Starting phenix.real_space_refine on Thu Jun 26 08:20:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yd0_33744/06_2025/7yd0_33744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yd0_33744/06_2025/7yd0_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_33744/06_2025/7yd0_33744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yd0_33744/06_2025/7yd0_33744.map" model { file = "/net/cci-nas-00/data/ceres_data/7yd0_33744/06_2025/7yd0_33744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yd0_33744/06_2025/7yd0_33744.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: 18.19, per 1000 atoms: 0.60 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: 8.03 Conformation dependent library (CDL) restraints added in 3.9 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: 4.20 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: 13.81 Time building geometry restraints manager: 9.58 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 72.610 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.670 ------------------------------------------------------------------------------- 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 : 7.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (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 TRP 0.005 0.001 TRP C 886 HIS 0.001 0.000 HIS C1064 PHE 0.007 0.001 PHE C 318 TYR 0.007 0.001 TYR B 265 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.28236 ( 832) hydrogen bonds : angle 9.88869 ( 2268) SS BOND : bond 0.00118 ( 47) SS BOND : angle 0.44040 ( 94) covalent geometry : bond 0.00229 (31139) covalent geometry : angle 0.58915 (42441) *********************** 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 : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7389 (tp40) cc_final: 0.7188 (tp40) 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: 0.7037 (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: 0.7944 (tt) REVERT: A 281 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6432 (pp20) REVERT: A 296 LEU cc_start: 0.8649 (tp) cc_final: 0.8362 (tp) REVERT: A 307 THR cc_start: 0.7855 (m) cc_final: 0.7495 (p) REVERT: A 308 VAL cc_start: 0.8388 (p) cc_final: 0.8046 (m) REVERT: A 323 THR cc_start: 0.7828 (m) cc_final: 0.6383 (p) REVERT: A 332 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7203 (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: 0.8127 (mt) REVERT: A 664 ILE cc_start: 0.8295 (mt) cc_final: 0.8069 (mm) REVERT: A 725 GLU cc_start: 0.7213 (pt0) cc_final: 0.6768 (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: 0.7215 (m110) REVERT: A 752 LEU cc_start: 0.8319 (mm) cc_final: 0.7969 (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: 0.6494 (tt0) REVERT: A 776 LYS cc_start: 0.8079 (tmmt) cc_final: 0.7735 (tmmt) REVERT: A 800 PHE cc_start: 0.8071 (m-80) cc_final: 0.7723 (m-80) REVERT: A 821 LEU cc_start: 0.8211 (mm) cc_final: 0.7870 (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: 0.8577 (tt) REVERT: A 933 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8220 (mtmm) REVERT: A 935 GLN cc_start: 0.8044 (tt0) cc_final: 0.7831 (tt0) REVERT: A 947 LYS cc_start: 0.8216 (mtpt) cc_final: 0.8009 (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: 0.7358 (mtmt) REVERT: A 975 SER cc_start: 0.8570 (m) cc_final: 0.7959 (t) REVERT: A 977 LEU cc_start: 0.9005 (mp) cc_final: 0.8756 (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: 0.5934 (tm-30) REVERT: A 1019 ARG cc_start: 0.7297 (ttm110) cc_final: 0.5865 (ttm110) REVERT: A 1028 LYS cc_start: 0.8511 (mttt) cc_final: 0.8244 (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: 0.7652 (t) REVERT: B 29 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7858 (t) REVERT: B 54 LEU cc_start: 0.8075 (mt) cc_final: 0.7858 (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: 0.7147 (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: 0.7243 (tt) REVERT: B 193 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7094 (ttpt) REVERT: B 307 THR cc_start: 0.7695 (m) cc_final: 0.7290 (p) REVERT: B 319 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6735 (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: 0.4939 (t0) REVERT: B 528 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8327 (mmtt) REVERT: B 535 LYS cc_start: 0.8307 (tptt) cc_final: 0.8013 (mmmm) REVERT: B 543 PHE cc_start: 0.6697 (m-10) cc_final: 0.6369 (m-80) REVERT: B 546 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8305 (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: 0.6739 (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: 0.8164 (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: 0.8169 (p) REVERT: B 759 PHE cc_start: 0.7311 (t80) cc_final: 0.6909 (t80) REVERT: B 765 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7260 (ttp80) REVERT: B 800 PHE cc_start: 0.7974 (m-80) cc_final: 0.7358 (m-80) REVERT: B 868 GLU cc_start: 0.7300 (tp30) cc_final: 0.6907 (tp30) REVERT: B 884 SER cc_start: 0.8794 (m) cc_final: 0.8506 (p) REVERT: B 954 HIS cc_start: 0.7120 (m-70) cc_final: 0.6764 (m90) REVERT: B 955 ASN cc_start: 0.7523 (m-40) cc_final: 0.7314 (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: 0.7537 (p) REVERT: B 965 GLN cc_start: 0.7321 (mt0) cc_final: 0.7067 (mt0) REVERT: B 1003 SER cc_start: 0.8340 (m) cc_final: 0.8003 (t) REVERT: B 1017 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6489 (tm-30) REVERT: B 1028 LYS cc_start: 0.8405 (mttm) cc_final: 0.7698 (mtpp) REVERT: B 1072 GLU cc_start: 0.8014 (pm20) cc_final: 0.7747 (pm20) REVERT: B 1081 ILE cc_start: 0.7822 (pt) cc_final: 0.7490 (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: 0.7849 (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: 0.7577 (p) REVERT: C 90 VAL cc_start: 0.8670 (m) cc_final: 0.8305 (t) REVERT: C 106 PHE cc_start: 0.7862 (m-80) cc_final: 0.7637 (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: 0.7996 (m-80) cc_final: 0.7760 (m-80) REVERT: C 275 PHE cc_start: 0.7929 (m-80) cc_final: 0.7674 (m-10) REVERT: C 281 GLU cc_start: 0.7169 (pp20) cc_final: 0.6638 (pp20) REVERT: C 293 LEU cc_start: 0.8484 (tp) cc_final: 0.8280 (tp) 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: 0.8087 (t0) REVERT: C 546 LEU cc_start: 0.7762 (tm) cc_final: 0.7477 (tt) REVERT: C 574 ASP cc_start: 0.6982 (t70) cc_final: 0.5971 (t0) REVERT: C 578 ASP cc_start: 0.6509 (t0) cc_final: 0.5920 (t70) REVERT: C 586 ASP cc_start: 0.7116 (t0) cc_final: 0.6614 (t0) REVERT: C 644 GLN cc_start: 0.8065 (tp40) cc_final: 0.7222 (tp40) REVERT: C 651 ILE cc_start: 0.8449 (mt) cc_final: 0.8231 (mm) REVERT: C 675 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6431 (mm-40) REVERT: C 708 SER cc_start: 0.8372 (t) cc_final: 0.8112 (m) REVERT: C 712 ILE cc_start: 0.8278 (tp) cc_final: 0.8038 (tp) REVERT: C 723 THR cc_start: 0.8505 (t) cc_final: 0.8297 (p) REVERT: C 725 GLU cc_start: 0.7250 (tt0) cc_final: 0.6384 (tt0) REVERT: C 740 MET cc_start: 0.7477 (ttp) cc_final: 0.7217 (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: 0.7008 (tt0) REVERT: C 795 LYS cc_start: 0.8637 (mttt) cc_final: 0.8339 (mttm) REVERT: C 868 GLU cc_start: 0.6891 (tp30) cc_final: 0.6509 (tp30) REVERT: C 886 TRP cc_start: 0.8361 (p90) cc_final: 0.7967 (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: 0.7686 (m-40) REVERT: C 933 LYS cc_start: 0.8295 (mtpt) cc_final: 0.8003 (ttmm) REVERT: C 977 LEU cc_start: 0.7848 (mp) cc_final: 0.6875 (mp) REVERT: C 980 ILE cc_start: 0.8845 (mt) cc_final: 0.8533 (mm) REVERT: C 981 PHE cc_start: 0.7750 (m-10) cc_final: 0.7501 (m-80) REVERT: C 1000 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8127 (mtt-85) REVERT: C 1028 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7768 (mttt) REVERT: C 1050 MET cc_start: 0.7659 (ptt) cc_final: 0.7288 (ptm) REVERT: C 1073 LYS cc_start: 0.7681 (tttm) cc_final: 0.7379 (mtpp) REVERT: C 1086 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7744 (mmmm) REVERT: C 1129 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8310 (m) REVERT: D 80 VAL cc_start: 0.7724 (t) cc_final: 0.7497 (p) REVERT: D 117 THR cc_start: 0.4587 (OUTLIER) cc_final: 0.4300 (t) REVERT: D 185 LEU cc_start: 0.0759 (pp) cc_final: 0.0162 (tp) REVERT: E 75 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4866 (tt) REVERT: F 145 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1856 (pt) outliers start: 202 outliers final: 77 residues processed: 1042 average time/residue: 0.4495 time to fit residues: 734.5065 Evaluate side-chains 767 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 673 time to evaluate : 3.398 ------------------------------------------------------------------------------- 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 331 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 307 optimal weight: 0.0470 chunk 118 optimal weight: 0.0050 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 355 optimal weight: 2.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 641 ASN 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 A1002 GLN A1005 GLN A1011 GLN A1048 HIS A1054 GLN A1106 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.195070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145383 restraints weight = 57162.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148619 restraints weight = 25997.