Starting phenix.real_space_refine on Fri Mar 6 11:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.map" model { file = "/net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yd0_33744/03_2026/7yd0_33744.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 137 5.16 5 C 19426 2.51 5 N 5046 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30413 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "E" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "G" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Time building chain proxies: 6.58, per 1000 atoms: 0.22 Number of scatterers: 30413 At special positions: 0 Unit cell: (143.64, 211.736, 222.376, 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 137 16.00 O 5804 8.00 N 5046 7.00 C 19426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7394 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 62 sheets defined 18.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.781A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.599A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.772A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.558A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.519A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.598A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 857 removed outlier: 3.517A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.721A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.675A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 946 through 966 removed outlier: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.607A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.565A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.889A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.088A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.821A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.822A pdb=" N ASN B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.552A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.519A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.972A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.505A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.506A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.988A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 905 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.689A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.713A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.692A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.538A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.517A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.116A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.620A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.735A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.899A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.295A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.086A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.712A pdb=" N SER C1147 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.692A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.688A pdb=" N ASP G 84 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G 85 " --> pdb=" O ALA G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.563A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.542A pdb=" N PHE A 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 7.294A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.538A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.982A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 94 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 188 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 189 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 204 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.629A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 319 removed outlier: 4.856A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.635A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.407A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.983A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.716A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.716A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.320A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.786A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.989A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.666A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.655A pdb=" N ALA B 263 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 92 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 188 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 187 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 191 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.767A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.659A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.646A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.071A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.017A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.305A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.305A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.069A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.266A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.616A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.570A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.999A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.504A pdb=" N VAL C 90 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 192 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.504A pdb=" N VAL C 90 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 192 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 189 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.618A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.545A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.795A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.625A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.461A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.415A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.836A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.216A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.715A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 41 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.784A pdb=" N TYR D 152 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.537A pdb=" N VAL E 10 " --> pdb=" O THR E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF9, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.479A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 89 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.560A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.782A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 114 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.780A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.590A pdb=" N VAL G 10 " --> pdb=" O THR G 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG7, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.615A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 89 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 148 through 149 851 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.71 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5171 1.33 - 1.45: 8423 1.45 - 1.57: 17375 1.57 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 31139 Sorted by residual: bond pdb=" CA ALA A 27 " pdb=" C ALA A 27 " ideal model delta sigma weight residual 1.523 1.454 0.070 1.34e-02 5.57e+03 2.69e+01 bond pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta sigma weight residual 1.457 1.509 -0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA TYR B 28 " pdb=" C TYR B 28 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.24e-02 6.50e+03 7.50e+00 bond pdb=" C TYR B 28 " pdb=" O TYR B 28 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.24e-02 6.50e+03 5.84e+00 bond pdb=" CA ALA B 27 " pdb=" CB ALA B 27 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.54e-02 4.22e+03 5.29e+00 ... (remaining 31134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 41808 2.12 - 4.25: 582 4.25 - 6.37: 40 6.37 - 8.50: 5 8.50 - 10.62: 6 Bond angle restraints: 42441 Sorted by residual: angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 108.48 117.35 -8.87 1.44e+00 4.82e-01 3.80e+01 angle pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" C PHE B 329 " ideal model delta sigma weight residual 110.10 100.97 9.13 1.53e+00 4.27e-01 3.56e+01 angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 112.90 107.88 5.02 9.60e-01 1.09e+00 2.73e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 112.47 123.09 -10.62 2.06e+00 2.36e-01 2.66e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.12 4.59 9.50e-01 1.11e+00 2.34e+01 ... (remaining 42436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 17706 17.11 - 34.22: 735 34.22 - 51.33: 141 51.33 - 68.44: 23 68.44 - 85.55: 9 Dihedral angle restraints: 18614 sinusoidal: 7130 harmonic: 11484 Sorted by residual: dihedral pdb=" CA PHE B 135 " pdb=" C PHE B 135 " pdb=" N CYS B 136 " pdb=" CA CYS B 136 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C PHE B 329 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" CB PHE B 329 " ideal model delta harmonic sigma weight residual -122.60 -112.96 -9.64 0 2.50e+00 1.60e-01 1.49e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual -73.00 -11.24 -61.76 1 2.00e+01 2.50e-03 1.26e+01 ... (remaining 18611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4398 0.072 - 0.145: 456 0.145 - 0.217: 6 0.217 - 0.290: 2 0.290 - 0.362: 1 Chirality restraints: 4863 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4860 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 330 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO A 987 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 24 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO C 25 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 25 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 25 " -0.031 5.00e-02 4.00e+02 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4233 2.76 - 3.29: 29294 3.29 - 3.83: 50066 3.83 - 4.36: 58495 4.36 - 4.90: 100729 Nonbonded interactions: 242817 Sorted by model distance: nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER A1003 " model vdw 2.223 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR G 5 " pdb=" OG1 THR G 23 " model vdw 2.243 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 21 " model vdw 2.252 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.258 3.040 ... (remaining 242812 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' selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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 group one per residue 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: 2.160 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.120 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 31186 Z= 0.148 Angle : 0.589 10.622 42535 Z= 0.363 Chirality : 0.040 0.362 4863 Planarity : 0.004 0.083 5471 Dihedral : 9.452 85.553 11079 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 5.95 % Allowed : 6.77 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.10), residues: 3888 helix: -2.90 (0.13), residues: 636 sheet: -2.93 (0.16), residues: 829 loop : -3.55 (0.10), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.007 0.001 TYR B 265 PHE 0.007 0.001 PHE C 318 TRP 0.005 0.001 TRP C 886 HIS 0.001 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00229 (31139) covalent geometry : angle 0.58915 (42441) SS BOND : bond 0.00118 ( 47) SS BOND : angle 0.44040 ( 94) hydrogen bonds : bond 0.28236 ( 832) hydrogen bonds : angle 9.88869 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 888 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5251 (OUTLIER) cc_final: 0.4843 (t-90) REVERT: A 97 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7021 (tmmt) REVERT: A 106 PHE cc_start: 0.7912 (m-80) cc_final: 0.7550 (m-80) REVERT: A 233 ILE cc_start: 0.3069 (OUTLIER) cc_final: 0.2787 (mm) REVERT: A 276 LEU cc_start: 0.8257 (tp) cc_final: 0.7943 (tt) REVERT: A 281 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6433 (pp20) REVERT: A 296 LEU cc_start: 0.8649 (tp) cc_final: 0.8361 (tp) REVERT: A 307 THR cc_start: 0.7855 (m) cc_final: 0.7496 (p) REVERT: A 308 VAL cc_start: 0.8388 (p) cc_final: 0.8045 (m) REVERT: A 323 THR cc_start: 0.7828 (m) cc_final: 0.6384 (p) REVERT: A 332 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7204 (tp) REVERT: A 578 ASP cc_start: 0.7648 (t0) cc_final: 0.7008 (t0) REVERT: A 587 ILE cc_start: 0.8370 (mt) cc_final: 0.8126 (mt) REVERT: A 664 ILE cc_start: 0.8295 (mt) cc_final: 0.8068 (mm) REVERT: A 725 GLU cc_start: 0.7213 (pt0) cc_final: 0.6769 (pt0) REVERT: A 734 THR cc_start: 0.8210 (t) cc_final: 0.7878 (m) REVERT: A 745 ASP cc_start: 0.5924 (m-30) cc_final: 0.5713 (m-30) REVERT: A 751 ASN cc_start: 0.7796 (m-40) cc_final: 0.7217 (m110) REVERT: A 752 LEU cc_start: 0.8319 (mm) cc_final: 0.7971 (mt) REVERT: A 762 GLN cc_start: 0.7513 (pt0) cc_final: 0.7027 (pt0) REVERT: A 773 GLU cc_start: 0.7072 (tt0) cc_final: 0.6495 (tt0) REVERT: A 776 LYS cc_start: 0.8079 (tmmt) cc_final: 0.7734 (tmmt) REVERT: A 800 PHE cc_start: 0.8071 (m-80) cc_final: 0.7724 (m-80) REVERT: A 821 LEU