54 % Allowed : 20.61 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.34 (0.15), residues: 3077 helix: 1.18 (0.22), residues: 612 sheet: -0.61 (0.20), residues: 631 loop : -1.80 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 433 HIS 0.008 0.001 HIS B 951 PHE 0.023 0.001 PHE C 538 TYR 0.021 0.001 TYR C1135 ARG 0.005 0.000 ARG C 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 21) link_NAG-ASN : angle 3.94960 ( 63) link_BETA1-4 : bond 0.00311 ( 7) link_BETA1-4 : angle 0.96544 ( 21) hydrogen bonds : bond 0.03441 ( 766) hydrogen bonds : angle 5.31763 ( 2166) SS BOND : bond 0.00330 ( 30) SS BOND : angle 1.52208 ( 60) covalent geometry : bond 0.00285 (25640) covalent geometry : angle 0.55095 (34862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27835.72 seconds wall clock time: 487 minutes 28.37 seconds (29248.37 seconds total)