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149587 restraints weight = 14262.072| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 31186 Z= 0.130 Angle : 0.619 13.976 42535 Z= 0.316 Chirality : 0.045 0.340 4863 Planarity : 0.005 0.070 5471 Dihedral : 6.759 75.799 4415 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.68 % Allowed : 13.14 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.12), residues: 3888 helix: -0.58 (0.19), residues: 652 sheet: -2.35 (0.16), residues: 835 loop : -3.12 (0.11), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.004 0.001 HIS C 49 PHE 0.023 0.001 PHE A 192 TYR 0.026 0.001 TYR C 91 ARG 0.012 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 832) hydrogen bonds : angle 6.35135 ( 2268) SS BOND : bond 0.00407 ( 47) SS BOND : angle 2.95019 ( 94) covalent geometry : bond 0.00280 (31139) covalent geometry : angle 0.60352 (42441) *********************** 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 896 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 703 time to evaluate : 3.167 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 97 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7102 (tmmt) REVERT: A 113 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6287 (tppt) REVERT: A 187 LEU cc_start: 0.7259 (tp) cc_final: 0.7036 (tp) REVERT: A 233 ILE cc_start: 0.3069 (OUTLIER) cc_final: 0.2812 (mm) REVERT: A 276 LEU cc_start: 0.8272 (tp) cc_final: 0.7876 (tt) REVERT: A 280 ASN cc_start: 0.6828 (t0) cc_final: 0.6551 (t0) REVERT: A 307 THR cc_start: 0.7785 (m) cc_final: 0.7441 (p) REVERT: A 308 VAL cc_start: 0.8399 (p) cc_final: 0.8034 (m) REVERT: A 332 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7492 (tp) REVERT: A 334 ASN cc_start: 0.7332 (t0) cc_final: 0.6842 (t0) REVERT: A 358 ILE cc_start: 0.8057 (pt) cc_final: 0.7687 (mt) REVERT: A 518 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2339 (pp) REVERT: A 578 ASP cc_start: 0.7531 (t0) cc_final: 0.7241 (t0) REVERT: A 751 ASN cc_start: 0.7626 (m-40) cc_final: 0.7067 (m110) REVERT: A 752 LEU cc_start: 0.8367 (mm) cc_final: 0.7902 (mp) REVERT: A 755 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6782 (mp-120) REVERT: A 762 GLN cc_start: 0.7205 (pt0) cc_final: 0.6879 (pt0) REVERT: A 776 LYS cc_start: 0.8122 (tmmt) cc_final: 0.7754 (tmmt) REVERT: A 784 GLN cc_start: 0.7719 (mt0) cc_final: 0.7368 (mt0) REVERT: A 795 LYS cc_start: 0.8424 (mttm) cc_final: 0.8140 (mttm) REVERT: A 804 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7429 (mm-40) REVERT: A 825 LYS cc_start: 0.8378 (mtpm) cc_final: 0.8058 (mtpt) REVERT: A 922 LEU cc_start: 0.8752 (tp) cc_final: 0.8482 (tt) REVERT: A 933 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8050 (mtpp) REVERT: A 950 ASP cc_start: 0.6884 (t0) cc_final: 0.6391 (t0) REVERT: A 954 HIS cc_start: 0.7932 (m-70) cc_final: 0.7421 (m170) REVERT: A 961 THR cc_start: 0.8725 (p) cc_final: 0.8510 (t) REVERT: A 964 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7591 (mtmt) REVERT: A 975 SER cc_start: 0.8730 (m) cc_final: 0.8113 (t) REVERT: A 976 VAL cc_start: 0.8618 (m) cc_final: 0.8209 (p) REVERT: A 978 ASN cc_start: 0.8016 (m110) cc_final: 0.7517 (t0) REVERT: A 1017 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6588 (tm-30) REVERT: A 1019 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6650 (ttp80) REVERT: A 1028 LYS cc_start: 0.8425 (mttt) cc_final: 0.7833 (mtpp) REVERT: A 1031 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 1058 HIS cc_start: 0.7813 (m-70) cc_final: 0.7582 (m-70) REVERT: A 1097 SER cc_start: 0.8677 (t) cc_final: 0.8126 (p) REVERT: A 1117 THR cc_start: 0.8214 (p) cc_final: 0.7904 (t) REVERT: A 1130 ILE cc_start: 0.8979 (pt) cc_final: 0.8727 (pt) REVERT: B 54 LEU cc_start: 0.8397 (mt) cc_final: 0.8105 (mm) REVERT: B 66 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7391 (t-90) REVERT: B 83 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6900 (p) REVERT: B 127 VAL cc_start: 0.7998 (t) cc_final: 0.7349 (m) REVERT: B 188 ARG cc_start: 0.7163 (ptp90) cc_final: 0.6710 (ptp-170) REVERT: B 193 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7116 (ttmt) REVERT: B 223 LEU cc_start: 0.7828 (mp) cc_final: 0.7510 (mt) REVERT: B 307 THR cc_start: 0.7804 (m) cc_final: 0.7332 (p) REVERT: B 356 LYS cc_start: 0.8468 (tmmt) cc_final: 0.7960 (tmmt) REVERT: B 398 ASP cc_start: 0.6071 (t70) cc_final: 0.5462 (t0) REVERT: B 402 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5517 (tp) REVERT: B 535 LYS cc_start: 0.8381 (tptt) cc_final: 0.8052 (mmmm) REVERT: B 547 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7736 (mtpp) REVERT: B 562 PHE cc_start: 0.7142 (p90) cc_final: 0.6940 (p90) REVERT: B 563 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6308 (mm-40) REVERT: B 585 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7464 (mt) REVERT: B 616 ASN cc_start: 0.5603 (t0) cc_final: 0.5197 (t0) REVERT: B 659 SER cc_start: 0.8565 (m) cc_final: 0.8222 (p) REVERT: B 750 SER cc_start: 0.8315 (m) cc_final: 0.7987 (p) REVERT: B 759 PHE cc_start: 0.7274 (t80) cc_final: 0.6665 (t80) REVERT: B 776 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7964 (ttmt) REVERT: B 868 GLU cc_start: 0.7193 (tp30) cc_final: 0.6740 (tp30) REVERT: B 884 SER cc_start: 0.8697 (m) cc_final: 0.8434 (p) REVERT: B 954 HIS cc_start: 0.7189 (m-70) cc_final: 0.6882 (m90) REVERT: B 983 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7328 (mtm180) REVERT: B 1003 SER cc_start: 0.8483 (m) cc_final: 0.8027 (t) REVERT: B 1081 ILE cc_start: 0.7910 (pt) cc_final: 0.7661 (mt) REVERT: B 1117 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 1118 ASP cc_start: 0.7330 (t70) cc_final: 0.6848 (t0) REVERT: B 1127 ASP cc_start: 0.7163 (t0) cc_final: 0.6775 (t0) REVERT: B 1141 LEU cc_start: 0.8326 (tt) cc_final: 0.7978 (tt) REVERT: C 96 GLU cc_start: 0.6697 (pt0) cc_final: 0.6427 (pt0) REVERT: C 121 ASN cc_start: 0.7934 (p0) cc_final: 0.7576 (p0) REVERT: C 128 ILE cc_start: 0.7681 (mt) cc_final: 0.7399 (mp) REVERT: C 129 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6868 (ttpt) REVERT: C 164 ASN cc_start: 0.7698 (t0) cc_final: 0.7391 (t0) REVERT: C 228 ASP cc_start: 0.7536 (t70) cc_final: 0.7238 (t70) REVERT: C 275 PHE cc_start: 0.7806 (m-80) cc_final: 0.7503 (m-80) REVERT: C 281 GLU cc_start: 0.7057 (pp20) cc_final: 0.6820 (pp20) REVERT: C 408 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7254 (ppp-140) REVERT: C 546 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7213 (tp) REVERT: C 574 ASP cc_start: 0.7324 (t70) cc_final: 0.6330 (t0) REVERT: C 578 ASP cc_start: 0.6617 (t0) cc_final: 0.6067 (t70) REVERT: C 586 ASP cc_start: 0.6974 (t0) cc_final: 0.6425 (t0) REVERT: C 592 PHE cc_start: 0.8243 (p90) cc_final: 0.8019 (p90) REVERT: C 675 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6805 (mm-40) REVERT: C 708 SER cc_start: 0.8446 (t) cc_final: 0.8154 (m) REVERT: C 712 ILE cc_start: 0.8338 (tp) cc_final: 0.8106 (tp) REVERT: C 723 THR cc_start: 0.8534 (t) cc_final: 0.8287 (p) REVERT: C 725 GLU cc_start: 0.7141 (tt0) cc_final: 0.6844 (tt0) REVERT: C 737 ASP cc_start: 0.6857 (t0) cc_final: 0.6518 (t70) REVERT: C 773 GLU cc_start: 0.7216 (tt0) cc_final: 0.6896 (tt0) REVERT: C 776 LYS cc_start: 0.8280 (ttpm) cc_final: 0.7884 (ttpp) REVERT: C 780 GLU cc_start: 0.7200 (pt0) cc_final: 0.6878 (pt0) REVERT: C 790 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7827 (mtpt) REVERT: C 795 LYS cc_start: 0.8660 (mttt) cc_final: 0.8368 (mttm) REVERT: C 810 SER cc_start: 0.8690 (m) cc_final: 0.8071 (p) REVERT: C 854 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7514 (tptp) REVERT: C 868 GLU cc_start: 0.6978 (tp30) cc_final: 0.6665 (tp30) REVERT: C 886 TRP cc_start: 0.8426 (p90) cc_final: 0.7915 (p90) REVERT: C 904 TYR cc_start: 0.7784 (m-10) cc_final: 0.7461 (m-10) REVERT: C 919 ASN cc_start: 0.7984 (m-40) cc_final: 0.7751 (m-40) REVERT: C 933 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7979 (ttmm) REVERT: C 957 GLN cc_start: 0.7572 (tm130) cc_final: 0.7141 (tm130) REVERT: C 977 LEU cc_start: 0.7629 (mp) cc_final: 0.7089 (mp) REVERT: C 980 ILE cc_start: 0.8854 (mt) cc_final: 0.8404 (mm) REVERT: C 998 THR cc_start: 0.8354 (t) cc_final: 0.8120 (t) REVERT: C 1014 ARG cc_start: 0.7794 (tpp80) cc_final: 0.7507 (ttm-80) REVERT: C 1066 THR cc_start: 0.8377 (p) cc_final: 0.8170 (p) REVERT: C 1129 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (m) REVERT: D 80 VAL cc_start: 0.8364 (t) cc_final: 0.7987 (p) REVERT: D 182 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4408 (tt) REVERT: G 142 PHE cc_start: 0.4587 (OUTLIER) cc_final: 0.4344 (t80) outliers start: 193 outliers final: 103 residues processed: 829 average time/residue: 0.4235 time to fit residues: 553.7739 Evaluate side-chains 757 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 638 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 233 ILE 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 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU 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 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 VAL 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 332 ILE 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 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 585 LEU 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 895 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP 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 118 LEU 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 546 LEU 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 948 LEU 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 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 210 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 371 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 282 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 437 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 949 GLN A 955 ASN A1106 GLN B 542 ASN B1005 GLN C 914 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.191634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142329 restraints weight = 56231.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146547 restraints weight = 22628.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149206 restraints weight = 12001.702| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 31186 Z= 0.110 Angle : 0.585 11.180 42535 Z= 0.293 Chirality : 0.044 0.286 4863 Planarity : 0.004 0.072 5471 Dihedral : 6.061 76.249 4363 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.63 % Allowed : 15.08 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.12), residues: 3888 helix: 0.13 (0.20), residues: 658 sheet: -1.91 (0.17), residues: 799 loop : -2.92 (0.11), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS A1048 PHE 0.029 0.001 PHE A 190 TYR 0.020 0.001 TYR B 451 ARG 0.005 0.000 ARG B 765 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 832) hydrogen bonds : angle 5.80771 ( 2268) SS BOND : bond 0.00412 ( 47) SS BOND : angle 1.95683 ( 94) covalent geometry : bond 0.00246 (31139) covalent geometry : angle 0.57828 (42441) *********************** 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 839 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 648 time to evaluate : 3.137 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 113 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6166 (tppt) REVERT: A 189 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6280 (mm-30) REVERT: A 204 LYS cc_start: 0.8362 (tttp) cc_final: 0.8018 (ttmm) REVERT: A 233 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2891 (mm) REVERT: A 276 LEU cc_start: 0.8277 (tp) cc_final: 0.7854 (tt) REVERT: A 280 ASN cc_start: 0.6888 (t0) cc_final: 0.6606 (t0) REVERT: A 307 THR cc_start: 0.7687 (m) cc_final: 0.7347 (p) REVERT: A 308 VAL cc_start: 0.8400 (p) cc_final: 0.8022 (m) REVERT: A 334 ASN cc_start: 0.7547 (t0) cc_final: 0.7037 (t0) REVERT: A 480 CYS cc_start: 0.5042 (OUTLIER) cc_final: 0.4333 (p) REVERT: A 751 ASN cc_start: 0.7514 (m-40) cc_final: 0.6967 (m110) REVERT: A 752 LEU cc_start: 0.8277 (mm) cc_final: 0.7800 (mp) REVERT: A 755 GLN cc_start: 0.7113 (mp-120) cc_final: 0.6780 (mp-120) REVERT: A 776 LYS cc_start: 0.8134 (tmmt) cc_final: 0.7769 (tmmt) REVERT: A 790 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7529 (mtpt) REVERT: A 800 PHE cc_start: 0.7857 (m-80) cc_final: 0.7284 (m-80) REVERT: A 804 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7325 (mm-40) REVERT: A 825 LYS cc_start: 0.8313 (mtpm) cc_final: 0.8081 (mttm) REVERT: A 855 PHE cc_start: 0.8558 (m-80) cc_final: 0.8218 (m-80) REVERT: A 922 LEU cc_start: 0.8732 (tp) cc_final: 0.8476 (tt) REVERT: A 933 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8183 (mtmm) REVERT: A 935 GLN cc_start: 0.8026 (tt0) cc_final: 0.7746 (tt0) REVERT: A 950 ASP cc_start: 0.6870 (t0) cc_final: 0.6279 (t0) REVERT: A 953 ASN cc_start: 0.8224 (m-40) cc_final: 0.7204 (m110) REVERT: A 957 GLN cc_start: 0.7315 (pt0) cc_final: 0.6899 (pm20) REVERT: A 961 THR cc_start: 0.8781 (p) cc_final: 0.8550 (t) REVERT: A 964 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7500 (mtmt) REVERT: A 975 SER cc_start: 0.8660 (m) cc_final: 0.8087 (t) REVERT: A 976 VAL cc_start: 0.8642 (m) cc_final: 0.8182 (p) REVERT: A 978 ASN cc_start: 0.7972 (m110) cc_final: 0.7387 (t0) REVERT: A 980 ILE cc_start: 0.8888 (mt) cc_final: 0.8474 (tp) REVERT: A 1017 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6575 (tm-30) REVERT: A 1019 ARG cc_start: 0.7013 (ttm110) cc_final: 0.6752 (ttp80) REVERT: A 1058 HIS cc_start: 0.7768 (m-70) cc_final: 0.7565 (m-70) REVERT: A 1073 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7431 (ttpp) REVERT: A 1097 SER cc_start: 0.8654 (t) cc_final: 0.8131 (p) REVERT: A 1117 THR cc_start: 0.8187 (p) cc_final: 0.7939 (t) REVERT: A 1130 ILE cc_start: 0.8981 (pt) cc_final: 0.8707 (pt) REVERT: B 54 LEU cc_start: 0.8459 (mt) cc_final: 0.8249 (mm) REVERT: B 66 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: B 83 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6886 (p) REVERT: B 99 ASN cc_start: 0.7724 (p0) cc_final: 0.7479 (p0) REVERT: B 127 VAL cc_start: 0.8201 (t) cc_final: 0.7499 (m) REVERT: B 165 ASN cc_start: 0.6148 (OUTLIER) cc_final: 0.5773 (p0) REVERT: B 177 MET cc_start: 0.6141 (mmt) cc_final: 0.5320 (mmt) REVERT: B 193 LYS cc_start: 0.7581 (mtmt) cc_final: 0.7212 (ttpt) REVERT: B 223 LEU cc_start: 0.7777 (mp) cc_final: 0.7525 (mt) REVERT: B 281 GLU cc_start: 0.7002 (pp20) cc_final: 0.6647 (pp20) REVERT: B 297 SER cc_start: 0.7994 (m) cc_final: 0.7517 (p) REVERT: B 307 THR cc_start: 0.7847 (m) cc_final: 0.7386 (p) REVERT: B 355 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8046 (mmm-85) REVERT: B 356 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8191 (tmtt) REVERT: B 398 ASP cc_start: 0.6698 (t70) cc_final: 0.5949 (t0) REVERT: B 402 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5911 (tp) REVERT: B 535 LYS cc_start: 0.8364 (tptt) cc_final: 0.8076 (mmmm) REVERT: B 542 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8122 (t0) REVERT: B 547 LYS cc_start: 0.8450 (ttmm) cc_final: 0.7644 (mtpp) REVERT: B 563 GLN cc_start: 0.6793 (mm-40) cc_final: 0.6389 (mm-40) REVERT: B 592 PHE cc_start: 0.7829 (p90) cc_final: 0.7581 (p90) REVERT: B 643 PHE cc_start: 0.7987 (t80) cc_final: 0.7732 (t80) REVERT: B 659 SER cc_start: 0.8599 (m) cc_final: 0.8250 (p) REVERT: B 750 SER cc_start: 0.8377 (m) cc_final: 0.7957 (p) REVERT: B 759 PHE cc_start: 0.7055 (t80) cc_final: 0.6597 (t80) REVERT: B 776 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8007 (ttmt) REVERT: B 868 GLU cc_start: 0.7085 (tp30) cc_final: 0.6641 (tp30) REVERT: B 884 SER cc_start: 0.8646 (m) cc_final: 0.8420 (p) REVERT: B 954 HIS cc_start: 0.7161 (m-70) cc_final: 0.6772 (m90) REVERT: B 961 THR cc_start: 0.8237 (p) cc_final: 0.7902 (t) REVERT: B 983 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7193 (mtm180) REVERT: B 993 ILE cc_start: 0.9054 (tp) cc_final: 0.8842 (tp) REVERT: B 1003 SER cc_start: 0.8395 (m) cc_final: 0.7956 (t) REVERT: B 1005 GLN cc_start: 0.7751 (tp40) cc_final: 0.7365 (tp-100) REVERT: B 1014 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7160 (ttm110) REVERT: B 1081 ILE cc_start: 0.7927 (pt) cc_final: 0.7690 (mt) REVERT: B 1117 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 1118 ASP cc_start: 0.7275 (t70) cc_final: 0.6796 (t0) REVERT: B 1127 ASP cc_start: 0.7236 (t0) cc_final: 0.6784 (t0) REVERT: B 1141 LEU cc_start: 0.8284 (tt) cc_final: 0.7962 (tt) REVERT: C 120 VAL cc_start: 0.7977 (t) cc_final: 0.7707 (p) REVERT: C 129 LYS cc_start: 0.7444 (ttpt) cc_final: 0.6896 (ttpt) REVERT: C 164 ASN cc_start: 0.7912 (t0) cc_final: 0.7665 (t0) REVERT: C 228 ASP cc_start: 0.7408 (t70) cc_final: 0.7118 (t70) REVERT: C 275 PHE cc_start: 0.7750 (m-80) cc_final: 0.7354 (m-10) REVERT: C 281 GLU cc_start: 0.7256 (pp20) cc_final: 0.6710 (pp20) REVERT: C 327 VAL cc_start: 0.8482 (t) cc_final: 0.8232 (m) REVERT: C 334 ASN cc_start: 0.7104 (t0) cc_final: 0.6255 (p0) REVERT: C 408 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6875 (ppp-140) REVERT: C 546 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7171 (tp) REVERT: C 574 ASP cc_start: 0.7350 (t70) cc_final: 0.6386 (t0) REVERT: C 578 ASP cc_start: 0.6589 (t0) cc_final: 0.6202 (t70) REVERT: C 586 ASP cc_start: 0.6966 (t0) cc_final: 0.6379 (t0) REVERT: C 644 GLN cc_start: 0.7242 (tp40) cc_final: 0.6725 (tp40) REVERT: C 675 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6741 (mm-40) REVERT: C 708 SER cc_start: 0.8418 (t) cc_final: 0.8083 (m) REVERT: C 712 ILE cc_start: 0.8385 (tp) cc_final: 0.8175 (tp) REVERT: C 723 THR cc_start: 0.8468 (t) cc_final: 0.8256 (p) REVERT: C 725 GLU cc_start: 0.7168 (tt0) cc_final: 0.6857 (tt0) REVERT: C 737 ASP cc_start: 0.6670 (t0) cc_final: 0.6410 (t70) REVERT: C 790 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7855 (mtpt) REVERT: C 795 LYS cc_start: 0.8653 (mttt) cc_final: 0.8377 (mttm) REVERT: C 810 SER cc_start: 0.8693 (m) cc_final: 0.8084 (p) REVERT: C 854 LYS cc_start: 0.7769 (tmmt) cc_final: 0.7520 (tptp) REVERT: C 868 GLU cc_start: 0.6941 (tp30) cc_final: 0.6613 (tp30) REVERT: C 886 TRP cc_start: 0.8381 (p90) cc_final: 0.7870 (p90) REVERT: C 902 MET cc_start: 0.7749 (tpp) cc_final: 0.7376 (mmm) REVERT: C 919 ASN cc_start: 0.7974 (m-40) cc_final: 0.7757 (m-40) REVERT: C 933 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7964 (ttmm) REVERT: C 957 GLN cc_start: 0.7481 (tm130) cc_final: 0.7086 (tm130) REVERT: C 977 LEU cc_start: 0.7508 (mp) cc_final: 0.6710 (mp) REVERT: C 980 ILE cc_start: 0.8808 (mt) cc_final: 0.8547 (mm) REVERT: C 981 PHE cc_start: 0.7821 (m-80) cc_final: 0.7350 (m-80) REVERT: C 1014 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7400 (ttm-80) REVERT: C 1019 ARG cc_start: 0.7173 (ttm110) cc_final: 0.6610 (ttp80) REVERT: C 1086 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7796 (mmmt) REVERT: C 1107 ARG cc_start: 0.7329 (mtt90) cc_final: 0.6796 (mtt90) REVERT: D 80 VAL cc_start: 0.8432 (t) cc_final: 0.8064 (p) REVERT: D 82 LEU cc_start: 0.2840 (tp) cc_final: 0.2189 (tp) REVERT: D 182 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.4024 (tt) REVERT: E 194 TYR cc_start: 0.2912 (OUTLIER) cc_final: 0.1624 (m-80) REVERT: F 182 LEU cc_start: 0.7869 (tp) cc_final: 0.7230 (tt) REVERT: G 142 PHE cc_start: 0.4559 (OUTLIER) cc_final: 0.4262 (t80) outliers start: 191 outliers final: 115 residues processed: 775 average time/residue: 0.4350 time to fit residues: 536.3127 Evaluate side-chains 756 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 625 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP 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 273 ARG 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 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 949 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 62 VAL 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 165 ASN Chi-restraints excluded: chain B residue 205 HIS 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 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG 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 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 576 VAL Chi-restraints excluded: chain B residue 588 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 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 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 118 LEU 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 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 546 LEU 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 662 CYS 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 931 ILE 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 C residue 1141 LEU 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 20 LEU 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 Chi-restraints excluded: chain G residue 200 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 214 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 388 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 165 ASN B 505 HIS B 690 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1048 HIS C 487 ASN C 762 GLN C 914 ASN C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1101 HIS D 79 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.184326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133847 restraints weight = 55345.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137914 restraints weight = 22640.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140470 restraints weight = 12073.294| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.178 31186 Z= 0.431 Angle : 0.786 11.664 42535 Z= 0.414 Chirality : 0.052 0.334 4863 Planarity : 0.006 0.069 5471 Dihedral : 6.668 59.404 4353 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.03 % Favored : 89.94 % Rotamer: Outliers : 6.24 % Allowed : 15.79 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 3888 helix: -0.17 (0.19), residues: 657 sheet: -2.06 (0.16), residues: 812 loop : -2.85 (0.11), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.022 0.002 HIS C1101 PHE 0.047 0.003 PHE A 906 TYR 0.039 0.003 TYR C1067 ARG 0.011 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 832) hydrogen bonds : angle 6.07746 ( 2268) SS BOND : bond 0.00817 ( 47) SS BOND : angle 2.11024 ( 94) covalent geometry : bond 0.00933 (31139) covalent geometry : angle 0.78107 (42441) *********************** 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 886 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 674 time to evaluate : 5.