cc_start: 0.8211 (mm) cc_final: 0.7871 (mt) REVERT: A 825 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8096 (mtpp) REVERT: A 922 LEU cc_start: 0.8865 (tp) cc_final: 0.8576 (tt) REVERT: A 933 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8221 (mtmm) REVERT: A 935 GLN cc_start: 0.8044 (tt0) cc_final: 0.7833 (tt0) REVERT: A 947 LYS cc_start: 0.8216 (mtpt) cc_final: 0.8010 (mtpp) REVERT: A 950 ASP cc_start: 0.6701 (t0) cc_final: 0.6161 (t0) REVERT: A 957 GLN cc_start: 0.7498 (pt0) cc_final: 0.7219 (pt0) REVERT: A 964 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7356 (mtmt) REVERT: A 975 SER cc_start: 0.8570 (m) cc_final: 0.7961 (t) REVERT: A 977 LEU cc_start: 0.9005 (mp) cc_final: 0.8749 (mt) REVERT: A 980 ILE cc_start: 0.8755 (mt) cc_final: 0.8527 (tt) REVERT: A 1017 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5933 (tm-30) REVERT: A 1019 ARG cc_start: 0.7297 (ttm110) cc_final: 0.5866 (ttm110) REVERT: A 1028 LYS cc_start: 0.8511 (mttt) cc_final: 0.8240 (mttm) REVERT: A 1097 SER cc_start: 0.8607 (t) cc_final: 0.8299 (p) REVERT: A 1117 THR cc_start: 0.8197 (p) cc_final: 0.7823 (t) REVERT: A 1123 SER cc_start: 0.7855 (m) cc_final: 0.7651 (t) REVERT: B 29 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7859 (t) REVERT: B 54 LEU cc_start: 0.8075 (mt) cc_final: 0.7861 (mm) REVERT: B 83 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (p) REVERT: B 106 PHE cc_start: 0.7351 (m-80) cc_final: 0.7146 (m-80) REVERT: B 127 VAL cc_start: 0.8452 (t) cc_final: 0.7865 (m) REVERT: B 187 LEU cc_start: 0.7494 (tp) cc_final: 0.7251 (tt) REVERT: B 193 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7091 (ttpt) REVERT: B 307 THR cc_start: 0.7695 (m) cc_final: 0.7291 (p) REVERT: B 319 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6736 (ttm-80) REVERT: B 356 LYS cc_start: 0.8521 (tmmt) cc_final: 0.7924 (tmmt) REVERT: B 398 ASP cc_start: 0.5600 (t70) cc_final: 0.4937 (t0) REVERT: B 528 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8328 (mmtt) REVERT: B 535 LYS cc_start: 0.8307 (tptt) cc_final: 0.8014 (mmmm) REVERT: B 543 PHE cc_start: 0.6697 (m-10) cc_final: 0.6373 (m-80) REVERT: B 546 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8304 (tm) REVERT: B 562 PHE cc_start: 0.7200 (p90) cc_final: 0.6822 (p90) REVERT: B 603 ASN cc_start: 0.7114 (t0) cc_final: 0.6738 (t0) REVERT: B 616 ASN cc_start: 0.4918 (t0) cc_final: 0.4063 (t0) REVERT: B 659 SER cc_start: 0.8498 (m) cc_final: 0.8165 (p) REVERT: B 725 GLU cc_start: 0.7134 (tt0) cc_final: 0.6827 (tt0) REVERT: B 750 SER cc_start: 0.8425 (m) cc_final: 0.8172 (p) REVERT: B 759 PHE cc_start: 0.7311 (t80) cc_final: 0.6908 (t80) REVERT: B 765 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7261 (ttp80) REVERT: B 790 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7835 (mtpp) REVERT: B 868 GLU cc_start: 0.7300 (tp30) cc_final: 0.6908 (tp30) REVERT: B 884 SER cc_start: 0.8794 (m) cc_final: 0.8523 (p) REVERT: B 954 HIS cc_start: 0.7120 (m-70) cc_final: 0.6765 (m90) REVERT: B 955 ASN cc_start: 0.7523 (m-40) cc_final: 0.7313 (m-40) REVERT: B 957 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7124 (tm130) REVERT: B 961 THR cc_start: 0.8167 (m) cc_final: 0.7533 (p) REVERT: B 965 GLN cc_start: 0.7321 (mt0) cc_final: 0.7070 (mt0) REVERT: B 1003 SER cc_start: 0.8340 (m) cc_final: 0.8005 (t) REVERT: B 1017 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6488 (tm-30) REVERT: B 1028 LYS cc_start: 0.8405 (mttm) cc_final: 0.7696 (mtpp) REVERT: B 1072 GLU cc_start: 0.8014 (pm20) cc_final: 0.7745 (pm20) REVERT: B 1081 ILE cc_start: 0.7822 (pt) cc_final: 0.7491 (mt) REVERT: B 1118 ASP cc_start: 0.7093 (t70) cc_final: 0.6717 (t0) REVERT: B 1123 SER cc_start: 0.8249 (t) cc_final: 0.7848 (p) REVERT: B 1141 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 33 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7578 (p) REVERT: C 90 VAL cc_start: 0.8670 (m) cc_final: 0.8307 (t) REVERT: C 106 PHE cc_start: 0.7862 (m-80) cc_final: 0.7636 (m-80) REVERT: C 117 LEU cc_start: 0.7983 (tp) cc_final: 0.7773 (tt) REVERT: C 128 ILE cc_start: 0.7763 (mt) cc_final: 0.7553 (mp) REVERT: C 190 PHE cc_start: 0.7997 (m-80) cc_final: 0.7761 (m-80) REVERT: C 275 PHE cc_start: 0.7929 (m-80) cc_final: 0.7671 (m-10) REVERT: C 281 GLU cc_start: 0.7169 (pp20) cc_final: 0.6640 (pp20) REVERT: C 293 LEU cc_start: 0.8483 (tp) cc_final: 0.8278 (tp) REVERT: C 298 GLU cc_start: 0.7256 (tt0) cc_final: 0.7055 (tt0) REVERT: C 408 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6663 (ppp-140) REVERT: C 542 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8085 (t0) REVERT: C 546 LEU cc_start: 0.7762 (tm) cc_final: 0.7478 (tt) REVERT: C 574 ASP cc_start: 0.6982 (t70) cc_final: 0.5975 (t0) REVERT: C 578 ASP cc_start: 0.6509 (t0) cc_final: 0.5921 (t70) REVERT: C 586 ASP cc_start: 0.7116 (t0) cc_final: 0.6615 (t0) REVERT: C 644 GLN cc_start: 0.8065 (tp40) cc_final: 0.7217 (tp40) REVERT: C 651 ILE cc_start: 0.8449 (mt) cc_final: 0.8234 (pt) REVERT: C 675 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6433 (mm-40) REVERT: C 708 SER cc_start: 0.8372 (t) cc_final: 0.8102 (m) REVERT: C 712 ILE cc_start: 0.8278 (tp) cc_final: 0.8031 (tp) REVERT: C 723 THR cc_start: 0.8505 (t) cc_final: 0.8302 (p) REVERT: C 725 GLU cc_start: 0.7250 (tt0) cc_final: 0.6327 (tt0) REVERT: C 727 LEU cc_start: 0.8173 (mt) cc_final: 0.7918 (mp) REVERT: C 740 MET cc_start: 0.7477 (ttp) cc_final: 0.7218 (ttp) REVERT: C 764 LYS cc_start: 0.8053 (mttt) cc_final: 0.7813 (ttmm) REVERT: C 765 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7365 (ttp-110) REVERT: C 772 VAL cc_start: 0.8840 (t) cc_final: 0.8580 (m) REVERT: C 773 GLU cc_start: 0.7278 (tt0) cc_final: 0.7011 (tt0) REVERT: C 795 LYS cc_start: 0.8637 (mttt) cc_final: 0.8341 (mttm) REVERT: C 868 GLU cc_start: 0.6891 (tp30) cc_final: 0.6510 (tp30) REVERT: C 886 TRP cc_start: 0.8361 (p90) cc_final: 0.7964 (p90) REVERT: C 904 TYR cc_start: 0.7969 (m-10) cc_final: 0.7648 (m-10) REVERT: C 905 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7358 (mtt180) REVERT: C 919 ASN cc_start: 0.7978 (m-40) cc_final: 0.7691 (m-40) REVERT: C 933 LYS cc_start: 0.8295 (mtpt) cc_final: 0.8002 (ttmm) REVERT: C 977 LEU cc_start: 0.7848 (mp) cc_final: 0.6875 (mp) REVERT: C 980 ILE cc_start: 0.8844 (mt) cc_final: 0.8531 (mm) REVERT: C 981 PHE cc_start: 0.7750 (m-10) cc_final: 0.7502 (m-80) REVERT: C 1000 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8125 (mtt-85) REVERT: C 1028 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7782 (mttt) REVERT: C 1050 MET cc_start: 0.7659 (ptt) cc_final: 0.7289 (ptm) REVERT: C 1086 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7746 (mmmm) REVERT: C 1129 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8309 (m) REVERT: D 80 VAL cc_start: 0.7724 (t) cc_final: 0.7498 (p) REVERT: D 117 THR cc_start: 0.4587 (OUTLIER) cc_final: 0.4299 (t) REVERT: D 185 LEU cc_start: 0.0758 (pp) cc_final: 0.0162 (tp) REVERT: E 75 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4867 (tt) REVERT: F 145 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1855 (pt) outliers start: 202 outliers final: 77 residues processed: 1042 average time/residue: 0.1875 time to fit residues: 308.5329 Evaluate side-chains 764 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 670 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 186 ASN A 218 GLN A 239 GLN A 334 ASN A 370 ASN A 409 GLN A 437 ASN A 564 GLN A 709 ASN A 784 GLN A 853 GLN A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN A1011 GLN A1048 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 173 GLN B 186 ASN B 245 HIS B 409 GLN B 414 GLN B 481 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 709 ASN B 762 GLN B 824 ASN B 853 GLN B 901 GLN B 907 ASN B 957 GLN B 965 GLN B 978 ASN B1011 GLN B1048 HIS B1054 GLN C 173 GLN C 181 GLN C 280 ASN C 370 ASN C 409 GLN C 417 ASN C 540 ASN C 563 GLN C 644 GLN C 901 GLN C 913 GLN C 914 ASN C 935 GLN C1002 GLN C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 41 GLN D 199 GLN E 40 GLN E 71 ASN E 81 GLN E 111 GLN E 197 GLN F 41 GLN F 199 GLN G 39 GLN G 40 GLN G 81 GLN G 111 GLN G 197 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139611 restraints weight = 55807.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143871 restraints weight = 22524.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146403 restraints weight = 11925.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147885 restraints weight = 7852.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148940 restraints weight = 6034.719| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31186 Z= 0.183 Angle : 0.646 13.617 42535 Z= 0.332 Chirality : 0.046 0.332 4863 Planarity : 0.005 0.068 5471 Dihedral : 6.869 75.850 4415 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.68 % Allowed : 13.17 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.12), residues: 3888 helix: -0.60 (0.19), residues: 657 sheet: -2.38 (0.16), residues: 831 loop : -3.11 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 509 TYR 0.027 0.001 TYR C 91 PHE 0.021 0.002 PHE G 142 TRP 0.015 0.001 TRP A 436 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00393 (31139) covalent geometry : angle 0.63368 (42441) SS BOND : bond 0.00457 ( 47) SS BOND : angle 2.78844 ( 94) hydrogen bonds : bond 0.04937 ( 832) hydrogen bonds : angle 6.27564 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 704 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7120 (tmmt) REVERT: A 187 LEU cc_start: 0.7053 (tp) cc_final: 0.6799 (tp) REVERT: A 194 ASN cc_start: 0.7036 (t0) cc_final: 0.6827 (t0) REVERT: A 233 ILE cc_start: 0.3147 (OUTLIER) cc_final: 0.2899 (mm) REVERT: A 276 LEU cc_start: 0.8330 (tp) cc_final: 0.7960 (tt) REVERT: A 280 ASN cc_start: 0.7002 (t0) cc_final: 0.6717 (t0) REVERT: A 306 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: A 307 THR cc_start: 0.7788 (m) cc_final: 0.7438 (p) REVERT: A 332 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 334 ASN cc_start: 0.7572 (t0) cc_final: 0.7092 (t0) REVERT: A 578 ASP cc_start: 0.7637 (t0) cc_final: 0.7251 (t0) REVERT: A 725 GLU cc_start: 0.7184 (pt0) cc_final: 0.6508 (pt0) REVERT: A 751 ASN cc_start: 0.7715 (m-40) cc_final: 0.7205 (m110) REVERT: A 752 LEU cc_start: 0.8445 (mm) cc_final: 0.8156 (mt) REVERT: A 755 GLN cc_start: 0.7209 (mp-120) cc_final: 0.6914 (mp-120) REVERT: A 762 GLN cc_start: 0.7257 (pt0) cc_final: 0.6899 (pt0) REVERT: A 776 LYS cc_start: 0.8164 (tmmt) cc_final: 0.7803 (tmmt) REVERT: A 784 GLN cc_start: 0.7719 (mt0) cc_final: 0.7403 (mt0) REVERT: A 790 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7561 (mtpt) REVERT: A 795 LYS cc_start: 0.8488 (mttm) cc_final: 0.8238 (mttm) REVERT: A 804 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7089 (mm-40) REVERT: A 825 LYS cc_start: 0.8347 (mtpm) cc_final: 0.8055 (mtpt) REVERT: A 922 LEU cc_start: 0.8782 (tp) cc_final: 0.8508 (tt) REVERT: A 933 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8209 (mtmm) REVERT: A 950 ASP cc_start: 0.6935 (t0) cc_final: 0.6460 (t0) REVERT: A 954 HIS cc_start: 0.7976 (m-70) cc_final: 0.7500 (m170) REVERT: A 964 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7666 (mtmt) REVERT: A 975 SER cc_start: 0.8756 (m) cc_final: 0.8101 (t) REVERT: A 976 VAL cc_start: 0.8700 (m) cc_final: 0.8298 (p) REVERT: A 979 ASP cc_start: 0.7355 (m-30) cc_final: 0.7133 (m-30) REVERT: A 980 ILE cc_start: 0.8806 (mt) cc_final: 0.8451 (tp) REVERT: A 1017 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 1019 ARG cc_start: 0.7261 (ttm110) cc_final: 0.6653 (ttp80) REVERT: A 1028 LYS cc_start: 0.8416 (mttt) cc_final: 0.7745 (mtpp) REVERT: A 1031 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 1058 HIS cc_start: 0.7840 (m-70) cc_final: 0.7592 (m-70) REVERT: A 1117 THR cc_start: 0.8288 (p) cc_final: 0.8004 (t) REVERT: A 1130 ILE cc_start: 0.9000 (pt) cc_final: 0.8737 (pt) REVERT: B 54 LEU cc_start: 0.8478 (mt) cc_final: 0.8203 (mm) REVERT: B 66 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7609 (t-90) REVERT: B 83 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6936 (p) REVERT: B 127 VAL cc_start: 0.8261 (t) cc_final: 0.7528 (m) REVERT: B 193 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7328 (ttmt) REVERT: B 297 SER cc_start: 0.8071 (m) cc_final: 0.7570 (p) REVERT: B 307 THR cc_start: 0.7921 (m) cc_final: 0.7439 (p) REVERT: B 356 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8174 (tmmt) REVERT: B 398 ASP cc_start: 0.6527 (t70) cc_final: 0.5924 (t0) REVERT: B 402 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5862 (tp) REVERT: B 535 LYS cc_start: 0.8336 (tptt) cc_final: 0.7993 (mmmm) REVERT: B 563 GLN cc_start: 0.6580 (mm-40) cc_final: 0.6354 (mm-40) REVERT: B 659 SER cc_start: 0.8595 (m) cc_final: 0.8335 (p) REVERT: B 719 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 750 SER cc_start: 0.8354 (m) cc_final: 0.8003 (p) REVERT: B 759 PHE cc_start: 0.7256 (t80) cc_final: 0.6658 (t80) REVERT: B 868 GLU cc_start: 0.7122 (tp30) cc_final: 0.6658 (tp30) REVERT: B 884 SER cc_start: 0.8686 (m) cc_final: 0.8466 (p) REVERT: B 904 TYR cc_start: 0.7365 (m-10) cc_final: 0.7155 (m-10) REVERT: B 954 HIS cc_start: 0.7187 (m-70) cc_final: 0.6877 (m90) REVERT: B 1003 SER cc_start: 0.8458 (m) cc_final: 0.7941 (t) REVERT: B 1054 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: B 1081 ILE cc_start: 0.8005 (pt) cc_final: 