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6620 (tptp) REVERT: A 233 ILE cc_start: 0.3559 (OUTLIER) cc_final: 0.3330 (mm) REVERT: A 276 LEU cc_start: 0.8491 (tp) cc_final: 0.8063 (tt) REVERT: A 280 ASN cc_start: 0.7317 (t0) cc_final: 0.6849 (t0) REVERT: A 307 THR cc_start: 0.7596 (m) cc_final: 0.7332 (p) REVERT: A 314 GLN cc_start: 0.7499 (tp40) cc_final: 0.7225 (tt0) REVERT: A 334 ASN cc_start: 0.7530 (t0) cc_final: 0.7103 (t0) REVERT: A 465 GLU cc_start: 0.6298 (tt0) cc_final: 0.6009 (tt0) REVERT: A 737 ASP cc_start: 0.7652 (t0) cc_final: 0.7390 (t70) REVERT: A 751 ASN cc_start: 0.7800 (m-40) cc_final: 0.7330 (m110) REVERT: A 752 LEU cc_start: 0.8673 (mm) cc_final: 0.8212 (mt) REVERT: A 755 GLN cc_start: 0.7447 (mp-120) cc_final: 0.7069 (mp-120) REVERT: A 776 LYS cc_start: 0.8286 (tmmt) cc_final: 0.7910 (tmmt) REVERT: A 790 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7757 (mtpt) REVERT: A 795 LYS cc_start: 0.8744 (mptt) cc_final: 0.8337 (mptt) REVERT: A 801 ASN cc_start: 0.5723 (OUTLIER) cc_final: 0.5490 (t0) REVERT: A 804 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7560 (mm-40) REVERT: A 820 ASP cc_start: 0.7305 (m-30) cc_final: 0.6841 (m-30) REVERT: A 825 LYS cc_start: 0.8333 (mtpm) cc_final: 0.8084 (mttm) REVERT: A 921 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8026 (ttpp) REVERT: A 922 LEU cc_start: 0.8839 (tp) cc_final: 0.8511 (tt) REVERT: A 933 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8270 (mtmm) REVERT: A 935 GLN cc_start: 0.8254 (tt0) cc_final: 0.8015 (tt0) REVERT: A 949 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: A 950 ASP cc_start: 0.7194 (t0) cc_final: 0.6631 (t0) REVERT: A 957 GLN cc_start: 0.7542 (pt0) cc_final: 0.7174 (pm20) REVERT: A 964 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7842 (mtmt) REVERT: A 975 SER cc_start: 0.8747 (m) cc_final: 0.8117 (t) REVERT: A 976 VAL cc_start: 0.8794 (m) cc_final: 0.8217 (p) REVERT: A 979 ASP cc_start: 0.7620 (m-30) cc_final: 0.7146 (m-30) REVERT: A 980 ILE cc_start: 0.8899 (mt) cc_final: 0.8479 (tp) REVERT: A 981 PHE cc_start: 0.7718 (m-10) cc_final: 0.7513 (m-10) REVERT: A 1017 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 1019 ARG cc_start: 0.7283 (ttm110) cc_final: 0.7051 (ttp80) REVERT: A 1031 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 1058 HIS cc_start: 0.8127 (m-70) cc_final: 0.7871 (m-70) REVERT: A 1073 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7771 (tttm) REVERT: B 66 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: B 83 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7093 (p) REVERT: B 90 VAL cc_start: 0.8022 (m) cc_final: 0.7808 (t) REVERT: B 102 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6838 (mtp-110) REVERT: B 127 VAL cc_start: 0.8203 (t) cc_final: 0.7463 (m) REVERT: B 192 PHE cc_start: 0.8227 (m-80) cc_final: 0.7947 (m-10) REVERT: B 193 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7523 (ttmt) REVERT: B 212 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5898 (pp20) REVERT: B 281 GLU cc_start: 0.7099 (pp20) cc_final: 0.6802 (pp20) REVERT: B 307 THR cc_start: 0.8073 (m) cc_final: 0.7565 (p) REVERT: B 308 VAL cc_start: 0.8457 (t) cc_final: 0.8233 (m) REVERT: B 353 TRP cc_start: 0.6958 (m-10) cc_final: 0.6308 (m-10) REVERT: B 355 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8335 (ttt-90) REVERT: B 398 ASP cc_start: 0.6520 (t70) cc_final: 0.5852 (t0) REVERT: B 402 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6320 (tt) REVERT: B 542 ASN cc_start: 0.8684 (t0) cc_final: 0.8344 (t0) REVERT: B 562 PHE cc_start: 0.7595 (p90) cc_final: 0.6978 (p90) REVERT: B 563 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6571 (mm-40) REVERT: B 664 ILE cc_start: 0.8466 (mm) cc_final: 0.8182 (mt) REVERT: B 703 ASN cc_start: 0.8630 (t0) cc_final: 0.8370 (t0) REVERT: B 738 CYS cc_start: 0.5741 (OUTLIER) cc_final: 0.5531 (t) REVERT: B 750 SER cc_start: 0.8605 (m) cc_final: 0.8038 (p) REVERT: B 759 PHE cc_start: 0.7162 (t80) cc_final: 0.6548 (t80) REVERT: B 765 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7492 (ttp80) REVERT: B 776 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8107 (ttmt) REVERT: B 779 GLN cc_start: 0.8276 (tt0) cc_final: 0.7962 (tt0) REVERT: B 820 ASP cc_start: 0.7943 (t70) cc_final: 0.7560 (t0) REVERT: B 821 LEU cc_start: 0.8242 (mp) cc_final: 0.7583 (mp) REVERT: B 824 ASN cc_start: 0.7975 (m-40) cc_final: 0.7750 (m-40) REVERT: B 868 GLU cc_start: 0.7229 (tp30) cc_final: 0.6772 (tp30) REVERT: B 902 MET cc_start: 0.8097 (mmm) cc_final: 0.7894 (mmm) REVERT: B 935 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7341 (tp-100) REVERT: B 954 HIS cc_start: 0.7297 (m-70) cc_final: 0.6898 (m90) REVERT: B 983 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7845 (mtm180) REVERT: B 1003 SER cc_start: 0.8467 (m) cc_final: 0.8080 (t) REVERT: B 1005 GLN cc_start: 0.7758 (tp40) cc_final: 0.7378 (tp-100) REVERT: B 1014 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7194 (ttm110) REVERT: B 1118 ASP cc_start: 0.7626 (t70) cc_final: 0.7103 (t0) REVERT: B 1127 ASP cc_start: 0.7635 (t0) cc_final: 0.7200 (t0) REVERT: B 1141 LEU cc_start: 0.8356 (tt) cc_final: 0.8024 (tt) REVERT: C 99 ASN cc_start: 0.7550 (t0) cc_final: 0.6941 (t0) REVERT: C 106 PHE cc_start: 0.8138 (m-80) cc_final: 0.7875 (m-10) REVERT: C 120 VAL cc_start: 0.8071 (t) cc_final: 0.7758 (p) REVERT: C 121 ASN cc_start: 0.8011 (p0) cc_final: 0.7595 (p0) REVERT: C 128 ILE cc_start: 0.8206 (mt) cc_final: 0.7995 (mp) REVERT: C 129 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7073 (ttpt) REVERT: C 228 ASP cc_start: 0.7345 (t70) cc_final: 0.7032 (t0) REVERT: C 275 PHE cc_start: 0.8152 (m-80) cc_final: 0.7497 (m-10) REVERT: C 281 GLU cc_start: 0.6980 (pp20) cc_final: 0.6532 (pp20) REVERT: C 297 SER cc_start: 0.7824 (m) cc_final: 0.7342 (p) REVERT: C 327 VAL cc_start: 0.8302 (t) cc_final: 0.8044 (m) REVERT: C 390 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7573 (tt) REVERT: C 392 PHE cc_start: 0.7139 (m-10) cc_final: 0.6875 (m-10) REVERT: C 536 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8287 (p0) REVERT: C 549 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8041 (t) REVERT: C 558 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7613 (mmtp) REVERT: C 572 THR cc_start: 0.6906 (OUTLIER) cc_final: 0.6687 (p) REVERT: C 574 ASP cc_start: 0.7632 (t70) cc_final: 0.6800 (t0) REVERT: C 599 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 655 TYR cc_start: 0.7403 (t80) cc_final: 0.7122 (t80) REVERT: C 675 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7253 (mm-40) REVERT: C 723 THR cc_start: 0.8553 (t) cc_final: 0.8326 (p) REVERT: C 725 GLU cc_start: 0.7144 (tt0) cc_final: 0.6881 (tt0) REVERT: C 737 ASP cc_start: 0.7188 (t0) cc_final: 0.6888 (t70) REVERT: C 759 PHE cc_start: 0.6967 (t80) cc_final: 0.6452 (t80) REVERT: C 776 LYS cc_start: 0.8462 (ttpm) cc_final: 0.8144 (ttpp) REVERT: C 790 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7957 (ttmm) REVERT: C 795 LYS cc_start: 0.8819 (mttt) cc_final: 0.8521 (mttm) REVERT: C 810 SER cc_start: 0.8700 (m) cc_final: 0.8029 (p) REVERT: C 854 LYS cc_start: 0.8124 (tmmt) cc_final: 0.7885 (tptp) REVERT: C 858 LEU cc_start: 0.8606 (mm) cc_final: 0.8312 (mp) REVERT: C 868 GLU cc_start: 0.6892 (tp30) cc_final: 0.6556 (tp30) REVERT: C 922 LEU cc_start: 0.8958 (tp) cc_final: 0.8752 (tt) REVERT: C 933 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8178 (ttmm) REVERT: C 945 LEU cc_start: 0.8630 (mm) cc_final: 0.8407 (mp) REVERT: C 977 LEU cc_start: 0.7727 (mp) cc_final: 0.6856 (mp) REVERT: C 980 ILE cc_start: 0.8846 (mt) cc_final: 0.8638 (mm) REVERT: C 981 PHE cc_start: 0.8004 (m-80) cc_final: 0.7576 (m-80) REVERT: C 988 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: C 1014 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7638 (ttm-80) REVERT: C 1101 HIS cc_start: 0.8310 (m-70) cc_final: 0.8083 (m170) REVERT: D 80 VAL cc_start: 0.8704 (t) cc_final: 0.8308 (p) REVERT: D 182 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.3748 (tt) REVERT: E 75 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.5019 (tt) REVERT: E 194 TYR cc_start: 0.2808 (OUTLIER) cc_final: 0.1458 (m-80) REVERT: G 142 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.4526 (t80) outliers start: 212 outliers final: 132 residues processed: 816 average time/residue: 0.6147 time to fit residues: 808.4432 Evaluate side-chains 780 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 626 time to evaluate : 3.543 ------------------------------------------------------------------------------- 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 113 LYS 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 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 659 SER 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 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 1081 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 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 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 190 PHE 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 266 TYR 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 355 ARG 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 453 TYR 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 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 605 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR 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 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL 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 125 ASN 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 318 PHE Chi-restraints excluded: chain C residue 323 THR 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 536 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU 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 611 LEU 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 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN 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 996 LEU 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 114 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 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 75 LEU 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 Chi-restraints excluded: chain G residue 200 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 138 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 291 optimal weight: 0.8980 chunk 339 optimal weight: 0.0070 chunk 19 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 762 GLN A 784 GLN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 505 HIS B1002 GLN B1048 HIS C 542 ASN C 603 ASN C 690 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.188994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139850 restraints weight = 55409.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144191 restraints weight = 22263.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146762 restraints weight = 11784.302| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 31186 Z= 0.136 Angle : 0.623 12.657 42535 Z= 0.312 Chirality : 0.045 0.241 4863 Planarity : 0.005 0.106 5471 Dihedral : 6.063 58.915 4337 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.07 % Allowed : 18.17 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.13), residues: 3888 helix: 0.42 (0.20), residues: 662 sheet: -1.69 (0.17), residues: 831 loop : -2.72 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.018 0.001 HIS B 505 PHE 0.037 0.002 PHE C 168 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 832) hydrogen bonds : angle 5.55435 ( 2268) SS BOND : bond 0.00308 ( 47) SS BOND : angle 1.83609 ( 94) covalent geometry : bond 0.00306 (31139) covalent geometry : angle 0.61749 (42441) *********************** 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 814 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 642 time to evaluate : 3.207 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 113 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6470 (tptp) REVERT: A 233 ILE cc_start: 0.3296 (OUTLIER) cc_final: 0.3051 (mm) REVERT: A 273 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6306 (mtm180) REVERT: A 276 LEU cc_start: 0.8352 (tp) cc_final: 0.7825 (tt) REVERT: A 280 ASN cc_start: 0.7105 (t0) cc_final: 0.6673 (t0) REVERT: A 307 THR cc_start: 0.7496 (m) cc_final: 0.7183 (p) REVERT: A 314 GLN cc_start: 0.7395 (tp40) cc_final: 0.7148 (tt0) REVERT: A 334 ASN cc_start: 0.7518 (t0) cc_final: 0.7118 (t0) REVERT: A 737 ASP cc_start: 0.7217 (t0) cc_final: 0.6904 (t0) REVERT: A 752 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8204 (mt) REVERT: A 755 GLN cc_start: 0.7246 (mp-120) cc_final: 0.6951 (mp-120) REVERT: A 776 LYS cc_start: 0.8233 (tmmt) cc_final: 0.7891 (tmmt) REVERT: A 790 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7599 (mtpt) REVERT: A 795 LYS cc_start: 0.8683 (mptt) cc_final: 0.8337 (mptt) REVERT: A 804 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7377 (mm-40) REVERT: A 825 LYS cc_start: 0.8326 (mtpm) cc_final: 0.8035 (mttm) REVERT: A 855 PHE cc_start: 0.8548 (m-80) cc_final: 0.8150 (m-80) REVERT: A 922 LEU cc_start: 0.8758 (tp) cc_final: 0.8495 (tt) REVERT: A 933 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8235 (mtmm) REVERT: A 950 ASP cc_start: 0.7042 (t0) cc_final: 0.6559 (t0) REVERT: A 957 GLN cc_start: 0.7420 (pt0) cc_final: 0.7053 (pm20) REVERT: A 964 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7724 (mtmt) REVERT: A 975 SER cc_start: 0.8722 (m) cc_final: 0.8070 (t) REVERT: A 976 VAL cc_start: 0.8785 (m) cc_final: 0.8295 (m) REVERT: A 979 ASP cc_start: 0.7483 (m-30) cc_final: 0.6816 (m-30) REVERT: A 980 ILE cc_start: 0.8715 (mt) cc_final: 0.8478 (tt) REVERT: A 981 PHE cc_start: 0.7648 (m-10) cc_final: 0.7440 (m-10) REVERT: A 1017 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6606 (tm-30) REVERT: A 1019 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6921 (ttp80) REVERT: A 1073 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7684 (ttpp) REVERT: B 66 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7744 (t-90) REVERT: B 83 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7086 (p) REVERT: B 91 TYR cc_start: 0.7518 (t80) cc_final: 0.7073 (t80) REVERT: B 127 VAL cc_start: 0.8179 (t) cc_final: 0.7403 (m) REVERT: B 193 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7630 (ttmt) REVERT: B 212 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5879 (pp20) REVERT: B 223 LEU cc_start: 0.8038 (mp) cc_final: 0.7755 (mt) REVERT: B 297 SER cc_start: 0.7885 (m) cc_final: 0.7600 (p) REVERT: B 338 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: B 355 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8270 (ttt-90) REVERT: B 356 LYS cc_start: 0.8640 (tmmt) cc_final: 0.8252 (tmtt) REVERT: B 398 ASP cc_start: 0.6613 (t70) cc_final: 0.5905 (t0) REVERT: B 465 GLU cc_start: 0.6745 (tt0) cc_final: 0.6492 (tt0) REVERT: B 562 PHE cc_start: 0.7446 (p90) cc_final: 0.6994 (p90) REVERT: B 563 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6480 (mm-40) REVERT: B 564 GLN cc_start: 0.7332 (mm-40) cc_final: 0.7107 (mm-40) REVERT: B 643 PHE cc_start: 0.7824 (t80) cc_final: 0.7588 (t80) REVERT: B 644 GLN cc_start: 0.8295 (tp40) cc_final: 0.8012 (tp40) REVERT: B 664 ILE cc_start: 0.8425 (mm) cc_final: 0.8052 (mt) REVERT: B 703 ASN cc_start: 0.8545 (t0) cc_final: 0.8315 (t0) REVERT: B 719 THR cc_start: 0.8168 (t) cc_final: 0.7943 (p) REVERT: B 750 SER cc_start: 0.8427 (m) cc_final: 0.8029 (p) REVERT: B 759 PHE cc_start: 0.7099 (t80) cc_final: 0.6563 (t80) REVERT: B 765 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7390 (ttp80) REVERT: B 776 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8094 (ttmt) REVERT: B 779 GLN cc_start: 0.8152 (tt0) cc_final: 0.7879 (tt0) REVERT: B 820 ASP cc_start: 0.7592 (t70) cc_final: 0.7248 (t0) REVERT: B 821 LEU cc_start: 0.8026 (mp) cc_final: 0.7560 (mp) REVERT: B 868 GLU cc_start: 0.7066 (tp30) cc_final: 0.6663 (tp30) REVERT: B 896 ILE cc_start: 0.8468 (tt) cc_final: 0.8189 (tt) REVERT: B 902 MET cc_start: 0.8015 (mmm) cc_final: 0.7770 (mmm) REVERT: B 935 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7193 (tp-100) REVERT: B 954 HIS cc_start: 0.7175 (m-70) cc_final: 0.6804 (m90) REVERT: B 957 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7636 (tp-100) REVERT: B 961 THR cc_start: 0.8121 (p) cc_final: 0.7891 (t) REVERT: B 1003 SER cc_start: 0.8481 (m) cc_final: 0.7982 (t) REVERT: B 1005 GLN cc_start: 0.7747 (tp40) cc_final: 0.7461 (tp-100) REVERT: B 1014 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7137 (ttm110) REVERT: B 1118 ASP cc_start: 0.7383 (t70) cc_final: 0.6835 (t0) REVERT: B 1127 ASP cc_start: 0.7584 (t0) cc_final: 0.7112 (t0) REVERT: B 1141 LEU cc_start: 0.8301 (tt) cc_final: 0.7963 (tt) REVERT: C 96 GLU cc_start: 0.6306 (pt0) cc_final: 0.6039 (pt0) REVERT: C 99 ASN cc_start: 0.7347 (t0) cc_final: 0.7013 (t0) REVERT: C 106 PHE cc_start: 0.7980 (m-80) cc_final: 0.7629 (m-10) REVERT: C 121 ASN cc_start: 0.8010 (p0) cc_final: 0.7511 (p0) REVERT: C 129 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6877 (tppt) REVERT: C 228 ASP cc_start: 0.7285 (t70) cc_final: 0.7038 (t0) REVERT: C 275 PHE cc_start: 0.7922 (m-80) cc_final: 0.7353 (m-10) REVERT: C 281 GLU cc_start: 0.6960 (pp20) cc_final: 0.6619 (pp20) REVERT: C 297 SER cc_start: 0.7665 (m) cc_final: 0.7254 (p) REVERT: C 390 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7629 (tt) REVERT: C 408 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7017 (ppp-140) REVERT: C 546 LEU cc_start: 0.7504 (tp) cc_final: 0.7264 (tt) REVERT: C 549 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7863 (t) REVERT: C 558 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7566 (mmtp) REVERT: C 564 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6750 (mm-40) REVERT: C 572 THR cc_start: 0.6729 (OUTLIER) cc_final: 0.6496 (p) REVERT: C 574 ASP cc_start: 0.7482 (t70) cc_final: 0.6489 (t0) REVERT: C 578 ASP cc_start: 0.6529 (t0) cc_final: 0.6153 (t70) REVERT: C 599 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8445 (p) REVERT: C 723 THR cc_start: 0.8487 (t) cc_final: 0.8258 (p) REVERT: C 725 GLU cc_start: 0.7206 (tt0) cc_final: 0.6920 (tt0) REVERT: C 737 ASP cc_start: 0.6839 (t0) cc_final: 0.6512 (t70) REVERT: C 759 PHE cc_start: 0.6482 (t80) cc_final: 0.6272 (t80) REVERT: C 776 LYS cc_start: 0.8372 (ttpm) cc_final: 0.8061 (ttpp) REVERT: C 790 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7878 (ttmm) REVERT: C 795 LYS cc_start: 0.8785 (mttt) cc_final: 0.8438 (mttm) REVERT: C 810 SER cc_start: 0.8766 (m) cc_final: 0.8123 (p) REVERT: C 854 LYS cc_start: 0.7884 (tmmt) cc_final: 0.7670 (tptp) REVERT: C 858 LEU cc_start: 0.8505 (mm) cc_final: 0.8236 (mp) REVERT: C 868 GLU cc_start: 0.6838 (tp30) cc_final: 0.6519 (tp30) REVERT: C 882 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8131 (mp) REVERT: C 886 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.7913 (p90) REVERT: C 933 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8093 (ttmm) REVERT: C 945 LEU cc_start: 0.8617 (mm) cc_final: 0.8415 (mp) REVERT: C 980 ILE cc_start: 0.8753 (mt) cc_final: 0.8453 (mm) REVERT: C 981 PHE cc_start: 0.7930 (m-80) cc_final: 0.7605 (m-80) REVERT: C 1014 ARG cc_start: 0.7767 (tpp80) cc_final: 0.7487 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7993 (mmmt) REVERT: C 1101 HIS cc_start: 0.8480 (m-70) cc_final: 0.8273 (m170) REVERT: D 80 VAL cc_start: 0.8624 (t) cc_final: 0.8234 (p) REVERT: D 182 LEU cc_start: 0.4502 (mp) cc_final: 0.3923 (tt) REVERT: E 194 TYR cc_start: 0.2735 (OUTLIER) cc_final: 0.1308 (m-80) REVERT: F 182 LEU cc_start: 0.7828 (tp) cc_final: 0.7088 (tt) REVERT: G 142 PHE cc_start: 0.4783 (OUTLIER) cc_final: 0.4318 (t80) outliers start: 172 outliers final: 114 residues processed: 766 average time/residue: 0.4256 time to fit residues: 518.1732 Evaluate side-chains 750 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 617 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 LYS 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 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 641 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 901 GLN 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 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 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 133 PHE Chi-restraints excluded: chain B residue 159 VAL 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 312 ILE Chi-restraints excluded: chain B residue 314 GLN 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 350 VAL Chi-restraints excluded: chain B residue 355 ARG 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 649 CYS 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 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 32 PHE 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 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 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 549 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 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 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP 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 75 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 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 75 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 309 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 388 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 784 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 953 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.188487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136816 restraints weight = 56292.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140790 restraints weight = 26210.