0.7780 (mt) REVERT: B 1117 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (p) REVERT: B 1118 ASP cc_start: 0.7348 (t70) cc_final: 0.6865 (t0) REVERT: B 1127 ASP cc_start: 0.7231 (t0) cc_final: 0.6859 (t0) REVERT: B 1141 LEU cc_start: 0.8305 (tt) cc_final: 0.7980 (tt) REVERT: C 121 ASN cc_start: 0.7880 (p0) cc_final: 0.7502 (p0) REVERT: C 128 ILE cc_start: 0.7910 (mt) cc_final: 0.7638 (mp) REVERT: C 129 LYS cc_start: 0.7392 (ttpt) cc_final: 0.6971 (ttpt) REVERT: C 164 ASN cc_start: 0.7995 (t0) cc_final: 0.7765 (t0) REVERT: C 189 GLU cc_start: 0.7573 (pt0) cc_final: 0.7344 (pt0) REVERT: C 190 PHE cc_start: 0.7781 (m-80) cc_final: 0.7523 (m-80) REVERT: C 228 ASP cc_start: 0.7484 (t70) cc_final: 0.7131 (t70) REVERT: C 275 PHE cc_start: 0.7840 (m-80) cc_final: 0.7374 (m-10) REVERT: C 281 GLU cc_start: 0.7063 (pp20) cc_final: 0.6850 (pp20) REVERT: C 408 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6737 (ppp-140) REVERT: C 574 ASP cc_start: 0.7466 (t70) cc_final: 0.6425 (t0) REVERT: C 578 ASP cc_start: 0.6660 (t0) cc_final: 0.6142 (t70) REVERT: C 586 ASP cc_start: 0.7010 (t0) cc_final: 0.6449 (t0) REVERT: C 592 PHE cc_start: 0.8253 (p90) cc_final: 0.7991 (p90) REVERT: C 674 TYR cc_start: 0.7878 (t80) cc_final: 0.7542 (t80) REVERT: C 675 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6825 (mm-40) REVERT: C 708 SER cc_start: 0.8460 (t) cc_final: 0.8114 (m) REVERT: C 712 ILE cc_start: 0.8420 (tp) cc_final: 0.8193 (tp) REVERT: C 723 THR cc_start: 0.8514 (t) cc_final: 0.8263 (p) REVERT: C 725 GLU cc_start: 0.7137 (tt0) cc_final: 0.6784 (tt0) REVERT: C 727 LEU cc_start: 0.8284 (mt) cc_final: 0.7942 (mp) REVERT: C 737 ASP cc_start: 0.6944 (t0) cc_final: 0.6626 (t70) REVERT: C 773 GLU cc_start: 0.7218 (tt0) cc_final: 0.6984 (tt0) REVERT: C 776 LYS cc_start: 0.8326 (ttpm) cc_final: 0.7916 (ttpp) REVERT: C 780 GLU cc_start: 0.7221 (pt0) cc_final: 0.6875 (pt0) REVERT: C 790 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7876 (mtpt) REVERT: C 795 LYS cc_start: 0.8701 (mttt) cc_final: 0.8413 (mttm) REVERT: C 810 SER cc_start: 0.8672 (m) cc_final: 0.8047 (p) REVERT: C 854 LYS cc_start: 0.7975 (tmmt) cc_final: 0.7597 (tptp) REVERT: C 868 GLU cc_start: 0.6911 (tp30) cc_final: 0.6625 (tp30) REVERT: C 886 TRP cc_start: 0.8426 (p90) cc_final: 0.7873 (p90) REVERT: C 904 TYR cc_start: 0.7904 (m-10) cc_final: 0.7588 (m-10) REVERT: C 933 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8039 (ttmm) REVERT: C 957 GLN cc_start: 0.7614 (tm130) cc_final: 0.7148 (tm130) REVERT: C 977 LEU cc_start: 0.7746 (mp) cc_final: 0.7222 (mp) REVERT: C 980 ILE cc_start: 0.8892 (mt) cc_final: 0.8566 (mm) REVERT: C 998 THR cc_start: 0.8362 (t) cc_final: 0.8129 (t) REVERT: C 1014 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7507 (ttm-80) REVERT: C 1019 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6758 (ttp80) REVERT: C 1129 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (m) REVERT: D 80 VAL cc_start: 0.8387 (t) cc_final: 0.8054 (p) REVERT: D 182 LEU cc_start: 0.4432 (OUTLIER) cc_final: 0.3725 (tt) REVERT: F 79 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5962 (pt0) REVERT: G 142 PHE cc_start: 0.4514 (OUTLIER) cc_final: 0.4238 (t80) outliers start: 193 outliers final: 104 residues processed: 835 average time/residue: 0.1869 time to fit residues: 247.7727 Evaluate side-chains 763 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 644 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1054 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 54 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 330 optimal weight: 0.0030 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 437 ASN A 564 GLN A 901 GLN A 913 GLN A 955 ASN B 121 ASN B 542 ASN B 755 GLN B 895 GLN B1005 GLN B1054 GLN C 914 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.191572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140136 restraints weight = 57011.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143828 restraints weight = 26368.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144523 restraints weight = 15836.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145492 restraints weight = 12294.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146089 restraints weight = 9996.653| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31186 Z= 0.157 Angle : 0.610 10.553 42535 Z= 0.309 Chirality : 0.045 0.296 4863 Planarity : 0.005 0.073 5471 Dihedral : 6.222 76.508 4362 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.83 % Allowed : 15.32 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.12), residues: 3888 helix: 0.05 (0.20), residues: 663 sheet: -1.98 (0.17), residues: 815 loop : -2.88 (0.11), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.023 0.001 TYR B 451 PHE 0.024 0.002 PHE C 168 TRP 0.016 0.001 TRP B 104 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00346 (31139) covalent geometry : angle 0.60454 (42441) SS BOND : bond 0.00328 ( 47) SS BOND : angle 1.84170 ( 94) hydrogen bonds : bond 0.04451 ( 832) hydrogen bonds : angle 5.79373 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 654 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8425 (tt) cc_final: 0.8145 (tt) REVERT: A 130 VAL cc_start: 0.7224 (p) cc_final: 0.6923 (m) REVERT: A 187 LEU cc_start: 0.7190 (tp) cc_final: 0.6982 (tp) REVERT: A 189 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6353 (mm-30) REVERT: A 204 LYS cc_start: 0.8482 (tttp) cc_final: 0.7939 (ttmt) REVERT: A 233 ILE cc_start: 0.3229 (OUTLIER) cc_final: 0.2966 (mm) REVERT: A 273 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6326 (mtm180) REVERT: A 276 LEU cc_start: 0.8400 (tp) cc_final: 0.8029 (tt) REVERT: A 280 ASN cc_start: 0.7136 (t0) cc_final: 0.6692 (t0) REVERT: A 307 THR cc_start: 0.7717 (m) cc_final: 0.7392 (p) REVERT: A 314 GLN cc_start: 0.7390 (tp40) cc_final: 0.7156 (tt0) REVERT: A 324 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6314 (mm-30) REVERT: A 334 ASN cc_start: 0.7431 (t0) cc_final: 0.6884 (t0) REVERT: A 578 ASP cc_start: 0.7574 (t0) cc_final: 0.7362 (t0) REVERT: A 751 ASN cc_start: 0.7625 (m-40) cc_final: 0.7130 (m110) REVERT: A 752 LEU cc_start: 0.8456 (mm) cc_final: 0.8174 (mt) REVERT: A 755 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6944 (mp-120) REVERT: A 776 LYS cc_start: 0.8217 (tmmt) cc_final: 0.7798 (tmmt) REVERT: A 790 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7616 (mtpt) REVERT: A 825 LYS cc_start: 0.8343 (mtpm) cc_final: 0.8068 (mttm) REVERT: A 855 PHE cc_start: 0.8513 (m-10) cc_final: 0.8187 (m-80) REVERT: A 922 LEU cc_start: 0.8722 (tp) cc_final: 0.8435 (tt) REVERT: A 933 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8191 (mtmm) REVERT: A 935 GLN cc_start: 0.8310 (tt0) cc_final: 0.8029 (tt0) REVERT: A 950 ASP cc_start: 0.6919 (t0) cc_final: 0.6339 (t0) REVERT: A 953 ASN cc_start: 0.8242 (m-40) cc_final: 0.7579 (m110) REVERT: A 957 GLN cc_start: 0.7442 (pt0) cc_final: 0.7059 (pm20) REVERT: A 964 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7627 (mtmt) REVERT: A 975 SER cc_start: 0.8777 (m) cc_final: 0.8173 (t) REVERT: A 976 VAL cc_start: 0.8679 (m) cc_final: 0.8201 (p) REVERT: A 979 ASP cc_start: 0.7437 (m-30) cc_final: 0.7183 (m-30) REVERT: A 980 ILE cc_start: 0.8837 (mt) cc_final: 0.8419 (tp) REVERT: A 1017 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6595 (tm-30) REVERT: A 1019 ARG cc_start: 0.7155 (ttm110) cc_final: 0.6812 (ttp80) REVERT: A 1058 HIS cc_start: 0.7885 (m-70) cc_final: 0.7614 (m-70) REVERT: A 1073 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7596 (ttpp) REVERT: A 1117 THR cc_start: 0.8321 (p) cc_final: 0.8073 (t) REVERT: A 1130 ILE cc_start: 0.8995 (pt) cc_final: 0.8694 (pt) REVERT: B 54 LEU cc_start: 0.8453 (mt) cc_final: 0.8241 (mm) REVERT: B 66 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7458 (t-90) REVERT: B 83 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.7041 (p) REVERT: B 127 VAL cc_start: 0.8057 (t) cc_final: 0.7306 (m) REVERT: B 188 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6877 (mtp85) REVERT: B 193 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7528 (ttmt) REVERT: B 294 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6547 (p0) REVERT: B 297 SER cc_start: 0.8037 (m) cc_final: 0.7514 (p) REVERT: B 307 THR cc_start: 0.7946 (m) cc_final: 0.7470 (p) REVERT: B 356 LYS cc_start: 0.8539 (tmmt) cc_final: 0.8088 (mmmm) REVERT: B 398 ASP cc_start: 0.6262 (t70) cc_final: 0.5630 (t0) REVERT: B 402 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.5832 (tt) REVERT: B 451 TYR cc_start: 0.7052 (m-80) cc_final: 0.6849 (m-80) REVERT: B 535 LYS cc_start: 0.8375 (tptt) cc_final: 0.7999 (mmmm) REVERT: B 542 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 562 PHE cc_start: 0.7404 (p90) cc_final: 0.7005 (p90) REVERT: B 563 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6654 (mm110) REVERT: B 592 PHE cc_start: 0.7876 (p90) cc_final: 0.7674 (p90) REVERT: B 725 GLU cc_start: 0.7281 (tt0) cc_final: 0.6679 (tt0) REVERT: B 740 MET cc_start: 0.8063 (mtp) cc_final: 0.7812 (ttm) REVERT: B 750 SER cc_start: 0.8532 (m) cc_final: 0.8081 (p) REVERT: B 759 PHE cc_start: 0.7100 (t80) cc_final: 0.6556 (t80) REVERT: B 868 GLU cc_start: 0.7125 (tp30) cc_final: 0.6675 (tp30) REVERT: B 954 HIS cc_start: 0.7274 (m-70) cc_final: 0.6973 (m90) REVERT: B 993 ILE cc_start: 0.8985 (tp) cc_final: 0.8757 (tp) REVERT: B 1003 SER cc_start: 0.8457 (m) cc_final: 0.8073 (t) REVERT: B 1005 GLN cc_start: 0.7788 (tp40) cc_final: 0.7413 (tp-100) REVERT: B 1118 ASP cc_start: 0.7454 (t70) cc_final: 0.6925 (t0) REVERT: B 1127 ASP cc_start: 0.7395 (t0) cc_final: 0.6987 (t0) REVERT: B 1141 LEU cc_start: 0.8305 (tt) cc_final: 0.7976 (tt) REVERT: C 92 PHE cc_start: 0.6877 (t80) cc_final: 0.6650 (t80) REVERT: C 96 GLU cc_start: 0.6425 (pt0) cc_final: 0.6187 (pt0) REVERT: C 120 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7682 (p) REVERT: C 128 ILE cc_start: 0.7888 (mt) cc_final: 0.7657 (mp) REVERT: C 129 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6859 (ttpt) REVERT: C 164 ASN cc_start: 0.7816 (t0) cc_final: 0.7589 (t0) REVERT: C 190 PHE cc_start: 0.7781 (m-80) cc_final: 0.7518 (m-80) REVERT: C 275 PHE cc_start: 0.7844 (m-80) cc_final: 0.7421 (m-10) REVERT: C 280 ASN cc_start: 0.7813 (t0) cc_final: 0.7508 (t0) REVERT: C 281 GLU cc_start: 0.7236 (pp20) cc_final: 0.6767 (pp20) REVERT: C 327 VAL cc_start: 0.8365 (t) cc_final: 0.8110 (m) REVERT: C 334 ASN cc_start: 0.7268 (t0) cc_final: 0.6265 (p0) REVERT: C 408 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7390 (ppp-140) REVERT: C 558 LYS cc_start: 0.7909 (mmtp) cc_final: 0.7521 (mmtp) REVERT: C 574 ASP cc_start: 0.7380 (t70) cc_final: 0.6531 (t0) REVERT: C 578 ASP cc_start: 0.6552 (t0) cc_final: 0.6128 (t70) REVERT: C 592 PHE cc_start: 0.8225 (p90) cc_final: 0.7957 (p90) REVERT: C 599 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 644 GLN cc_start: 0.7498 (tp40) cc_final: 0.7223 (tp40) REVERT: C 674 TYR cc_start: 0.7933 (t80) cc_final: 0.7513 (t80) REVERT: C 675 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6924 (mm-40) REVERT: C 708 SER cc_start: 0.8474 (t) cc_final: 0.8083 (m) REVERT: C 711 SER cc_start: 0.7563 (m) cc_final: 0.7309 (p) REVERT: C 712 ILE cc_start: 0.8435 (tp) cc_final: 0.8204 (tp) REVERT: C 723 THR cc_start: 0.8492 (t) cc_final: 0.8280 (p) REVERT: C 725 GLU cc_start: 0.7165 (tt0) cc_final: 0.6773 (tt0) REVERT: C 727 LEU cc_start: 0.8386 (mt) cc_final: 0.8085 (mp) REVERT: C 737 ASP cc_start: 0.6751 (t0) cc_final: 0.6471 (t70) REVERT: C 790 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7911 (mtpt) REVERT: C 795 LYS cc_start: 0.8773 (mttt) cc_final: 0.8474 (mttm) REVERT: C 810 SER cc_start: 0.8718 (m) cc_final: 0.8088 (p) REVERT: C 854 LYS cc_start: 0.7877 (tmmt) cc_final: 0.7616 (tptp) REVERT: C 868 GLU cc_start: 0.6925 (tp30) cc_final: 0.6600 (tp30) REVERT: C 886 TRP cc_start: 0.8364 (OUTLIER) cc_final: 0.7834 (p90) REVERT: C 902 MET cc_start: 0.7788 (tpp) cc_final: 0.7446 (mmm) REVERT: C 904 TYR cc_start: 0.7798 (m-10) cc_final: 0.7483 (m-10) REVERT: C 933 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7994 (ttmm) REVERT: C 957 GLN cc_start: 0.7593 (tm130) cc_final: 0.7153 (tm130) REVERT: C 977 LEU cc_start: 0.7512 (mp) cc_final: 0.6667 (mp) REVERT: C 980 ILE cc_start: 0.8863 (mt) cc_final: 0.8533 (mm) REVERT: C 981 PHE cc_start: 0.7981 (m-80) cc_final: 0.7501 (m-80) REVERT: C 1014 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7551 (ttm-80) REVERT: C 1019 ARG cc_start: 0.7242 (ttm110) cc_final: 0.6784 (ttp80) REVERT: C 1086 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7745 (mmmt) REVERT: D 80 VAL cc_start: 0.8581 (t) cc_final: 0.8180 (p) REVERT: D 82 LEU cc_start: 0.3097 (tp) cc_final: 0.2556 (tp) REVERT: D 182 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4422 (tt) REVERT: E 194 TYR cc_start: 0.3430 (OUTLIER) cc_final: 0.2205 (m-80) REVERT: G 142 PHE cc_start: 0.4683 (OUTLIER) cc_final: 0.4424 (t80) outliers start: 198 outliers final: 125 residues processed: 783 average time/residue: 0.1891 time to fit residues: 235.9632 Evaluate side-chains 771 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 629 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 304 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 354 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 335 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 762 GLN A 784 GLN A 913 GLN A 955 ASN B 505 HIS B 542 ASN B 690 GLN B 895 GLN C 487 ASN C 536 ASN C 580 GLN C 690 GLN C 914 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.191483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140104 restraints weight = 56538.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143447 restraints weight = 26006.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144210 restraints weight = 16906.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145845 restraints weight = 12165.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145980 restraints weight = 9043.195| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31186 Z= 0.135 Angle : 0.590 11.536 42535 Z= 0.296 Chirality : 0.044 0.242 4863 Planarity : 0.004 0.073 5471 Dihedral : 5.980 59.616 4349 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.57 % Allowed : 16.32 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.13), residues: 3888 helix: 0.37 (0.20), residues: 663 sheet: -1.77 (0.17), residues: 812 loop : -2.74 (0.11), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.021 0.001 TYR A1067 PHE 0.029 0.001 PHE A 190 TRP 0.014 0.001 TRP A 436 HIS 0.007 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00301 (31139) covalent geometry : angle 0.58486 (42441) SS BOND : bond 0.00317 ( 47) SS BOND : angle 1.68456 ( 94) hydrogen bonds : bond 0.04016 ( 832) hydrogen bonds : angle 5.56083 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 636 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8400 (tt) cc_final: 0.8038 (tt) REVERT: A 189 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6489 (mm-30) REVERT: A 233 ILE cc_start: 0.3281 (OUTLIER) cc_final: 0.2983 (mm) REVERT: A 273 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6455 (mtm180) REVERT: A 276 LEU cc_start: 0.8405 (tp) cc_final: 0.8199 (tp) REVERT: A 280 ASN cc_start: 0.7093 (t0) cc_final: 0.6666 (t0) REVERT: A 307 THR cc_start: 0.7600 (m) cc_final: 0.7259 (p) REVERT: A 314 GLN cc_start: 0.7404 (tp40) cc_final: 0.7141 (tt0) REVERT: A 324 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6282 (mm-30) REVERT: A 334 ASN cc_start: 0.7402 (t0) cc_final: 0.6884 (t0) REVERT: A 480 CYS cc_start: 0.4824 (OUTLIER) cc_final: 0.3952 (p) REVERT: A 565 PHE cc_start: 0.6840 (m-10) cc_final: 0.6521 (m-10) REVERT: A 578 ASP cc_start: 0.7638 (t0) cc_final: 0.7418 (t0) REVERT: A 751 ASN cc_start: 0.7577 (m-40) cc_final: 0.7083 (m110) REVERT: A 752 LEU cc_start: 0.8494 (mm) cc_final: 0.8200 (mt) REVERT: A 755 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6924 (mp-120) REVERT: A 776 LYS cc_start: 0.8234 (tmmt) cc_final: 0.7840 (tmmt) REVERT: A 790 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7611 (mtpt) REVERT: A 804 GLN cc_start: 0.7789 (mm-40) cc_final: 0.6983 (mm-40) REVERT: A 825 LYS cc_start: 0.8345 (mtpm) cc_final: 0.8045 (mttm) REVERT: A 855 PHE cc_start: 0.8469 (m-10) cc_final: 0.8181 (m-80) REVERT: A 922 LEU cc_start: 0.8722 (tp) cc_final: 0.8440 (tt) REVERT: A 933 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8216 (mtmm) REVERT: A 935 GLN cc_start: 0.8294 (tt0) cc_final: 0.7691 (mt0) REVERT: A 953 ASN cc_start: 0.8254 (m-40) cc_final: 0.7503 (m110) REVERT: A 957 GLN cc_start: 0.7453 (pt0) cc_final: 0.7116 (pm20) REVERT: A 964 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7600 (mtmt) REVERT: A 975 SER cc_start: 0.8780 (m) cc_final: 0.8150 (t) REVERT: A 976 VAL cc_start: 0.8659 (m) cc_final: 0.8187 (p) REVERT: A 979 ASP cc_start: 0.7473 (m-30) cc_final: 0.7211 (m-30) REVERT: A 980 ILE cc_start: 0.8815 (mt) cc_final: 0.8449 (tp) REVERT: A 1017 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 1019 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6802 (ttp80) REVERT: A 1031 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 1058 HIS cc_start: 0.7904 (m-70) cc_final: 0.7623 (m-70) REVERT: A 1073 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7603 (ttpp) REVERT: A 1117 THR cc_start: 0.8320 (p) cc_final: 0.8090 (t) REVERT: B 54 LEU cc_start: 0.8493 (mt) cc_final: 0.8277 (mm) REVERT: B 66 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7680 (t-90) REVERT: B 83 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7038 (p) REVERT: B 99 ASN cc_start: 0.7911 (p0) cc_final: 0.7679 (p0) REVERT: B 127 VAL cc_start: 0.8002 (t) cc_final: 0.7273 (m) REVERT: B 188 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6796 (mtm180) REVERT: B 193 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7583 (ttmt) REVERT: B 212 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5759 (pp20) REVERT: B 294 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6546 (p0) REVERT: B 297 SER cc_start: 0.8038 (m) cc_final: 0.7541 (p) REVERT: B 356 LYS cc_start: 0.8461 (tmmt) cc_final: 0.8069 (tmtt) REVERT: B 398 ASP cc_start: 0.6194 (t70) cc_final: 0.5521 (t0) REVERT: B 402 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.5945 (tt) REVERT: B 535 LYS cc_start: 0.8328 (tptt) cc_final: 0.7953 (mmmm) REVERT: B 542 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 562 PHE cc_start: 0.7401 (p90) cc_final: 0.6894 (p90) REVERT: B 563 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6620 (mm110) REVERT: B 643 PHE cc_start: 0.7885 (t80) cc_final: 0.7682 (t80) REVERT: B 750 SER cc_start: 0.8491 (m) cc_final: 0.7965 (p) REVERT: B 868 GLU cc_start: 0.7078 (tp30) cc_final: 0.6644 (tp30) REVERT: B 954 HIS cc_start: 0.7300 (m-70) cc_final: 0.6856 (m90) REVERT: B 961 THR cc_start: 0.8239 (p) cc_final: 0.7858 (t) REVERT: B 993 ILE cc_start: 0.8941 (tp) cc_final: 0.8609 (tp) REVERT: B 1003 SER cc_start: 0.8490 (m) cc_final: 0.8000 (t) REVERT: B 1050 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7101 (ptm) REVERT: B 1118 ASP cc_start: 0.7518 (t70) cc_final: 0.6956 (t0) REVERT: B 1127 ASP cc_start: 0.7406 (t0) cc_final: 0.7018 (t0) REVERT: B 1141 LEU cc_start: 0.8324 (tt) cc_final: 0.7968 (tt) REVERT: C 92 PHE cc_start: 0.6901 (t80) cc_final: 0.6689 (t80) REVERT: C 96 GLU cc_start: 0.6469 (pt0) cc_final: 0.6164 (pt0) REVERT: C 164 ASN cc_start: 0.7854 (t0) cc_final: 0.7607 (t0) REVERT: C 190 PHE cc_start: 0.7761 (m-80) cc_final: 0.7497 (m-80) REVERT: C 275 PHE cc_start: 0.7874 (m-80) cc_final: 0.7434 (m-10) REVERT: C 280 ASN cc_start: 0.7811 (t0) cc_final: 0.7525 (t0) REVERT: C 281 GLU cc_start: 0.7175 (pp20) cc_final: 0.6600 (pp20) REVERT: C 319 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7606 (ptp-110) REVERT: C 327 VAL cc_start: 0.8335 (t) cc_final: 0.8115 (m) REVERT: C 334 ASN cc_start: 0.7258 (t0) cc_final: 0.6026 (p0) REVERT: C 408 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7415 (ppp-140) REVERT: C 558 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7527 (mmtp) REVERT: C 572 THR cc_start: 0.6417 (OUTLIER) cc_final: 0.6205 (p) REVERT: C 574 ASP cc_start: 0.7344 (t70) cc_final: 0.6544 (t0) REVERT: C 578 ASP cc_start: 0.6360 (t0) cc_final: 0.5941 (t70) REVERT: C 599 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8287 (p) REVERT: C 655 TYR cc_start: 0.7165 (t80) cc_final: 0.6953 (t80) REVERT: C 674 TYR cc_start: 0.7923 (t80) cc_final: 0.7500 (t80) REVERT: C 675 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6907 (mm-40) REVERT: C 708 SER cc_start: 0.8474 (t) cc_final: 0.8047 (m) REVERT: C 711 SER cc_start: 0.7649 (m) cc_final: 0.7397 (p) REVERT: C 723 THR cc_start: 0.8514 (t) cc_final: 0.8281 (p) REVERT: C 725 GLU cc_start: 0.7158 (tt0) cc_final: 0.6800 (tt0) REVERT: C 727 LEU cc_start: 0.8432 (mt) cc_final: 0.8131 (mp) REVERT: C 737 ASP cc_start: 0.6680 (t0) cc_final: 0.6305 (t70) REVERT: C 780 GLU cc_start: 0.7273 (pt0) cc_final: 0.7043 (pt0) REVERT: C 790 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7925 (mtpt) REVERT: C 795 LYS cc_start: 0.8782 (mttt) cc_final: 0.8491 (mttm) REVERT: C 810 SER cc_start: 0.8715 (m) cc_final: 0.8067 (p) REVERT: C 854 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7602 (tptp) REVERT: C 868 GLU cc_start: 0.6840 (tp30) cc_final: 0.6557 (tp30) REVERT: C 886 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7823 (p90) REVERT: C 902 MET cc_start: 0.7816 (tpp) cc_final: 0.7479 (mmm) REVERT: C 904 TYR cc_start: 0.7760 (m-10) cc_final: 0.7535 (m-10) REVERT: C 933 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8037 (ttmm) REVERT: C 945 LEU cc_start: 0.8583 (mm) cc_final: 0.8364 (mp) REVERT: C 957 GLN cc_start: 0.7491 (tm130) cc_final: 0.7134 (tm130) REVERT: C 977 LEU cc_start: 0.7527 (mp) cc_final: 0.6989 (mp) REVERT: C 980 ILE cc_start: 0.8827 (mt) cc_final: 0.8513 (mm) REVERT: C 981 PHE cc_start: 0.8003 (m-80) cc_final: 0.7650 (m-80) REVERT: C 1002 GLN cc_start: 0.7806 (tp40) cc_final: 0.6958 (tm-30) REVERT: C 1014 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7547 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7693 (mmmt) REVERT: D 80 VAL cc_start: 0.8617 (t) cc_final: 0.8235 (p) REVERT: D 82 LEU cc_start: 0.2928 (tp) cc_final: 0.2443 (tp) REVERT: D 182 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4167 (tt) REVERT: E 194 TYR cc_start: 0.3303 (OUTLIER) cc_final: 0.2080 (m-80) REVERT: F 182 LEU cc_start: 0.8148 (tp) cc_final: 0.7569 (tt) REVERT: G 142 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.4555 (t80) outliers start: 189 outliers final: 127 residues processed: 760 average time/residue: 0.1911 time to fit residues: 231.5944 Evaluate side-chains 770 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 623 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 238 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 366 optimal weight: 20.0000 chunk 252 optimal weight: 0.0000 chunk 204 optimal weight: 3.9990 chunk 390 optimal weight: 0.0270 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 913 GLN A 955 ASN B 505 HIS B 542 ASN B 957 GLN C 540 ASN C 914 ASN C 957 GLN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS G 200 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.192183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139202 restraints weight = 56898.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142845 restraints weight = 24880.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144903 restraints weight = 14182.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145991 restraints weight = 9976.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146675 restraints weight = 8234.879| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31186 Z= 0.109 Angle : 0.574 12.756 42535 Z= 0.284 Chirality : 0.044 0.356 4863 Planarity : 0.004 0.100 5471 Dihedral : 5.969 59.884 4349 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.89 % Allowed : 16.79 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.13), residues: 3888 helix: 0.63 (0.21), residues: 661 sheet: -1.61 (0.17), residues: 828 loop : -2.63 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.019 0.001 TYR A1067 PHE 0.031 0.001 PHE C 168 TRP 0.010 0.001 TRP A 64 HIS 0.007 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00245 (31139) covalent geometry : angle 0.57097 (42441) SS BOND : bond 0.00254 ( 47) SS BOND : angle 1.45323 ( 94) hydrogen bonds : bond 0.03716 ( 832) hydrogen bonds : angle 5.37540 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 645 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7573 (tp40) cc_final: 0.7353 (tp40) REVERT: A 117 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 233 ILE cc_start: 0.3263 (OUTLIER) cc_final: 0.3013 (mm) REVERT: A 269 TYR cc_start: 0.6923 (m-10) cc_final: 0.6456 (m-80) REVERT: A 273 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6302 (mtm180) REVERT: A 276 LEU cc_start: 0.8389 (tp) cc_final: 0.7918 (tt) REVERT: A 280 ASN cc_start: 0.7060 (t0) cc_final: 0.6691 (t0) REVERT: A 307 THR cc_start: 0.7466 (m) cc_final: 0.7118 (p) REVERT: A 314 GLN cc_start: 0.7347 (tp40) cc_final: 0.7016 (tt0) REVERT: A 324 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6271 (mm-30) REVERT: A 334 ASN cc_start: 0.7472 (t0) cc_final: 0.6958 (t0) REVERT: A 466 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6956 (ttp80) REVERT: A 480 CYS cc_start: 0.4832 (OUTLIER) cc_final: 0.3938 (p) REVERT: A 565 PHE cc_start: 0.6843 (m-10) cc_final: 0.6534 (m-10) REVERT: A 574 ASP cc_start: 0.7586 (p0) cc_final: 0.7362 (p0) REVERT: A 751 ASN cc_start: 0.7450 (m-40) cc_final: 0.6999 (m110) REVERT: A 752 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 755 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6958 (mp-120) REVERT: A 776 LYS cc_start: 0.8225 (tmmt) cc_final: 0.7898 (tmmt) REVERT: A 790 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7512 (mtpt) REVERT: A 801 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5319 (t0) REVERT: A 825 LYS cc_start: 0.8290 (mtpm) cc_final: 0.8004 (mttm) REVERT: A 855 PHE cc_start: 0.8350 (m-10) cc_final: 0.8127 (m-80) REVERT: A 922 LEU cc_start: 0.8767 (tp) cc_final: 0.8469 (tt) REVERT: A 933 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8231 (mtmm) REVERT: A 953 ASN cc_start: 0.8241 (m-40) cc_final: 0.7480 (m110) REVERT: A 957 GLN cc_start: 0.7380 (pt0) cc_final: 0.7051 (pm20) REVERT: A 964 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7557 (mtmt) REVERT: A 975 SER cc_start: 0.8730 (m) cc_final: 0.8057 (t) REVERT: A 976 VAL cc_start: 0.8725 (m) cc_final: 0.8247 (p) REVERT: A 979 ASP cc_start: 0.7309 (m-30) cc_final: 0.6973 (m-30) REVERT: A 980 ILE cc_start: 0.8692 (mt) cc_final: 0.8446 (tp) REVERT: A 1017 