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141368 restraints weight = 16393.998| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31186 Z= 0.177 Angle : 0.617 11.532 42535 Z= 0.310 Chirality : 0.045 0.211 4863 Planarity : 0.005 0.122 5471 Dihedral : 6.056 57.842 4336 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.33 % Allowed : 18.38 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.13), residues: 3888 helix: 0.56 (0.21), residues: 648 sheet: -1.69 (0.17), residues: 840 loop : -2.59 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.007 0.001 HIS C1064 PHE 0.034 0.002 PHE A 190 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 832) hydrogen bonds : angle 5.45933 ( 2268) SS BOND : bond 0.00321 ( 47) SS BOND : angle 1.60756 ( 94) covalent geometry : bond 0.00396 (31139) covalent geometry : angle 0.61329 (42441) *********************** 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 814 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 633 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6459 (tptp) REVERT: A 233 ILE cc_start: 0.3434 (OUTLIER) cc_final: 0.3182 (mm) REVERT: A 273 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6295 (mtm180) REVERT: A 276 LEU cc_start: 0.8394 (tp) cc_final: 0.7855 (tt) REVERT: A 280 ASN cc_start: 0.7193 (t0) cc_final: 0.6702 (t0) REVERT: A 307 THR cc_start: 0.7587 (m) cc_final: 0.7193 (p) REVERT: A 314 GLN cc_start: 0.7455 (tp40) cc_final: 0.7189 (tt0) REVERT: A 334 ASN cc_start: 0.7367 (t0) cc_final: 0.6955 (t0) REVERT: A 357 ARG cc_start: 0.6020 (ptm-80) cc_final: 0.5634 (tmt170) REVERT: A 663 ASP cc_start: 0.7053 (m-30) cc_final: 0.6746 (m-30) REVERT: A 752 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 755 GLN cc_start: 0.7378 (mp-120) cc_final: 0.7098 (mp-120) REVERT: A 776 LYS cc_start: 0.8292 (tmmt) cc_final: 0.7890 (tmmt) REVERT: A 790 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7698 (mtpt) REVERT: A 795 LYS cc_start: 0.8686 (mptt) cc_final: 0.8313 (mptt) REVERT: A 825 LYS cc_start: 0.8321 (mtpm) cc_final: 0.8038 (mttm) REVERT: A 855 PHE cc_start: 0.8634 (m-80) cc_final: 0.8225 (m-80) REVERT: A 922 LEU cc_start: 0.8753 (tp) cc_final: 0.8474 (tt) REVERT: A 933 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8201 (mtmm) REVERT: A 935 GLN cc_start: 0.8376 (tt0) cc_final: 0.8042 (tt0) REVERT: A 957 GLN cc_start: 0.7471 (pt0) cc_final: 0.7092 (pm20) REVERT: A 964 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7782 (mtmt) REVERT: A 965 GLN cc_start: 0.8106 (mt0) cc_final: 0.7808 (mt0) REVERT: A 975 SER cc_start: 0.8709 (m) cc_final: 0.8098 (t) REVERT: A 976 VAL cc_start: 0.8747 (m) cc_final: 0.8477 (m) REVERT: A 980 ILE cc_start: 0.8699 (mt) cc_final: 0.8357 (tp) REVERT: A 981 PHE cc_start: 0.7724 (m-10) cc_final: 0.7519 (m-10) REVERT: A 1017 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 1019 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6983 (ttp80) REVERT: A 1073 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7755 (ttpp) REVERT: A 1110 TYR cc_start: 0.8293 (t80) cc_final: 0.7595 (t80) REVERT: B 63 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 66 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7577 (t-90) REVERT: B 83 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 193 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7623 (ttmt) REVERT: B 212 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5873 (pp20) REVERT: B 223 LEU cc_start: 0.8085 (mp) cc_final: 0.7854 (mt) REVERT: B 280 ASN cc_start: 0.8396 (p0) cc_final: 0.8182 (p0) REVERT: B 297 SER cc_start: 0.8041 (m) cc_final: 0.7802 (p) REVERT: B 307 THR cc_start: 0.8057 (m) cc_final: 0.7557 (p) REVERT: B 338 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6299 (t80) REVERT: B 355 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8318 (tpt-90) REVERT: B 356 LYS cc_start: 0.8554 (tmmt) cc_final: 0.8185 (tmtt) REVERT: B 398 ASP cc_start: 0.6188 (t70) cc_final: 0.5551 (t0) REVERT: B 562 PHE cc_start: 0.7522 (p90) cc_final: 0.7186 (p90) REVERT: B 563 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6510 (mm-40) REVERT: B 619 GLU cc_start: 0.6692 (tt0) cc_final: 0.6433 (tt0) REVERT: B 643 PHE cc_start: 0.7920 (t80) cc_final: 0.7716 (t80) REVERT: B 664 ILE cc_start: 0.8432 (mm) cc_final: 0.8079 (mt) REVERT: B 703 ASN cc_start: 0.8593 (t0) cc_final: 0.8328 (t0) REVERT: B 719 THR cc_start: 0.8183 (t) cc_final: 0.7935 (p) REVERT: B 750 SER cc_start: 0.8410 (m) cc_final: 0.8016 (p) REVERT: B 759 PHE cc_start: 0.7218 (t80) cc_final: 0.6500 (t80) REVERT: B 765 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7425 (ttp80) REVERT: B 776 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8102 (ttmt) REVERT: B 820 ASP cc_start: 0.7612 (t70) cc_final: 0.7241 (t0) REVERT: B 868 GLU cc_start: 0.7104 (tp30) cc_final: 0.6713 (tp30) REVERT: B 902 MET cc_start: 0.8058 (mmm) cc_final: 0.7821 (mmm) REVERT: B 957 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7506 (tp-100) REVERT: B 961 THR cc_start: 0.8265 (p) cc_final: 0.7926 (t) REVERT: B 988 GLU cc_start: 0.6651 (tp30) cc_final: 0.6430 (tp30) REVERT: B 1003 SER cc_start: 0.8480 (m) cc_final: 0.8001 (t) REVERT: B 1005 GLN cc_start: 0.7757 (tp40) cc_final: 0.7445 (tp-100) REVERT: B 1014 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7132 (ttm110) REVERT: B 1118 ASP cc_start: 0.7459 (t70) cc_final: 0.6900 (t0) REVERT: B 1127 ASP cc_start: 0.7641 (t0) cc_final: 0.7278 (t0) REVERT: B 1141 LEU cc_start: 0.8284 (tt) cc_final: 0.7934 (tt) REVERT: C 99 ASN cc_start: 0.7500 (t0) cc_final: 0.6863 (t0) REVERT: C 105 ILE cc_start: 0.8025 (mp) cc_final: 0.7627 (tp) REVERT: C 106 PHE cc_start: 0.7980 (m-80) cc_final: 0.7721 (m-10) REVERT: C 120 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7721 (p) REVERT: C 121 ASN cc_start: 0.8030 (p0) cc_final: 0.7680 (p0) REVERT: C 129 LYS cc_start: 0.7523 (ttpt) cc_final: 0.6866 (tppt) REVERT: C 170 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5694 (m-10) REVERT: C 194 ASN cc_start: 0.8095 (p0) cc_final: 0.7873 (p0) REVERT: C 228 ASP cc_start: 0.7347 (t70) cc_final: 0.7019 (t70) REVERT: C 275 PHE cc_start: 0.7997 (m-80) cc_final: 0.7370 (m-10) REVERT: C 281 GLU cc_start: 0.6951 (pp20) cc_final: 0.6605 (pp20) REVERT: C 297 SER cc_start: 0.7732 (m) cc_final: 0.7287 (p) REVERT: C 357 ARG cc_start: 0.7283 (ptp-170) cc_final: 0.6827 (ptp-170) REVERT: C 390 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7608 (tt) REVERT: C 408 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7454 (ppp-140) REVERT: C 558 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7523 (mmtp) REVERT: C 574 ASP cc_start: 0.7448 (t70) cc_final: 0.6430 (t0) REVERT: C 588 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 599 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8419 (p) REVERT: C 655 TYR cc_start: 0.7339 (t80) cc_final: 0.6953 (t80) REVERT: C 723 THR cc_start: 0.8497 (t) cc_final: 0.8277 (p) REVERT: C 725 GLU cc_start: 0.7269 (tt0) cc_final: 0.6970 (tt0) REVERT: C 737 ASP cc_start: 0.6893 (t0) cc_final: 0.6562 (t70) REVERT: C 776 LYS cc_start: 0.8353 (ttpm) cc_final: 0.8071 (ttpp) REVERT: C 790 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7921 (ttmm) REVERT: C 795 LYS cc_start: 0.8801 (mttt) cc_final: 0.8487 (mttm) REVERT: C 810 SER cc_start: 0.8771 (m) cc_final: 0.8058 (p) REVERT: C 854 LYS cc_start: 0.7941 (tmmt) cc_final: 0.7664 (tptp) REVERT: C 858 LEU cc_start: 0.8522 (mm) cc_final: 0.8225 (mp) REVERT: C 868 GLU cc_start: 0.6906 (tp30) cc_final: 0.6569 (tp30) REVERT: C 886 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7956 (p90) REVERT: C 933 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8119 (ttmm) REVERT: C 945 LEU cc_start: 0.8629 (mm) cc_final: 0.8425 (mp) REVERT: C 977 LEU cc_start: 0.7572 (mp) cc_final: 0.6698 (mp) REVERT: C 980 ILE cc_start: 0.8710 (mt) cc_final: 0.8402 (mm) REVERT: C 981 PHE cc_start: 0.8058 (m-80) cc_final: 0.7699 (m-80) REVERT: C 1002 GLN cc_start: 0.7793 (tp40) cc_final: 0.6940 (tm-30) REVERT: C 1014 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7526 (ttm-80) REVERT: C 1019 ARG cc_start: 0.7317 (ttm110) cc_final: 0.7090 (ttp80) REVERT: C 1086 LYS cc_start: 0.8242 (mmmt) cc_final: 0.8007 (mmmt) REVERT: D 80 VAL cc_start: 0.8716 (t) cc_final: 0.8346 (p) REVERT: D 182 LEU cc_start: 0.5042 (mp) cc_final: 0.4525 (tt) REVERT: E 194 TYR cc_start: 0.3536 (OUTLIER) cc_final: 0.2310 (m-80) REVERT: F 182 LEU cc_start: 0.8199 (tp) cc_final: 0.7626 (tt) REVERT: G 142 PHE cc_start: 0.4923 (OUTLIER) cc_final: 0.4639 (t80) outliers start: 181 outliers final: 124 residues processed: 759 average time/residue: 0.4285 time to fit residues: 516.8928 Evaluate side-chains 766 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 622 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 113 LYS 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 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 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR 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 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1076 THR 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 63 THR 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 196 ASP 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 312 ILE Chi-restraints excluded: chain B residue 314 GLN 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 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 605 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR 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 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL 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 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 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE 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 585 LEU Chi-restraints excluded: chain C residue 588 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 708 SER 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 921 LYS 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 1038 LYS 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 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 75 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 329 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 369 optimal weight: 0.0020 chunk 372 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 160 optimal weight: 0.0050 chunk 391 optimal weight: 5.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 784 GLN A 895 GLN A 913 GLN A 955 ASN B 317 ASN B 542 ASN C 280 ASN C 360 ASN C 540 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139063 restraints weight = 56515.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142877 restraints weight = 26587.