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 1058 HIS cc_start: 0.7817 (m-70) cc_final: 0.7616 (m-70) REVERT: A 1073 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7532 (ttpp) REVERT: A 1117 THR cc_start: 0.8397 (p) cc_final: 0.8161 (t) REVERT: B 66 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7742 (t-90) REVERT: B 83 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 91 TYR cc_start: 0.7339 (t80) cc_final: 0.6893 (t80) REVERT: B 99 ASN cc_start: 0.7769 (p0) cc_final: 0.7550 (p0) REVERT: B 127 VAL cc_start: 0.8119 (t) cc_final: 0.7409 (m) REVERT: B 165 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.5883 (p0) REVERT: B 188 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6758 (mtm180) REVERT: B 193 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7618 (ttmt) REVERT: B 212 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5759 (pp20) REVERT: B 297 SER cc_start: 0.8000 (m) cc_final: 0.7545 (p) REVERT: B 307 THR cc_start: 0.7956 (m) cc_final: 0.7466 (p) REVERT: B 338 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: B 355 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8234 (ttt-90) REVERT: B 356 LYS cc_start: 0.8591 (tmmt) cc_final: 0.8208 (tmtt) REVERT: B 398 ASP cc_start: 0.6560 (t70) cc_final: 0.5749 (t0) REVERT: B 402 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6172 (tt) REVERT: B 465 GLU cc_start: 0.6762 (tt0) cc_final: 0.6439 (tt0) REVERT: B 535 LYS cc_start: 0.8313 (tptt) cc_final: 0.8016 (mmmm) REVERT: B 562 PHE cc_start: 0.7377 (p90) cc_final: 0.6810 (p90) REVERT: B 563 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6619 (mm110) REVERT: B 750 SER cc_start: 0.8362 (m) cc_final: 0.7939 (p) REVERT: B 868 GLU cc_start: 0.6988 (tp30) cc_final: 0.6585 (tp30) REVERT: B 921 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7668 (mtpp) REVERT: B 954 HIS cc_start: 0.7139 (m-70) cc_final: 0.6797 (m90) REVERT: B 957 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7538 (tp-100) REVERT: B 961 THR cc_start: 0.8217 (p) cc_final: 0.7852 (t) REVERT: B 993 ILE cc_start: 0.8989 (tp) cc_final: 0.8723 (tp) REVERT: B 1003 SER cc_start: 0.8418 (m) cc_final: 0.7968 (t) REVERT: B 1019 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7241 (ttp80) REVERT: B 1118 ASP cc_start: 0.7447 (t70) cc_final: 0.6892 (t0) REVERT: B 1127 ASP cc_start: 0.7364 (t0) cc_final: 0.6953 (t0) REVERT: B 1141 LEU cc_start: 0.8246 (tt) cc_final: 0.7890 (tt) REVERT: C 96 GLU cc_start: 0.6335 (pt0) cc_final: 0.6100 (pt0) REVERT: C 120 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7662 (p) REVERT: C 128 ILE cc_start: 0.7859 (mt) cc_final: 0.7505 (pt) REVERT: C 129 LYS cc_start: 0.7410 (ttpt) cc_final: 0.6948 (ttpt) REVERT: C 164 ASN cc_start: 0.7929 (t0) cc_final: 0.7691 (t0) REVERT: C 190 PHE cc_start: 0.7588 (m-80) cc_final: 0.7332 (m-10) REVERT: C 223 LEU cc_start: 0.8099 (mp) cc_final: 0.7875 (mp) REVERT: C 237 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7088 (mtp-110) REVERT: C 275 PHE cc_start: 0.7847 (m-80) cc_final: 0.7414 (m-10) REVERT: C 280 ASN cc_start: 0.7745 (t0) cc_final: 0.7429 (t0) REVERT: C 281 GLU cc_start: 0.7117 (pp20) cc_final: 0.6559 (pp20) REVERT: C 327 VAL cc_start: 0.8277 (t) cc_final: 0.8040 (m) REVERT: C 334 ASN cc_start: 0.7325 (t0) cc_final: 0.6161 (p0) REVERT: C 408 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7378 (ppp-140) REVERT: C 558 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7489 (mmtp) REVERT: C 572 THR cc_start: 0.6446 (OUTLIER) cc_final: 0.6198 (p) REVERT: C 574 ASP cc_start: 0.7331 (t70) cc_final: 0.6507 (t0) REVERT: C 599 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 655 TYR cc_start: 0.7203 (t80) cc_final: 0.7003 (t80) REVERT: C 674 TYR cc_start: 0.7890 (t80) cc_final: 0.7455 (t80) REVERT: C 675 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6827 (mm-40) REVERT: C 708 SER cc_start: 0.8341 (t) cc_final: 0.7923 (m) REVERT: C 723 THR cc_start: 0.8483 (t) cc_final: 0.8246 (p) REVERT: C 725 GLU cc_start: 0.7183 (tt0) cc_final: 0.6850 (tt0) REVERT: C 727 LEU cc_start: 0.8412 (mt) cc_final: 0.8114 (mp) REVERT: C 737 ASP cc_start: 0.6575 (t0) cc_final: 0.6144 (t70) REVERT: C 790 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7861 (mtpt) REVERT: C 795 LYS cc_start: 0.8738 (mttt) cc_final: 0.8464 (mttm) REVERT: C 810 SER cc_start: 0.8723 (m) cc_final: 0.8082 (p) REVERT: C 868 GLU cc_start: 0.6802 (tp30) cc_final: 0.6546 (tp30) REVERT: C 886 TRP cc_start: 0.8337 (p90) cc_final: 0.7797 (p90) REVERT: C 933 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8034 (ttmm) REVERT: C 957 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6961 (tm-30) REVERT: C 977 LEU cc_start: 0.7563 (mp) cc_final: 0.6954 (mp) REVERT: C 980 ILE cc_start: 0.8783 (mt) cc_final: 0.8514 (mm) REVERT: C 981 PHE cc_start: 0.7812 (m-80) cc_final: 0.7561 (m-80) REVERT: C 1002 GLN cc_start: 0.7686 (tp40) cc_final: 0.6853 (tm-30) REVERT: C 1014 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7427 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7615 (mmmt) REVERT: C 1133 VAL cc_start: 0.8580 (m) cc_final: 0.8362 (m) REVERT: C 1134 ASN cc_start: 0.6107 (m-40) cc_final: 0.5904 (m-40) REVERT: D 182 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.4840 (tt) REVERT: E 194 TYR cc_start: 0.3624 (OUTLIER) cc_final: 0.2935 (m-80) REVERT: F 182 LEU cc_start: 0.8130 (tp) cc_final: 0.7811 (tt) REVERT: G 142 PHE cc_start: 0.5211 (OUTLIER) cc_final: 0.4955 (t80) outliers start: 200 outliers final: 127 residues processed: 778 average time/residue: 0.1864 time to fit residues: 230.9616 Evaluate side-chains 772 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 622 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 159 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 221 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 345 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 209 optimal weight: 0.8980 chunk 388 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 784 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 542 ASN B 755 GLN B1005 GLN C 784 GLN C 914 ASN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.191561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141521 restraints weight = 56729.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143926 restraints weight = 25909.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144988 restraints weight = 17535.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146758 restraints weight = 11982.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146516 restraints weight = 9159.389| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31186 Z= 0.122 Angle : 0.581 11.918 42535 Z= 0.287 Chirality : 0.044 0.263 4863 Planarity : 0.004 0.109 5471 Dihedral : 5.976 59.872 4346 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.21 % Allowed : 17.94 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3888 helix: 0.75 (0.21), residues: 649 sheet: -1.51 (0.17), residues: 822 loop : -2.51 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.020 0.001 TYR A1067 PHE 0.031 0.001 PHE C 168 TRP 0.011 0.001 TRP G 37 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00276 (31139) covalent geometry : angle 0.57749 (42441) SS BOND : bond 0.00271 ( 47) SS BOND : angle 1.48778 ( 94) hydrogen bonds : bond 0.03702 ( 832) hydrogen bonds : angle 5.26579 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 631 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8002 (tt) REVERT: A 233 ILE cc_start: 0.3372 (OUTLIER) cc_final: 0.3077 (mm) REVERT: A 269 TYR cc_start: 0.7003 (m-10) cc_final: 0.6333 (m-80) REVERT: A 276 LEU cc_start: 0.8409 (tp) cc_final: 0.7882 (tt) REVERT: A 280 ASN cc_start: 0.7129 (t0) cc_final: 0.6695 (t0) REVERT: A 314 GLN cc_start: 0.7409 (tp40) cc_final: 0.7076 (tt0) REVERT: A 324 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6246 (mm-30) REVERT: A 329 PHE cc_start: 0.7815 (m-10) cc_final: 0.7537 (m-10) REVERT: A 334 ASN cc_start: 0.7304 (t0) cc_final: 0.6773 (t0) REVERT: A 466 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6764 (ttp80) REVERT: A 480 CYS cc_start: 0.4649 (OUTLIER) cc_final: 0.3846 (p) REVERT: A 542 ASN cc_start: 0.8271 (t0) cc_final: 0.7868 (t0) REVERT: A 578 ASP cc_start: 0.7627 (t0) cc_final: 0.7194 (t70) REVERT: A 663 ASP cc_start: 0.7028 (m-30) cc_final: 0.6739 (m-30) REVERT: A 752 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 755 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6993 (mp-120) REVERT: A 773 GLU cc_start: 0.7326 (tt0) cc_final: 0.6322 (tt0) REVERT: A 776 LYS cc_start: 0.8251 (tmmt) cc_final: 0.7876 (tmmt) REVERT: A 790 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7582 (mtpt) REVERT: A 801 ASN cc_start: 0.5792 (OUTLIER) cc_final: 0.5349 (t0) REVERT: A 825 LYS cc_start: 0.8326 (mtpm) cc_final: 0.8031 (mttm) REVERT: A 855 PHE cc_start: 0.8441 (m-10) cc_final: 0.8132 (m-80) REVERT: A 922 LEU cc_start: 0.8706 (tp) cc_final: 0.8429 (tt) REVERT: A 933 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8191 (mtmm) REVERT: A 953 ASN cc_start: 0.8241 (m-40) cc_final: 0.7496 (m110) REVERT: A 957 GLN cc_start: 0.7420 (pt0) cc_final: 0.7038 (pm20) REVERT: A 964 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7660 (mtmt) REVERT: A 975 SER cc_start: 0.8776 (m) cc_final: 0.8112 (t) REVERT: A 976 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 979 ASP cc_start: 0.7489 (m-30) cc_final: 0.7121 (m-30) REVERT: A 1017 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 1019 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6733 (ttm110) REVERT: A 1058 HIS cc_start: 0.7902 (m-70) cc_final: 0.7636 (m-70) REVERT: A 1073 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7617 (ttpp) REVERT: A 1117 THR cc_start: 0.8391 (p) cc_final: 0.8136 (t) REVERT: B 66 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: B 83 VAL cc_start: 0.7339 (OUTLIER) cc_final: 0.7054 (p) REVERT: B 91 TYR cc_start: 0.7298 (t80) cc_final: 0.6882 (t80) REVERT: B 99 ASN cc_start: 0.7963 (p0) cc_final: 0.7670 (p0) REVERT: B 127 VAL cc_start: 0.7943 (t) cc_final: 0.7206 (m) REVERT: B 165 ASN cc_start: 0.6468 (OUTLIER) cc_final: 0.5948 (p0) REVERT: B 188 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6802 (mtm180) REVERT: B 193 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7562 (ttmt) REVERT: B 212 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5849 (pp20) REVERT: B 294 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6597 (p0) REVERT: B 297 SER cc_start: 0.7975 (m) cc_final: 0.7548 (p) REVERT: B 338 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: B 356 LYS cc_start: 0.8445 (tmmt) cc_final: 0.8071 (tmtt) REVERT: B 398 ASP cc_start: 0.6128 (t70) cc_final: 0.5585 (t0) REVERT: B 465 GLU cc_start: 0.6496 (tt0) cc_final: 0.6189 (tt0) REVERT: B 535 LYS cc_start: 0.8332 (tptt) cc_final: 0.8002 (mmmm) REVERT: B 562 PHE cc_start: 0.7501 (p90) cc_final: 0.7099 (p90) REVERT: B 563 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6498 (mm-40) REVERT: B 750 SER cc_start: 0.8331 (m) cc_final: 0.7976 (p) REVERT: B 777 ASN cc_start: 0.7725 (m-40) cc_final: 0.7403 (m110) REVERT: B 868 GLU cc_start: 0.7073 (tp30) cc_final: 0.6655 (tp30) REVERT: B 921 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7673 (mtpp) REVERT: B 954 HIS cc_start: 0.7236 (m-70) cc_final: 0.6842 (m90) REVERT: B 957 GLN cc_start: 0.7785 (tp-100) cc_final: 0.7274 (tp-100) REVERT: B 961 THR cc_start: 0.8263 (p) cc_final: 0.7910 (t) REVERT: B 969 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8221 (pttm) REVERT: B 993 ILE cc_start: 0.8950 (tp) cc_final: 0.8652 (tp) REVERT: B 1003 SER cc_start: 0.8426 (m) cc_final: 0.8001 (t) REVERT: B 1005 GLN cc_start: 0.7779 (tp40) cc_final: 0.7547 (tp-100) REVERT: B 1118 ASP cc_start: 0.7528 (t70) cc_final: 0.6955 (t0) REVERT: B 1127 ASP cc_start: 0.7484 (t0) cc_final: 0.7072 (t0) REVERT: B 1141 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7921 (tt) REVERT: C 96 GLU cc_start: 0.6649 (pt0) cc_final: 0.6250 (pt0) REVERT: C 120 VAL cc_start: 0.8038 (t) cc_final: 0.7604 (p) REVERT: C 128 ILE cc_start: 0.7839 (mt) cc_final: 0.7627 (mp) REVERT: C 129 LYS cc_start: 0.7479 (ttpt) cc_final: 0.6955 (ttpt) REVERT: C 164 ASN cc_start: 0.7890 (t0) cc_final: 0.7602 (t0) REVERT: C 170 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5692 (m-10) REVERT: C 223 LEU cc_start: 0.8170 (mp) cc_final: 0.7945 (mp) REVERT: C 228 ASP cc_start: 0.7558 (t0) cc_final: 0.7269 (t70) REVERT: C 275 PHE cc_start: 0.7939 (m-80) cc_final: 0.7433 (m-10) REVERT: C 281 GLU cc_start: 0.7035 (pp20) cc_final: 0.6319 (pp20) REVERT: C 327 VAL cc_start: 0.8214 (t) cc_final: 0.7976 (m) REVERT: C 408 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7516 (ppp-140) REVERT: C 558 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7486 (mmtp) REVERT: C 572 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.6192 (p) REVERT: C 574 ASP cc_start: 0.7327 (t70) cc_final: 0.6457 (t0) REVERT: C 599 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 602 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8000 (p) REVERT: C 619 GLU cc_start: 0.6454 (tt0) cc_final: 0.6193 (tt0) REVERT: C 675 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6868 (mm-40) REVERT: C 708 SER cc_start: 0.8216 (t) cc_final: 0.7870 (m) REVERT: C 723 THR cc_start: 0.8499 (t) cc_final: 0.8257 (p) REVERT: C 725 GLU cc_start: 0.7196 (tt0) cc_final: 0.6906 (tt0) REVERT: C 737 ASP cc_start: 0.6694 (t0) cc_final: 0.6305 (t70) REVERT: C 790 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7915 (mtpt) REVERT: C 795 LYS cc_start: 0.8772 (mttt) cc_final: 0.8483 (mttm) REVERT: C 810 SER cc_start: 0.8749 (m) cc_final: 0.8100 (p) REVERT: C 868 GLU cc_start: 0.6876 (tp30) cc_final: 0.6605 (tp30) REVERT: C 886 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7795 (p90) REVERT: C 902 MET cc_start: 0.7880 (tpp) cc_final: 0.7610 (tpp) REVERT: C 933 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8042 (ttmm) REVERT: C 957 GLN cc_start: 0.7419 (tm-30) cc_final: 0.6953 (tm-30) REVERT: C 977 LEU cc_start: 0.7553 (mp) cc_final: 0.6948 (mm) REVERT: C 980 ILE cc_start: 0.8767 (mt) cc_final: 0.8485 (mm) REVERT: C 981 PHE cc_start: 0.7995 (m-80) cc_final: 0.7614 (m-80) REVERT: C 996 LEU cc_start: 0.8659 (tp) cc_final: 0.8370 (mp) REVERT: C 1002 GLN cc_start: 0.7750 (tp40) cc_final: 0.6924 (tm-30) REVERT: C 1014 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7542 (ttm-80) REVERT: C 1050 MET cc_start: 0.7698 (ptm) cc_final: 0.7446 (ptt) REVERT: C 1086 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7589 (mmmt) REVERT: C 1107 ARG cc_start: 0.7363 (mtt90) cc_final: 0.6786 (mpt90) REVERT: D 182 LEU cc_start: 0.4924 (mp) cc_final: 0.4426 (tt) REVERT: E 194 TYR cc_start: 0.3633 (OUTLIER) cc_final: 0.2360 (m-80) REVERT: F 182 LEU cc_start: 0.8277 (tp) cc_final: 0.7779 (tt) outliers start: 177 outliers final: 123 residues processed: 756 average time/residue: 0.1873 time to fit residues: 226.1247 Evaluate side-chains 767 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 621 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 64 optimal weight: 4.9990 chunk 282 optimal weight: 0.0770 chunk 372 optimal weight: 0.0770 chunk 117 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 271 optimal weight: 0.2980 chunk 143 optimal weight: 9.9990 chunk 60 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 overall best weight: 0.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 913 GLN A 949 GLN A 954 HIS B 422 ASN B 542 ASN B 755 GLN C 784 GLN C 914 ASN C 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.193169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142589 restraints weight = 56884.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146085 restraints weight = 26902.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146959 restraints weight = 16824.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148523 restraints weight = 11127.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148567 restraints weight = 8398.898| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31186 Z= 0.098 Angle : 0.566 12.400 42535 Z= 0.280 Chirality : 0.044 0.274 4863 Planarity : 0.004 0.071 5471 Dihedral : 5.867 59.899 4344 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.15 % Allowed : 18.14 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.13), residues: 3888 helix: 0.96 (0.21), residues: 647 sheet: -1.35 (0.18), residues: 792 loop : -2.39 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.018 0.001 TYR A1067 PHE 0.031 0.001 PHE B 55 TRP 0.011 0.001 TRP A 436 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00220 (31139) covalent geometry : angle 0.56252 (42441) SS BOND : bond 0.00283 ( 47) SS BOND : angle 1.39469 ( 94) hydrogen bonds : bond 0.03452 ( 832) hydrogen bonds : angle 5.12989 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 643 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 233 ILE cc_start: 0.3247 (OUTLIER) cc_final: 0.2969 (mm) REVERT: A 269 TYR cc_start: 0.6978 (m-10) cc_final: 0.6332 (m-80) REVERT: A 273 ARG cc_start: 0.6801 (mtm-85) cc_final: 0.6588 (mtm180) REVERT: A 276 LEU cc_start: 0.8338 (tp) cc_final: 0.7783 (tt) REVERT: A 280 ASN cc_start: 0.7052 (t0) cc_final: 0.6637 (t0) REVERT: A 314 GLN cc_start: 0.7376 (tp40) cc_final: 0.7067 (tt0) REVERT: A 324 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6210 (mm-30) REVERT: A 329 PHE cc_start: 0.7792 (m-10) cc_final: 0.7531 (m-10) REVERT: A 334 ASN cc_start: 0.7298 (t0) cc_final: 0.6782 (t0) REVERT: A 342 PHE cc_start: 0.7436 (m-80) cc_final: 0.6983 (m-80) REVERT: A 466 ARG cc_start: 0.7073 (ttp80) cc_final: 0.6797 (ttp80) REVERT: A 480 CYS cc_start: 0.4660 (OUTLIER) cc_final: 0.3884 (p) REVERT: A 542 ASN cc_start: 0.8244 (t0) cc_final: 0.7658 (t0) REVERT: A 565 PHE cc_start: 0.6767 (m-10) cc_final: 0.6502 (m-10) REVERT: A 572 THR cc_start: 0.8238 (m) cc_final: 0.7360 (p) REVERT: A 578 ASP cc_start: 0.7567 (t0) cc_final: 0.7094 (t70) REVERT: A 663 ASP cc_start: 0.7005 (m-30) cc_final: 0.6705 (m-30) REVERT: A 752 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8011 (mt) REVERT: A 755 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6978 (mp-120) REVERT: A 776 LYS cc_start: 0.8258 (tmmt) cc_final: 0.7727 (tmmt) REVERT: A 780 GLU cc_start: 0.7123 (pt0) cc_final: 0.6692 (pt0) REVERT: A 790 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7572 (mtpt) REVERT: A 801 ASN cc_start: 0.5672 (OUTLIER) cc_final: 0.5240 (t0) REVERT: A 804 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7278 (mm-40) REVERT: A 825 LYS cc_start: 0.8292 (mtpm) cc_final: 0.8012 (mttm) REVERT: A 855 PHE cc_start: 0.8342 (m-10) cc_final: 0.8098 (m-80) REVERT: A 922 LEU cc_start: 0.8680 (tp) cc_final: 0.8393 (tt) REVERT: A 964 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7660 (mtmt) REVERT: A 965 GLN cc_start: 0.7851 (mt0) cc_final: 0.7530 (mt0) REVERT: A 975 SER cc_start: 0.8720 (m) cc_final: 0.8089 (t) REVERT: A 976 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 979 ASP cc_start: 0.7424 (m-30) cc_final: 0.6957 (m-30) REVERT: A 980 ILE cc_start: 0.8661 (mt) cc_final: 0.8401 (tp) REVERT: A 1017 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 1073 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7568 (ttpp) REVERT: A 1097 SER cc_start: 0.8563 (t) cc_final: 0.7961 (p) REVERT: A 1117 THR cc_start: 0.8410 (p) cc_final: 0.8145 (t) REVERT: B 42 VAL cc_start: 0.8499 (t) cc_final: 0.8180 (m) REVERT: B 65 PHE cc_start: 0.7827 (m-10) cc_final: 0.7613 (m-10) REVERT: B 66 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: B 83 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7064 (p) REVERT: B 91 TYR cc_start: 0.7195 (t80) cc_final: 0.6931 (t80) REVERT: B 99 ASN cc_start: 0.7857 (p0) cc_final: 0.7555 (p0) REVERT: B 127 VAL cc_start: 0.8013 (t) cc_final: 0.7261 (m) REVERT: B 165 ASN cc_start: 0.6327 (OUTLIER) cc_final: 0.5848 (p0) REVERT: B 188 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6820 (mtm180) REVERT: B 193 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7587 (ttmt) REVERT: B 212 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5856 (pp20) REVERT: B 294 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6592 (p0) REVERT: B 297 SER cc_start: 0.7924 (m) cc_final: 0.7565 (p) REVERT: B 307 THR cc_start: 0.7976 (m) cc_final: 0.7484 (p) REVERT: B 338 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: B 355 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8038 (ttt-90) REVERT: B 356 LYS cc_start: 0.8493 (tmmt) cc_final: 0.8051 (mmmm) REVERT: B 394 ASN cc_start: 0.6047 (t0) cc_final: 0.5538 (t0) REVERT: B 398 ASP cc_start: 0.6200 (t70) cc_final: 0.5419 (t0) REVERT: B 402 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6197 (tt) REVERT: B 465 GLU cc_start: 0.6581 (tt0) cc_final: 0.6232 (tt0) REVERT: B 535 LYS cc_start: 0.8344 (tptt) cc_final: 0.8084 (mmmm) REVERT: B 563 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6467 (mm-40) REVERT: B 750 SER cc_start: 0.8272 (m) cc_final: 0.7864 (p) REVERT: B 777 ASN cc_start: 0.7576 (m-40) cc_final: 0.7208 (m-40) REVERT: B 868 GLU cc_start: 0.7039 (tp30) cc_final: 0.6636 (tp30) REVERT: B 902 MET cc_start: 0.7889 (tpp) cc_final: 0.7583 (mmm) REVERT: B 904 TYR cc_start: 0.7225 (m-10) cc_final: 0.6824 (m-10) REVERT: B 914 ASN cc_start: 0.7966 (p0) cc_final: 0.7729 (p0) REVERT: B 921 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7624 (mtpp) REVERT: B 954 HIS cc_start: 0.7221 (m-70) cc_final: 0.6798 (m90) REVERT: B 957 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7190 (tp-100) REVERT: B 961 THR cc_start: 0.8255 (p) cc_final: 0.7861 (t) REVERT: B 969 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8215 (pttm) REVERT: B 993 ILE cc_start: 0.8952 (tp) cc_final: 0.8641 (tp) REVERT: B 1003 SER cc_start: 0.8386 (m) cc_final: 0.7993 (t) REVERT: B 1118 ASP cc_start: 0.7504 (t70) cc_final: 0.6932 (t0) REVERT: B 1127 ASP cc_start: 0.7433 (t0) cc_final: 0.7013 (t0) REVERT: B 1141 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 96 GLU cc_start: 0.6522 (pt0) cc_final: 0.6141 (pt0) REVERT: C 120 VAL cc_start: 0.7971 (t) cc_final: 0.7581 (m) REVERT: C 128 ILE cc_start: 0.7903 (mt) cc_final: 0.7685 (mp) REVERT: C 164 ASN cc_start: 0.7895 (t0) cc_final: 0.7610 (t0) REVERT: C 170 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: C 228 ASP cc_start: 0.7541 (t0) cc_final: 0.7256 (t70) REVERT: C 275 PHE cc_start: 0.7892 (m-80) cc_final: 0.7394 (m-10) REVERT: C 297 SER cc_start: 0.7633 (m) cc_final: 0.7242 (p) REVERT: C 327 VAL cc_start: 0.8188 (t) cc_final: 0.7972 (m) REVERT: C 408 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7377 (ppp-140) REVERT: C 558 LYS cc_start: 0.7800 (mmtp) cc_final: 0.7420 (mmtp) REVERT: C 572 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.6120 (p) REVERT: C 574 ASP cc_start: 0.7300 (t70) cc_final: 0.6374 (t0) REVERT: C 602 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 674 TYR cc_start: 0.8151 (t80) cc_final: 0.7907 (t80) REVERT: C 675 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6839 (mm-40) REVERT: C 708 SER cc_start: 0.8057 (t) cc_final: 0.7718 (m) REVERT: C 723 THR cc_start: 0.8493 (t) cc_final: 0.8261 (p) REVERT: C 725 GLU cc_start: 0.7368 (tt0) cc_final: 0.7049 (tt0) REVERT: C 790 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7917 (mtpt) REVERT: C 795 LYS cc_start: 0.8753 (mttt) cc_final: 0.8464 (mttm) REVERT: C 810 SER cc_start: 0.8776 (m) cc_final: 0.8106 (p) REVERT: C 868 GLU cc_start: 0.6890 (tp30) cc_final: 0.6611 (tp30) REVERT: C 886 TRP cc_start: 0.8335 (p90) cc_final: 0.7781 (p90) REVERT: C 933 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7995 (ttmm) REVERT: C 957 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 977 LEU cc_start: 0.7502 (mp) cc_final: 0.6899 (mm) REVERT: C 980 ILE cc_start: 0.8765 (mt) cc_final: 0.8495 (mm) REVERT: C 981 PHE cc_start: 0.7962 (m-80) cc_final: 0.7578 (m-80) REVERT: C 996 LEU cc_start: 0.8656 (tp) cc_final: 0.8359 (mp) REVERT: C 1002 GLN cc_start: 0.7724 (tp40) cc_final: 0.6906 (tm-30) REVERT: C 1014 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7427 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7521 (mmmt) REVERT: C 1107 ARG cc_start: 0.7305 (mtt90) cc_final: 0.6580 (mpt90) REVERT: C 1136 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7864 (p) REVERT: D 182 LEU cc_start: 0.4854 (mp) cc_final: 0.4365 (tt) REVERT: E 194 TYR cc_start: 0.3651 (OUTLIER) cc_final: 0.2376 (m-80) REVERT: F 182 LEU cc_start: 0.8260 (tp) cc_final: 0.7744 (tt) REVERT: G 183 LEU cc_start: -0.4125 (OUTLIER) cc_final: -0.4469 (tp) outliers start: 175 outliers final: 119 residues processed: 767 average time/residue: 0.1927 time to fit residues: 234.9398 Evaluate side-chains 763 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 619 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 84 optimal weight: 0.5980 chunk 387 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 328 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 363 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 784 GLN A 913 GLN A 953 ASN B 542 ASN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 280 ASN C 360 ASN C 784 GLN C 914 ASN C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.190990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139824 restraints weight = 56654.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143459 restraints weight = 26398.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144054 restraints weight = 16819.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145589 restraints weight = 11895.