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143588 restraints weight = 16749.321| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31186 Z= 0.115 Angle : 0.596 11.833 42535 Z= 0.295 Chirality : 0.044 0.267 4863 Planarity : 0.005 0.132 5471 Dihedral : 5.940 58.644 4335 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.89 % Allowed : 19.12 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.13), residues: 3888 helix: 0.75 (0.21), residues: 651 sheet: -1.49 (0.17), residues: 836 loop : -2.48 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.006 0.001 HIS B1048 PHE 0.036 0.001 PHE A 190 TYR 0.024 0.001 TYR C 91 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 832) hydrogen bonds : angle 5.29839 ( 2268) SS BOND : bond 0.00264 ( 47) SS BOND : angle 1.49236 ( 94) covalent geometry : bond 0.00260 (31139) covalent geometry : angle 0.59220 (42441) *********************** 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 802 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 636 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6370 (tptp) REVERT: A 233 ILE cc_start: 0.3347 (OUTLIER) cc_final: 0.3117 (mm) REVERT: A 269 TYR cc_start: 0.7121 (m-10) cc_final: 0.6873 (m-10) REVERT: A 273 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6280 (mtm180) REVERT: A 276 LEU cc_start: 0.8331 (tp) cc_final: 0.7805 (tt) REVERT: A 280 ASN cc_start: 0.7188 (t0) cc_final: 0.6693 (t0) REVERT: A 307 THR cc_start: 0.7530 (m) cc_final: 0.7153 (p) REVERT: A 314 GLN cc_start: 0.7390 (tp40) cc_final: 0.7036 (tt0) REVERT: A 334 ASN cc_start: 0.7341 (t0) cc_final: 0.6908 (t0) REVERT: A 542 ASN cc_start: 0.8293 (t0) cc_final: 0.7799 (t0) REVERT: A 547 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8122 (mtpp) REVERT: A 663 ASP cc_start: 0.7121 (m-30) cc_final: 0.6834 (m-30) REVERT: A 752 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 755 GLN cc_start: 0.7370 (mp-120) cc_final: 0.7126 (mp-120) REVERT: A 776 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7886 (tmmt) REVERT: A 790 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7656 (mtpt) REVERT: A 795 LYS cc_start: 0.8652 (mptt) cc_final: 0.8328 (mptt) REVERT: A 825 LYS cc_start: 0.8386 (mtpm) cc_final: 0.8105 (mttm) REVERT: A 854 LYS cc_start: 0.8771 (tptp) cc_final: 0.8535 (tptp) REVERT: A 855 PHE cc_start: 0.8509 (m-80) cc_final: 0.8135 (m-80) REVERT: A 922 LEU cc_start: 0.8709 (tp) cc_final: 0.8428 (tt) REVERT: A 933 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8202 (mtmm) REVERT: A 935 GLN cc_start: 0.8318 (tt0) cc_final: 0.8015 (tt0) REVERT: A 953 ASN cc_start: 0.8156 (m110) cc_final: 0.7335 (m-40) REVERT: A 957 GLN cc_start: 0.7422 (pt0) cc_final: 0.7102 (pm20) REVERT: A 964 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7718 (mtmt) REVERT: A 975 SER cc_start: 0.8659 (m) cc_final: 0.8019 (t) REVERT: A 976 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 978 ASN cc_start: 0.8142 (m110) cc_final: 0.7935 (m110) REVERT: A 979 ASP cc_start: 0.7510 (m-30) cc_final: 0.7257 (m-30) REVERT: A 980 ILE cc_start: 0.8682 (mt) cc_final: 0.8372 (tt) REVERT: A 981 PHE cc_start: 0.7735 (m-10) cc_final: 0.7513 (m-10) REVERT: A 1017 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6816 (tm-30) REVERT: A 1019 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6964 (ttp80) REVERT: A 1031 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6623 (mp0) REVERT: A 1073 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7644 (ttpp) REVERT: A 1110 TYR cc_start: 0.8251 (t80) cc_final: 0.7583 (t80) REVERT: B 63 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8235 (p) REVERT: B 66 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7593 (t-90) REVERT: B 83 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7161 (p) REVERT: B 127 VAL cc_start: 0.8084 (t) cc_final: 0.7326 (m) REVERT: B 193 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7656 (ttmt) REVERT: B 212 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5894 (pp20) REVERT: B 223 LEU cc_start: 0.8086 (mp) cc_final: 0.7824 (mt) REVERT: B 280 ASN cc_start: 0.8372 (p0) cc_final: 0.8162 (p0) REVERT: B 297 SER cc_start: 0.7962 (m) cc_final: 0.7723 (p) REVERT: B 338 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6171 (t80) REVERT: B 355 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8256 (tpt-90) REVERT: B 356 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8166 (tmmt) REVERT: B 398 ASP cc_start: 0.6170 (t70) cc_final: 0.5511 (t0) REVERT: B 402 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6169 (tt) REVERT: B 465 GLU cc_start: 0.6623 (tt0) cc_final: 0.6308 (tt0) REVERT: B 562 PHE cc_start: 0.7457 (p90) cc_final: 0.6917 (p90) REVERT: B 563 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6609 (mm-40) REVERT: B 703 ASN cc_start: 0.8575 (t0) cc_final: 0.8314 (t0) REVERT: B 719 THR cc_start: 0.8039 (t) cc_final: 0.7826 (p) REVERT: B 750 SER cc_start: 0.8318 (m) cc_final: 0.7931 (p) REVERT: B 759 PHE cc_start: 0.7311 (t80) cc_final: 0.6527 (t80) REVERT: B 765 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7224 (ttp80) REVERT: B 776 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8124 (ttmt) REVERT: B 777 ASN cc_start: 0.7746 (m-40) cc_final: 0.7418 (m110) REVERT: B 779 GLN cc_start: 0.8164 (tt0) cc_final: 0.7923 (tt0) REVERT: B 820 ASP cc_start: 0.7564 (t70) cc_final: 0.7284 (t0) REVERT: B 825 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7709 (mtpp) REVERT: B 868 GLU cc_start: 0.7051 (tp30) cc_final: 0.6698 (tp30) REVERT: B 954 HIS cc_start: 0.7351 (m170) cc_final: 0.6897 (m90) REVERT: B 957 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7292 (tp-100) REVERT: B 961 THR cc_start: 0.8310 (p) cc_final: 0.7902 (t) REVERT: B 988 GLU cc_start: 0.6696 (tp30) cc_final: 0.6441 (tp30) REVERT: B 1003 SER cc_start: 0.8469 (m) cc_final: 0.7912 (t) REVERT: B 1005 GLN cc_start: 0.7727 (tp40) cc_final: 0.7392 (tp-100) REVERT: B 1014 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7272 (ttm110) REVERT: B 1019 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7259 (ttp80) REVERT: B 1095 PHE cc_start: 0.7505 (m-10) cc_final: 0.7181 (m-10) REVERT: B 1118 ASP cc_start: 0.7404 (t70) cc_final: 0.6864 (t0) REVERT: B 1127 ASP cc_start: 0.7628 (t0) cc_final: 0.7343 (t0) REVERT: B 1141 LEU cc_start: 0.8271 (tt) cc_final: 0.7913 (tt) REVERT: C 96 GLU cc_start: 0.6483 (pt0) cc_final: 0.6062 (pt0) REVERT: C 99 ASN cc_start: 0.7445 (t0) cc_final: 0.7024 (t0) REVERT: C 106 PHE cc_start: 0.7778 (m-80) cc_final: 0.7435 (m-10) REVERT: C 120 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7617 (p) REVERT: C 121 ASN cc_start: 0.8052 (p0) cc_final: 0.7658 (p0) REVERT: C 164 ASN cc_start: 0.7599 (t0) cc_final: 0.7260 (t0) REVERT: C 168 PHE cc_start: 0.7799 (t80) cc_final: 0.7068 (t80) REVERT: C 170 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5802 (m-10) REVERT: C 194 ASN cc_start: 0.8098 (p0) cc_final: 0.7863 (p0) REVERT: C 223 LEU cc_start: 0.8054 (mp) cc_final: 0.7841 (mp) REVERT: C 228 ASP cc_start: 0.7342 (t70) cc_final: 0.7123 (t70) REVERT: C 275 PHE cc_start: 0.7919 (m-80) cc_final: 0.7356 (m-10) REVERT: C 281 GLU cc_start: 0.7100 (pp20) cc_final: 0.6390 (pp20) REVERT: C 340 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 408 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7450 (ppp-140) REVERT: C 558 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7492 (mmtp) REVERT: C 574 ASP cc_start: 0.7397 (t70) cc_final: 0.6339 (t0) REVERT: C 578 ASP cc_start: 0.6551 (t0) cc_final: 0.6114 (t70) REVERT: C 588 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (p) REVERT: C 602 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 619 GLU cc_start: 0.6857 (tt0) cc_final: 0.6500 (tt0) REVERT: C 655 TYR cc_start: 0.7347 (t80) cc_final: 0.6922 (t80) REVERT: C 702 GLU cc_start: 0.7021 (mp0) cc_final: 0.6749 (mp0) REVERT: C 723 THR cc_start: 0.8512 (t) cc_final: 0.8284 (p) REVERT: C 725 GLU cc_start: 0.7292 (tt0) cc_final: 0.6986 (tt0) REVERT: C 737 ASP cc_start: 0.6795 (t0) cc_final: 0.6457 (t70) REVERT: C 790 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7973 (mtpt) REVERT: C 795 LYS cc_start: 0.8783 (mttt) cc_final: 0.8452 (mttm) REVERT: C 810 SER cc_start: 0.8780 (m) cc_final: 0.8017 (p) REVERT: C 811 LYS cc_start: 0.8442 (tptp) cc_final: 0.8177 (tptm) REVERT: C 854 LYS cc_start: 0.7857 (tmmt) cc_final: 0.7598 (tptp) REVERT: C 858 LEU cc_start: 0.8471 (mm) cc_final: 0.8179 (mp) REVERT: C 868 GLU cc_start: 0.6893 (tp30) cc_final: 0.6572 (tp30) REVERT: C 886 TRP cc_start: 0.8293 (OUTLIER) cc_final: 0.7831 (p90) REVERT: C 933 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8075 (ttmm) REVERT: C 957 GLN cc_start: 0.7486 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 977 LEU cc_start: 0.7535 (mp) cc_final: 0.6847 (mp) REVERT: C 980 ILE cc_start: 0.8680 (mt) cc_final: 0.8361 (mm) REVERT: C 981 PHE cc_start: 0.8033 (m-80) cc_final: 0.7700 (m-80) REVERT: C 1002 GLN cc_start: 0.7765 (tp40) cc_final: 0.6911 (tm-30) REVERT: C 1014 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7504 (ttm110) REVERT: C 1019 ARG cc_start: 0.7294 (ttm110) cc_final: 0.7060 (ttp80) REVERT: C 1086 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7655 (mmmt) REVERT: E 194 TYR cc_start: 0.3634 (OUTLIER) cc_final: 0.2378 (m-80) REVERT: F 182 LEU cc_start: 0.8185 (tp) cc_final: 0.7627 (tt) outliers start: 166 outliers final: 117 residues processed: 755 average time/residue: 0.4368 time to fit residues: 525.5529 Evaluate side-chains 746 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 609 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS 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 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 390 LEU 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 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR 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 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1076 THR 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 63 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 133 PHE Chi-restraints excluded: chain B residue 159 VAL 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 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE 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 505 HIS Chi-restraints excluded: chain B residue 517 LEU 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 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 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 277 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 585 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 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN 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 1038 LYS 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 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 217 ARG Chi-restraints excluded: chain G residue 75 LEU 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 189 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 379 optimal weight: 50.0000 chunk 258 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 350 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 762 GLN A 784 GLN A 913 GLN A 965 GLN B 317 ASN B 542 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.189025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137495 restraints weight = 56466.