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145885 restraints weight = 8985.867| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31186 Z= 0.142 Angle : 0.589 12.045 42535 Z= 0.293 Chirality : 0.044 0.197 4863 Planarity : 0.004 0.069 5471 Dihedral : 5.890 59.531 4342 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.21 % Allowed : 18.56 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3888 helix: 0.92 (0.21), residues: 651 sheet: -1.31 (0.18), residues: 798 loop : -2.34 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.021 0.001 TYR A1067 PHE 0.031 0.001 PHE B 55 TRP 0.008 0.001 TRP E 37 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00321 (31139) covalent geometry : angle 0.58527 (42441) SS BOND : bond 0.00324 ( 47) SS BOND : angle 1.56595 ( 94) hydrogen bonds : bond 0.03655 ( 832) hydrogen bonds : angle 5.14185 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 632 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 204 LYS cc_start: 0.8549 (tttt) cc_final: 0.7695 (ttpt) REVERT: A 233 ILE cc_start: 0.3347 (OUTLIER) cc_final: 0.3048 (mm) REVERT: A 269 TYR cc_start: 0.7090 (m-10) cc_final: 0.6409 (m-80) REVERT: A 273 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6353 (mtm180) REVERT: A 276 LEU cc_start: 0.8416 (tp) cc_final: 0.7876 (tt) REVERT: A 280 ASN cc_start: 0.7113 (t0) cc_final: 0.6698 (t0) REVERT: A 314 GLN cc_start: 0.7440 (tp40) cc_final: 0.7110 (tt0) REVERT: A 324 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 329 PHE cc_start: 0.7824 (m-10) cc_final: 0.7526 (m-10) REVERT: A 334 ASN cc_start: 0.7262 (t0) cc_final: 0.6776 (t0) REVERT: A 342 PHE cc_start: 0.7464 (m-80) cc_final: 0.6970 (m-80) REVERT: A 466 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6956 (ttp80) REVERT: A 542 ASN cc_start: 0.8284 (t0) cc_final: 0.7749 (t0) REVERT: A 663 ASP cc_start: 0.7071 (m-30) cc_final: 0.6746 (m-30) REVERT: A 735 SER cc_start: 0.8048 (m) cc_final: 0.7804 (t) REVERT: A 752 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (mt) REVERT: A 755 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7063 (mp-120) REVERT: A 776 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7731 (tmmt) REVERT: A 780 GLU cc_start: 0.7113 (pt0) cc_final: 0.6686 (pt0) REVERT: A 790 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7648 (mtpt) REVERT: A 801 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5298 (t0) REVERT: A 804 GLN cc_start: 0.7731 (mm-40) cc_final: 0.6990 (mm-40) REVERT: A 825 LYS cc_start: 0.8308 (mtpm) cc_final: 0.8020 (mttm) REVERT: A 855 PHE cc_start: 0.8424 (m-10) cc_final: 0.8085 (m-80) REVERT: A 922 LEU cc_start: 0.8703 (tp) cc_final: 0.8426 (tt) REVERT: A 935 GLN cc_start: 0.8258 (tt0) cc_final: 0.7714 (tt0) REVERT: A 964 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7708 (mtmt) REVERT: A 965 GLN cc_start: 0.7885 (mt0) cc_final: 0.7559 (mt0) REVERT: A 975 SER cc_start: 0.8753 (m) cc_final: 0.8116 (t) REVERT: A 976 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 979 ASP cc_start: 0.7508 (m-30) cc_final: 0.7075 (m-30) REVERT: A 980 ILE cc_start: 0.8680 (mt) cc_final: 0.8413 (tt) REVERT: A 992 GLN cc_start: 0.8421 (tp40) cc_final: 0.7747 (mp10) REVERT: A 1017 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 1019 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6866 (ttm110) REVERT: A 1034 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 1073 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7655 (ttpp) REVERT: A 1117 THR cc_start: 0.8396 (p) cc_final: 0.8184 (t) REVERT: B 66 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7683 (t-90) REVERT: B 83 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.7067 (p) REVERT: B 91 TYR cc_start: 0.7252 (t80) cc_final: 0.6833 (t80) REVERT: B 99 ASN cc_start: 0.7908 (p0) cc_final: 0.7622 (p0) REVERT: B 127 VAL cc_start: 0.8027 (t) cc_final: 0.7285 (m) REVERT: B 165 ASN cc_start: 0.6388 (OUTLIER) cc_final: 0.5904 (p0) REVERT: B 188 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6828 (mtm180) REVERT: B 193 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7599 (ttmt) REVERT: B 212 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5872 (pp20) REVERT: B 294 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6630 (p0) REVERT: B 297 SER cc_start: 0.7965 (m) cc_final: 0.7631 (p) REVERT: B 307 THR cc_start: 0.8026 (m) cc_final: 0.7527 (p) REVERT: B 338 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: B 356 LYS cc_start: 0.8489 (tmmt) cc_final: 0.8042 (mmmm) REVERT: B 398 ASP cc_start: 0.6100 (t70) cc_final: 0.5584 (t0) REVERT: B 402 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6185 (tt) REVERT: B 465 GLU cc_start: 0.6559 (tt0) cc_final: 0.6294 (tt0) REVERT: B 535 LYS cc_start: 0.8331 (tptt) cc_final: 0.8028 (mmmm) REVERT: B 539 VAL cc_start: 0.7829 (m) cc_final: 0.7604 (m) REVERT: B 563 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6639 (mm-40) REVERT: B 750 SER cc_start: 0.8223 (m) cc_final: 0.7904 (p) REVERT: B 777 ASN cc_start: 0.7641 (m-40) cc_final: 0.7389 (m110) REVERT: B 779 GLN cc_start: 0.8175 (tt0) cc_final: 0.7883 (tt0) REVERT: B 868 GLU cc_start: 0.7099 (tp30) cc_final: 0.6699 (tp30) REVERT: B 902 MET cc_start: 0.7957 (tpp) cc_final: 0.7717 (mmm) REVERT: B 914 ASN cc_start: 0.8036 (p0) cc_final: 0.7800 (p0) REVERT: B 921 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7692 (mtpp) REVERT: B 961 THR cc_start: 0.8278 (p) cc_final: 0.7890 (t) REVERT: B 969 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8223 (pttm) REVERT: B 993 ILE cc_start: 0.8989 (tp) cc_final: 0.8651 (tp) REVERT: B 1003 SER cc_start: 0.8412 (m) cc_final: 0.7996 (t) REVERT: B 1118 ASP cc_start: 0.7545 (t70) cc_final: 0.6997 (t0) REVERT: B 1127 ASP cc_start: 0.7492 (t0) cc_final: 0.7077 (t0) REVERT: B 1141 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7903 (tt) REVERT: C 96 GLU cc_start: 0.6673 (pt0) cc_final: 0.6275 (pt0) REVERT: C 99 ASN cc_start: 0.7261 (t0) cc_final: 0.6884 (t0) REVERT: C 128 ILE cc_start: 0.7976 (mt) cc_final: 0.7743 (mp) REVERT: C 164 ASN cc_start: 0.7955 (t0) cc_final: 0.7652 (t0) REVERT: C 170 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: C 194 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7859 (p0) REVERT: C 223 LEU cc_start: 0.8250 (mp) cc_final: 0.7955 (mp) REVERT: C 228 ASP cc_start: 0.7500 (t0) cc_final: 0.7247 (t70) REVERT: C 275 PHE cc_start: 0.7958 (m-80) cc_final: 0.7422 (m-10) REVERT: C 297 SER cc_start: 0.7647 (m) cc_final: 0.7223 (p) REVERT: C 408 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7406 (ppp-140) REVERT: C 558 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7467 (mmtp) REVERT: C 574 ASP cc_start: 0.7341 (t70) cc_final: 0.6426 (t0) REVERT: C 599 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8360 (p) REVERT: C 602 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 655 TYR cc_start: 0.7393 (t80) cc_final: 0.7070 (t80) REVERT: C 674 TYR cc_start: 0.8240 (t80) cc_final: 0.7905 (t80) REVERT: C 675 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6958 (mm-40) REVERT: C 723 THR cc_start: 0.8401 (t) cc_final: 0.8173 (p) REVERT: C 725 GLU cc_start: 0.7328 (tt0) cc_final: 0.7009 (tt0) REVERT: C 790 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7952 (mtpt) REVERT: C 795 LYS cc_start: 0.8813 (mttt) cc_final: 0.8518 (mttm) REVERT: C 810 SER cc_start: 0.8765 (m) cc_final: 0.8094 (p) REVERT: C 868 GLU cc_start: 0.6908 (tp30) cc_final: 0.6620 (tp30) REVERT: C 886 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7799 (p90) REVERT: C 933 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8041 (ttmm) REVERT: C 957 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7059 (tm-30) REVERT: C 977 LEU cc_start: 0.7546 (mp) cc_final: 0.6889 (mm) REVERT: C 980 ILE cc_start: 0.8750 (mt) cc_final: 0.8456 (mm) REVERT: C 981 PHE cc_start: 0.8000 (m-80) cc_final: 0.7596 (m-80) REVERT: C 996 LEU cc_start: 0.8660 (tp) cc_final: 0.8348 (mp) REVERT: C 1002 GLN cc_start: 0.7750 (tp40) cc_final: 0.6928 (tm-30) REVERT: C 1014 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7464 (ttm-80) REVERT: C 1050 MET cc_start: 0.7700 (ptm) cc_final: 0.7462 (ptt) REVERT: C 1086 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7570 (mmmt) REVERT: C 1133 VAL cc_start: 0.8568 (m) cc_final: 0.8298 (m) REVERT: C 1134 ASN cc_start: 0.6563 (m-40) cc_final: 0.5955 (m110) REVERT: C 1136 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (p) REVERT: D 182 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4471 (tt) REVERT: E 194 TYR cc_start: 0.3721 (OUTLIER) cc_final: 0.2459 (m-80) REVERT: F 182 LEU cc_start: 0.8265 (tp) cc_final: 0.7777 (tt) outliers start: 177 outliers final: 124 residues processed: 755 average time/residue: 0.1889 time to fit residues: 227.7918 Evaluate side-chains 772 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 622 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 357 optimal weight: 5.9990 chunk 374 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 291 optimal weight: 0.0570 chunk 373 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 544 ASN A 784 GLN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 542 ASN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 914 ASN C1048 HIS F 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.187128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135580 restraints weight = 56140.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139243 restraints weight = 26097.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139902 restraints weight = 16693.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141526 restraints weight = 11498.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141675 restraints weight = 8543.472| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 31186 Z= 0.275 Angle : 0.677 12.061 42535 Z= 0.345 Chirality : 0.048 0.264 4863 Planarity : 0.005 0.067 5471 Dihedral : 6.157 56.819 4338 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.18 % Allowed : 18.70 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.13), residues: 3888 helix: 0.62 (0.20), residues: 651 sheet: -1.48 (0.17), residues: 837 loop : -2.42 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.025 0.002 TYR A1067 PHE 0.028 0.002 PHE A1089 TRP 0.015 0.002 TRP B 64 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00603 (31139) covalent geometry : angle 0.67098 (42441) SS BOND : bond 0.00384 ( 47) SS BOND : angle 2.09788 ( 94) hydrogen bonds : bond 0.04356 ( 832) hydrogen bonds : angle 5.39359 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 643 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 204 LYS cc_start: 0.8562 (tttt) cc_final: 0.7906 (ttpt) REVERT: A 227 VAL cc_start: 0.8301 (m) cc_final: 0.8043 (t) REVERT: A 233 ILE cc_start: 0.3587 (OUTLIER) cc_final: 0.3309 (mm) REVERT: A 276 LEU cc_start: 0.8507 (tp) cc_final: 0.8121 (tt) REVERT: A 280 ASN cc_start: 0.7282 (t0) cc_final: 0.6852 (t0) REVERT: A 314 GLN cc_start: 0.7518 (tp40) cc_final: 0.7190 (tt0) REVERT: A 324 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6325 (mm-30) REVERT: A 334 ASN cc_start: 0.7227 (t0) cc_final: 0.6788 (t0) REVERT: A 387 LEU cc_start: 0.8104 (tp) cc_final: 0.7680 (mt) REVERT: A 466 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7077 (ttp80) REVERT: A 586 ASP cc_start: 0.7407 (t0) cc_final: 0.7189 (t0) REVERT: A 751 ASN cc_start: 0.7642 (m-40) cc_final: 0.7171 (m-40) REVERT: A 752 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 755 GLN cc_start: 0.7498 (mp-120) cc_final: 0.7220 (mp-120) REVERT: A 776 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7893 (tmmt) REVERT: A 790 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7700 (mtpt) REVERT: A 801 ASN cc_start: 0.5646 (OUTLIER) cc_final: 0.5251 (t0) REVERT: A 804 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7127 (mm-40) REVERT: A 825 LYS cc_start: 0.8361 (mtpm) cc_final: 0.8081 (mttm) REVERT: A 922 LEU cc_start: 0.8789 (tp) cc_final: 0.8482 (tt) REVERT: A 935 GLN cc_start: 0.8314 (tt0) cc_final: 0.7763 (tt0) REVERT: A 964 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7819 (mtmt) REVERT: A 965 GLN cc_start: 0.8056 (mt0) cc_final: 0.7674 (mt0) REVERT: A 975 SER cc_start: 0.8761 (m) cc_final: 0.8098 (t) REVERT: A 976 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 978 ASN cc_start: 0.8248 (m110) cc_final: 0.8042 (m110) REVERT: A 979 ASP cc_start: 0.7635 (m-30) cc_final: 0.7221 (m-30) REVERT: A 980 ILE cc_start: 0.8680 (mt) cc_final: 0.8436 (tt) REVERT: A 981 PHE cc_start: 0.7727 (m-10) cc_final: 0.7489 (m-10) REVERT: A 992 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: A 1017 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 1019 ARG cc_start: 0.7347 (ttm110) cc_final: 0.7005 (ttm110) REVERT: A 1073 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7699 (ttpp) REVERT: A 1107 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7395 (mpt180) REVERT: A 1110 TYR cc_start: 0.8214 (t80) cc_final: 0.7443 (t80) REVERT: A 1117 THR cc_start: 0.8506 (p) cc_final: 0.8287 (t) REVERT: B 66 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7763 (t-90) REVERT: B 83 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7320 (p) REVERT: B 88 ASP cc_start: 0.7619 (m-30) cc_final: 0.7358 (m-30) REVERT: B 99 ASN cc_start: 0.8071 (p0) cc_final: 0.7852 (p0) REVERT: B 127 VAL cc_start: 0.8066 (t) cc_final: 0.7336 (m) REVERT: B 165 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6123 (p0) REVERT: B 188 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6858 (mtm180) REVERT: B 193 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7591 (ttmt) REVERT: B 212 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5941 (pp20) REVERT: B 224 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 273 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7294 (mtm180) REVERT: B 294 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6653 (p0) REVERT: B 297 SER cc_start: 0.8105 (m) cc_final: 0.7749 (p) REVERT: B 307 THR cc_start: 0.8074 (m) cc_final: 0.7613 (p) REVERT: B 308 VAL cc_start: 0.8482 (t) cc_final: 0.8270 (m) REVERT: B 355 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8432 (ttt-90) REVERT: B 398 ASP cc_start: 0.6123 (t70) cc_final: 0.5613 (t0) REVERT: B 542 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8258 (t0) REVERT: B 588 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 719 THR cc_start: 0.8282 (t) cc_final: 0.8042 (p) REVERT: B 750 SER cc_start: 0.8333 (m) cc_final: 0.7907 (p) REVERT: B 824 ASN cc_start: 0.7930 (m-40) cc_final: 0.7723 (m-40) REVERT: B 868 GLU cc_start: 0.7155 (tp30) cc_final: 0.6738 (tp30) REVERT: B 954 HIS cc_start: 0.7392 (m170) cc_final: 0.6972 (m90) REVERT: B 961 THR cc_start: 0.8330 (p) cc_final: 0.7961 (t) REVERT: B 993 ILE cc_start: 0.8994 (tp) cc_final: 0.8650 (tp) REVERT: B 1003 SER cc_start: 0.8427 (m) cc_final: 0.8006 (t) REVERT: B 1118 ASP cc_start: 0.7538 (t70) cc_final: 0.6982 (t0) REVERT: B 1127 ASP cc_start: 0.7601 (t0) cc_final: 0.7247 (t0) REVERT: B 1141 LEU cc_start: 0.8265 (tt) cc_final: 0.7885 (tt) REVERT: C 99 ASN cc_start: 0.7544 (t0) cc_final: 0.6809 (t0) REVERT: C 121 ASN cc_start: 0.8057 (p0) cc_final: 0.7685 (p0) REVERT: C 128 ILE cc_start: 0.8008 (mt) cc_final: 0.7775 (mp) REVERT: C 164 ASN cc_start: 0.8043 (t0) cc_final: 0.7765 (t0) REVERT: C 228 ASP cc_start: 0.7436 (t0) cc_final: 0.7222 (t70) REVERT: C 275 PHE cc_start: 0.8068 (m-80) cc_final: 0.7449 (m-10) REVERT: C 297 SER cc_start: 0.7684 (m) cc_final: 0.7241 (p) REVERT: C 327 VAL cc_start: 0.8153 (t) cc_final: 0.7919 (m) REVERT: C 408 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7407 (ppp-140) REVERT: C 558 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7471 (mmtp) REVERT: C 574 ASP cc_start: 0.7462 (t70) cc_final: 0.6472 (t0) REVERT: C 599 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8331 (p) REVERT: C 602 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8070 (p) REVERT: C 619 GLU cc_start: 0.6986 (tt0) cc_final: 0.6722 (tt0) REVERT: C 655 TYR cc_start: 0.7482 (t80) cc_final: 0.7171 (t80) REVERT: C 723 THR cc_start: 0.8418 (t) cc_final: 0.8197 (p) REVERT: C 725 GLU cc_start: 0.7302 (tt0) cc_final: 0.6989 (tt0) REVERT: C 776 LYS cc_start: 0.8436 (ttpm) cc_final: 0.8101 (ttpp) REVERT: C 790 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7934 (ttmm) REVERT: C 795 LYS cc_start: 0.8809 (mttt) cc_final: 0.8504 (mttm) REVERT: C 810 SER cc_start: 0.8793 (m) cc_final: 0.8105 (p) REVERT: C 868 GLU cc_start: 0.6921 (tp30) cc_final: 0.6689 (tp30) REVERT: C 886 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7798 (p90) REVERT: C 933 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8147 (ttmm) REVERT: C 957 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7127 (tm-30) REVERT: C 980 ILE cc_start: 0.8758 (mt) cc_final: 0.8448 (mm) REVERT: C 981 PHE cc_start: 0.8045 (m-80) cc_final: 0.7663 (m-80) REVERT: C 996 LEU cc_start: 0.8664 (tp) cc_final: 0.8360 (mp) REVERT: C 1002 GLN cc_start: 0.7819 (tp40) cc_final: 0.7012 (tm-30) REVERT: C 1014 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7642 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7731 (mmmt) REVERT: C 1133 VAL cc_start: 0.8508 (m) cc_final: 0.8183 (m) REVERT: C 1134 ASN cc_start: 0.5690 (m-40) cc_final: 0.4091 (m110) REVERT: E 194 TYR cc_start: 0.3757 (OUTLIER) cc_final: 0.2428 (m-80) outliers start: 176 outliers final: 131 residues processed: 756 average time/residue: 0.1915 time to fit residues: 230.9626 Evaluate side-chains 766 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 614 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 166 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 324 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 388 ASN A 422 ASN A 784 GLN A 901 GLN A 913 GLN A 953 ASN B 542 ASN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 784 GLN C 914 ASN F 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.189776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138746 restraints weight = 56354.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142789 restraints weight = 26027.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143284 restraints weight = 15723.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144764 restraints weight = 11014.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144884 restraints weight = 8280.954| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31186 Z= 0.135 Angle : 0.634 12.563 42535 Z= 0.316 Chirality : 0.045 0.225 4863 Planarity : 0.005 0.071 5471 Dihedral : 6.042 57.309 4334 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.39 % Allowed : 20.24 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3888 helix: 0.84 (0.21), residues: 642 sheet: -1.30 (0.17), residues: 826 loop : -2.33 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.032 0.001 TYR A 265 PHE 0.031 0.002 PHE B 168 TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00308 (31139) covalent geometry : angle 0.63031 (42441) SS BOND : bond 0.00370 ( 47) SS BOND : angle 1.64084 ( 94) hydrogen bonds : bond 0.03771 ( 832) hydrogen bonds : angle 5.30216 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 622 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8137 (tt) REVERT: A 193 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7608 (ptpp) REVERT: A 227 VAL cc_start: 0.8212 (m) cc_final: 0.7955 (t) REVERT: A 233 ILE cc_start: 0.3481 (OUTLIER) cc_final: 0.3232 (mm) REVERT: A 276 LEU cc_start: 0.8454 (tp) cc_final: 0.8054 (tt) REVERT: A 280 ASN cc_start: 0.7228 (t0) cc_final: 0.6805 (t0) REVERT: A 314 GLN cc_start: 0.7449 (tp40) cc_final: 0.7132 (tt0) REVERT: A 324 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6336 (mm-30) REVERT: A 334 ASN cc_start: 0.7257 (t0) cc_final: 0.6811 (t0) REVERT: A 387 LEU cc_start: 0.8120 (tp) cc_final: 0.7675 (mt) REVERT: A 466 ARG cc_start: 0.7223 (ttp80) cc_final: 0.7002 (ttp80) REVERT: A 542 ASN cc_start: 0.8345 (t0) cc_final: 0.7727 (t0) REVERT: A 737 ASP cc_start: 0.7445 (p0) cc_final: 0.7088 (p0) REVERT: A 752 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8259 (mt) REVERT: A 755 GLN cc_start: 0.7376 (mp-120) cc_final: 0.7090 (mp-120) REVERT: A 776 LYS cc_start: 0.8243 (tmmt) cc_final: 0.7899 (tmmt) REVERT: A 790 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7659 (mtpt) REVERT: A 801 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5221 (t0) REVERT: A 804 GLN cc_start: 0.7714 (mm-40) cc_final: 0.6998 (mm-40) REVERT: A 825 LYS cc_start: 0.8359 (mtpm) cc_final: 0.8073 (mttm) REVERT: A 855 PHE cc_start: 0.8438 (m-80) cc_final: 0.8066 (m-80) REVERT: A 922 LEU cc_start: 0.8724 (tp) cc_final: 0.8441 (tt) REVERT: A 935 GLN cc_start: 0.8211 (tt0) cc_final: 0.7674 (tt0) REVERT: A 964 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7750 (mtmt) REVERT: A 965 GLN cc_start: 0.7959 (mt0) cc_final: 0.7646 (mt0) REVERT: A 975 SER cc_start: 0.8726 (m) cc_final: 0.8125 (t) REVERT: A 976 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 978 ASN cc_start: 0.8241 (m110) cc_final: 0.8002 (m110) REVERT: A 979 ASP cc_start: 0.7528 (m-30) cc_final: 0.7070 (m-30) REVERT: A 980 ILE cc_start: 0.8586 (mt) cc_final: 0.8370 (tt) REVERT: A 1017 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 1019 ARG cc_start: 0.7163 (ttm110) cc_final: 0.6880 (ttm110) REVERT: A 1031 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6822 (mp0) REVERT: A 1073 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7716 (ttpp) REVERT: A 1107 ARG cc_start: 0.7563 (mpt180) cc_final: 0.7218 (mpt180) REVERT: A 1110 TYR cc_start: 0.8188 (t80) cc_final: 0.7434 (t80) REVERT: A 1117 THR cc_start: 0.8442 (p) cc_final: 0.8213 (t) REVERT: B 66 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7668 (t-90) REVERT: B 83 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7330 (p) REVERT: B 99 ASN cc_start: 0.8004 (p0) cc_final: 0.7743 (p0) REVERT: B 188 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6871 (mtm180) REVERT: B 193 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7700 (ttmt) REVERT: B 212 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5953 (pp20) REVERT: B 294 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6602 (p0) REVERT: B 297 SER cc_start: 0.8011 (m) cc_final: 0.7722 (p) REVERT: B 307 THR cc_start: 0.8063 (m) cc_final: 0.7553 (p) REVERT: B 355 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8359 (ttt-90) REVERT: B 356 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8071 (tmmt) REVERT: B 398 ASP cc_start: 0.6245 (t70) cc_final: 0.5659 (t0) REVERT: B 465 GLU cc_start: 0.6631 (tt0) cc_final: 0.6287 (tt0) REVERT: B 542 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8137 (t0) REVERT: B 563 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6657 (mm-40) REVERT: B 719 THR cc_start: 0.8233 (t) cc_final: 0.8021 (p) REVERT: B 750 SER cc_start: 0.8266 (m) cc_final: 0.7932 (p) REVERT: B 779 GLN cc_start: 0.8127 (tt0) cc_final: 0.7898 (tt0) REVERT: B 868 GLU cc_start: 0.7024 (tp30) cc_final: 0.6661 (tp30) REVERT: B 954 HIS cc_start: 0.7337 (m170) cc_final: 0.6902 (m90) REVERT: B 957 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7197 (tp-100) REVERT: B 961 THR cc_start: 0.8283 (p) cc_final: 0.7921 (t) REVERT: B 993 ILE cc_start: 0.8935 (tp) cc_final: 0.8631 (tp) REVERT: B 1003 SER cc_start: 0.8410 (m) cc_final: 0.8015 (t) REVERT: B 1073 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7422 (ttmm) REVERT: B 1118 ASP cc_start: 0.7469 (t70) cc_final: 0.6921 (t0) REVERT: B 1127 ASP cc_start: 0.7514 (t0) cc_final: 0.7212 (t0) REVERT: B 1141 LEU cc_start: 0.8220 (tt) cc_final: 0.7855 (tt) REVERT: C 96 GLU cc_start: 0.6678 (pt0) cc_final: 0.6277 (pt0) REVERT: C 99 ASN cc_start: 0.7420 (t0) cc_final: 0.6958 (t0) REVERT: C 120 VAL cc_start: 0.8027 (t) cc_final: 0.7616 (m) REVERT: C 121 ASN cc_start: 0.8061 (p0) cc_final: 0.7642 (p0) REVERT: C 128 ILE cc_start: 0.8008 (mt) cc_final: 0.7746 (mp) REVERT: C 164 ASN cc_start: 0.8057 (t0) cc_final: 0.7785 (t0) REVERT: C 228 ASP cc_start: 0.7423 (t0) cc_final: 0.7211 (t70) REVERT: C 237 ARG cc_start: 0.7466 (mtp-110) cc_final: 0.7247 (mtp85) REVERT: C 275 PHE cc_start: 0.7941 (m-80) cc_final: 0.7409 (m-10) REVERT: C 297 SER cc_start: 0.7612 (m) cc_final: 0.7214 (p) REVERT: C 327 VAL cc_start: 0.8098 (t) cc_final: 0.7883 (m) REVERT: C 408 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7414 (ppp-140) REVERT: C 558 LYS cc_start: 0.7840 (mmtp) cc_final: 0.7433 (mmtp) REVERT: C 574 ASP cc_start: 0.7456 (t70) cc_final: 0.6469 (t0) REVERT: C 599 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8361 (p) REVERT: C 602 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8051 (p) REVERT: C 655 TYR cc_start: 0.7451 (t80) cc_final: 0.7151 (t80) REVERT: C 723 THR cc_start: 0.8390 (t) cc_final: 0.8175 (p) REVERT: C 725 GLU cc_start: 0.7335 (tt0) cc_final: 0.7001 (tt0) REVERT: C 762 GLN cc_start: 0.7767 (mt0) cc_final: 0.7506 (mt0) REVERT: C 776 LYS cc_start: 0.8409 (ttpm) cc_final: 0.8088 (ttpp) REVERT: C 790 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7976 (mtpt) REVERT: C 795 LYS cc_start: 0.8771 (mttt) cc_final: 0.8463 (mttm) REVERT: C 868 GLU cc_start: 0.6890 (tp30) cc_final: 0.6660 (tp30) REVERT: C 886 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7749 (p90) REVERT: C 933 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8077 (ttmm) REVERT: C 977 LEU cc_start: 0.7517 (mp) cc_final: 0.6658 (mm) REVERT: C 980 ILE cc_start: 0.8732 (mt) cc_final: 0.8465 (mm) REVERT: C 981 PHE cc_start: 0.7985 (m-80) cc_final: 0.7537 (m-80) REVERT: C 996 LEU cc_start: 0.8667 (tp) cc_final: 0.8344 (mp) REVERT: C 1002 GLN cc_start: 0.7804 (tp40) cc_final: 0.6951 (tm-30) REVERT: C 1014 ARG cc_start: 0.7819 (tpp80) cc_final: 0.7536 (ttm110) REVERT: C 1086 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7312 (mmmt) REVERT: D 182 LEU cc_start: 0.5047 (tp) cc_final: 0.4608 (tp) REVERT: E 47 LYS cc_start: 0.4088 (OUTLIER) cc_final: 0.2971 (ttmm) REVERT: E 194 TYR cc_start: 0.3790 (OUTLIER) cc_final: 0.2505 (m-80) outliers start: 149 outliers final: 121 residues processed: 728 average time/residue: 0.1936 time to fit residues: 224.2904 Evaluate side-chains 751 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 611 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 9.9990 chunk 260 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 390 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 342 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 219 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 422 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 542 ASN C 762 GLN C 784 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.189564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138443 restraints weight = 56733.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142306 restraints weight = 26174.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143062 restraints weight = 16343.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144537 restraints weight = 11087.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144720 restraints weight = 8439.387| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 31186 Z= 0.188 Angle : 0.819 59.199 42535 Z= 0.452 Chirality : 0.049 1.370 4863 Planarity : 0.005 0.125 5471 Dihedral : 5.976 57.319 4331 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.36 % Allowed : 20.50 % Favored : 75.14 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3888 helix: 0.83 (0.21), residues: 643 sheet: -1.31 (0.17), residues: 817 loop : -2.33 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 273 TYR 0.029 0.001 TYR A 265 PHE 0.031 0.002 PHE C 855 TRP 0.011 0.001 TRP A 64 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00415 (31139) covalent geometry : angle 0.81527 (42441) SS BOND : bond 0.00500 ( 47) SS BOND : angle 1.92302 ( 94) hydrogen bonds : bond 0.03797 ( 832) hydrogen bonds : angle 5.30763 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7343.49 seconds wall clock time: 126 minutes 40.10 seconds (7600.10 seconds total)