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141181 restraints weight = 26832.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141950 restraints weight = 17070.807| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31186 Z= 0.158 Angle : 0.614 14.148 42535 Z= 0.306 Chirality : 0.045 0.226 4863 Planarity : 0.005 0.084 5471 Dihedral : 5.902 57.929 4331 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.74 % Allowed : 19.85 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.13), residues: 3888 helix: 0.69 (0.21), residues: 661 sheet: -1.39 (0.17), residues: 830 loop : -2.40 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS C1064 PHE 0.036 0.002 PHE A 190 TYR 0.022 0.001 TYR A 265 ARG 0.007 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 832) hydrogen bonds : angle 5.27888 ( 2268) SS BOND : bond 0.00398 ( 47) SS BOND : angle 1.60093 ( 94) covalent geometry : bond 0.00353 (31139) covalent geometry : angle 0.61029 (42441) *********************** 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 784 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 623 time to evaluate : 3.648 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 113 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6381 (tptp) REVERT: A 204 LYS cc_start: 0.8438 (tttt) cc_final: 0.7573 (ttpt) REVERT: A 233 ILE cc_start: 0.3489 (OUTLIER) cc_final: 0.3233 (mm) REVERT: A 269 TYR cc_start: 0.7178 (m-10) cc_final: 0.6897 (m-10) REVERT: A 273 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6296 (mtm180) REVERT: A 276 LEU cc_start: 0.8389 (tp) cc_final: 0.7837 (tt) REVERT: A 280 ASN cc_start: 0.7173 (t0) cc_final: 0.6689 (t0) REVERT: A 307 THR cc_start: 0.7608 (m) cc_final: 0.7197 (p) REVERT: A 314 GLN cc_start: 0.7427 (tp40) cc_final: 0.7107 (tt0) REVERT: A 334 ASN cc_start: 0.7339 (t0) cc_final: 0.6900 (t0) REVERT: A 387 LEU cc_start: 0.8142 (tp) cc_final: 0.7655 (mt) REVERT: A 542 ASN cc_start: 0.8333 (t0) cc_final: 0.8063 (t0) REVERT: A 663 ASP cc_start: 0.7109 (m-30) cc_final: 0.6821 (m-30) REVERT: A 752 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8264 (mt) REVERT: A 755 GLN cc_start: 0.7445 (mp-120) cc_final: 0.7174 (mp-120) REVERT: A 776 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7890 (tmmt) REVERT: A 790 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7692 (mtpt) REVERT: A 795 LYS cc_start: 0.8669 (mptt) cc_final: 0.8335 (mptt) REVERT: A 825 LYS cc_start: 0.8386 (mtpm) cc_final: 0.8116 (mttm) REVERT: A 854 LYS cc_start: 0.8814 (tptp) cc_final: 0.8549 (tptp) REVERT: A 855 PHE cc_start: 0.8555 (m-80) cc_final: 0.8282 (m-80) REVERT: A 922 LEU cc_start: 0.8725 (tp) cc_final: 0.8443 (tt) REVERT: A 933 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8200 (mtmm) REVERT: A 935 GLN cc_start: 0.8357 (tt0) cc_final: 0.8110 (tt0) REVERT: A 957 GLN cc_start: 0.7452 (pt0) cc_final: 0.7075 (pm20) REVERT: A 964 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7789 (mtmt) REVERT: A 975 SER cc_start: 0.8654 (m) cc_final: 0.8028 (t) REVERT: A 976 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 979 ASP cc_start: 0.7550 (m-30) cc_final: 0.7277 (m-30) REVERT: A 980 ILE cc_start: 0.8678 (mt) cc_final: 0.8403 (tt) REVERT: A 981 PHE cc_start: 0.7762 (m-10) cc_final: 0.7528 (m-10) REVERT: A 1017 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6839 (tm-30) REVERT: A 1019 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7028 (ttp80) REVERT: A 1073 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7729 (ttpp) REVERT: A 1110 TYR cc_start: 0.8226 (t80) cc_final: 0.7645 (t80) REVERT: B 34 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7745 (mtt-85) REVERT: B 63 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 66 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7528 (t-90) REVERT: B 83 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7182 (p) REVERT: B 127 VAL cc_start: 0.8108 (t) cc_final: 0.7361 (m) REVERT: B 193 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7689 (ttmt) REVERT: B 212 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6128 (pp20) REVERT: B 223 LEU cc_start: 0.8045 (mp) cc_final: 0.7778 (mt) REVERT: B 297 SER cc_start: 0.7994 (m) cc_final: 0.7785 (p) REVERT: B 307 THR cc_start: 0.8046 (m) cc_final: 0.7548 (p) REVERT: B 338 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6302 (t80) REVERT: B 355 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8048 (tpt-90) REVERT: B 356 LYS cc_start: 0.8541 (tmmt) cc_final: 0.8088 (mmmm) REVERT: B 398 ASP cc_start: 0.6064 (t70) cc_final: 0.5389 (t0) REVERT: B 402 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6176 (tt) REVERT: B 465 GLU cc_start: 0.6609 (tt0) cc_final: 0.6309 (tt0) REVERT: B 562 PHE cc_start: 0.7485 (p90) cc_final: 0.7008 (p90) REVERT: B 563 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6627 (mm-40) REVERT: B 703 ASN cc_start: 0.8552 (t0) cc_final: 0.8289 (t0) REVERT: B 714 ILE cc_start: 0.7881 (mp) cc_final: 0.7658 (mm) REVERT: B 719 THR cc_start: 0.8134 (t) cc_final: 0.7903 (p) REVERT: B 750 SER cc_start: 0.8349 (m) cc_final: 0.7995 (p) REVERT: B 759 PHE cc_start: 0.7310 (t80) cc_final: 0.6523 (t80) REVERT: B 765 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7246 (ttp80) REVERT: B 776 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8137 (ttmt) REVERT: B 779 GLN cc_start: 0.8199 (tt0) cc_final: 0.7955 (tt0) REVERT: B 804 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8312 (mm-40) REVERT: B 820 ASP cc_start: 0.7476 (t70) cc_final: 0.7224 (t0) REVERT: B 825 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7754 (mtpp) REVERT: B 868 GLU cc_start: 0.7093 (tp30) cc_final: 0.6734 (tp30) REVERT: B 902 MET cc_start: 0.8064 (mmm) cc_final: 0.7717 (mmm) REVERT: B 954 HIS cc_start: 0.7373 (m170) cc_final: 0.6921 (m90) REVERT: B 957 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7458 (tp40) REVERT: B 961 THR cc_start: 0.8322 (p) cc_final: 0.7864 (t) REVERT: B 1003 SER cc_start: 0.8440 (m) cc_final: 0.8104 (t) REVERT: B 1005 GLN cc_start: 0.7726 (tp40) cc_final: 0.7423 (tp-100) REVERT: B 1014 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7329 (ttm110) REVERT: B 1019 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7169 (ttp-110) REVERT: B 1073 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7376 (ttmm) REVERT: B 1118 ASP cc_start: 0.7443 (t70) cc_final: 0.6883 (t0) REVERT: B 1127 ASP cc_start: 0.7618 (t0) cc_final: 0.7303 (t0) REVERT: B 1141 LEU cc_start: 0.8250 (tt) cc_final: 0.7892 (tt) REVERT: C 96 GLU cc_start: 0.6634 (pt0) cc_final: 0.6280 (pt0) REVERT: C 99 ASN cc_start: 0.7605 (t0) cc_final: 0.7064 (t0) REVERT: C 106 PHE cc_start: 0.7854 (m-80) cc_final: 0.7479 (m-10) REVERT: C 120 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7621 (p) REVERT: C 121 ASN cc_start: 0.8087 (p0) cc_final: 0.7687 (p0) REVERT: C 129 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6687 (tppt) REVERT: C 164 ASN cc_start: 0.7586 (t0) cc_final: 0.7347 (t0) REVERT: C 168 PHE cc_start: 0.7838 (t80) cc_final: 0.7198 (t80) REVERT: C 170 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5936 (m-80) REVERT: C 228 ASP cc_start: 0.7345 (t70) cc_final: 0.7138 (t70) REVERT: C 237 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.7150 (mtp-110) REVERT: C 275 PHE cc_start: 0.7961 (m-80) cc_final: 0.7379 (m-10) REVERT: C 281 GLU cc_start: 0.6905 (pp20) cc_final: 0.6505 (pp20) REVERT: C 297 SER cc_start: 0.7678 (m) cc_final: 0.7259 (p) REVERT: C 357 ARG cc_start: 0.7344 (ptp-170) cc_final: 0.6834 (ptp-170) REVERT: C 408 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7393 (ppp-140) REVERT: C 558 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7518 (mmtp) REVERT: C 571 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6183 (t0) REVERT: C 574 ASP cc_start: 0.7387 (t70) cc_final: 0.6359 (t0) REVERT: C 578 ASP cc_start: 0.6638 (t0) cc_final: 0.6245 (t70) REVERT: C 588 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 599 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8454 (p) REVERT: C 602 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8029 (p) REVERT: C 655 TYR cc_start: 0.7420 (t80) cc_final: 0.6963 (t80) REVERT: C 702 GLU cc_start: 0.7043 (mp0) cc_final: 0.6813 (mp0) REVERT: C 723 THR cc_start: 0.8449 (t) cc_final: 0.8212 (p) REVERT: C 725 GLU cc_start: 0.7371 (tt0) cc_final: 0.7059 (tt0) REVERT: C 737 ASP cc_start: 0.6831 (t0) cc_final: 0.6550 (t70) REVERT: C 765 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7604 (ttp-110) REVERT: C 776 LYS cc_start: 0.8352 (ttpm) cc_final: 0.8052 (ttpp) REVERT: C 790 LYS cc_start: 0.8261 (mtpt) cc_final: 0.8005 (mtpt) REVERT: C 795 LYS cc_start: 0.8803 (mttt) cc_final: 0.8492 (mttm) REVERT: C 810 SER cc_start: 0.8764 (m) cc_final: 0.7986 (p) REVERT: C 854 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7653 (tptp) REVERT: C 858 LEU cc_start: 0.8473 (mm) cc_final: 0.8187 (mp) REVERT: C 868 GLU cc_start: 0.6917 (tp30) cc_final: 0.6583 (tp30) REVERT: C 886 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7892 (p90) REVERT: C 933 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8102 (ttmm) REVERT: C 957 GLN cc_start: 0.7517 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 977 LEU cc_start: 0.7531 (mp) cc_final: 0.6845 (mp) REVERT: C 980 ILE cc_start: 0.8678 (mt) cc_final: 0.8354 (mm) REVERT: C 981 PHE cc_start: 0.8066 (m-80) cc_final: 0.7729 (m-80) REVERT: C 1014 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7547 (ttm110) REVERT: C 1086 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7667 (mmmt) REVERT: D 182 LEU cc_start: 0.5201 (mt) cc_final: 0.4663 (tp) REVERT: E 194 TYR cc_start: 0.3715 (OUTLIER) cc_final: 0.2464 (m-80) REVERT: F 182 LEU cc_start: 0.8173 (tp) cc_final: 0.7657 (tt) outliers start: 161 outliers final: 122 residues processed: 735 average time/residue: 0.5123 time to fit residues: 604.9269 Evaluate side-chains 764 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 619 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS 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 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 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 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR 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 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1076 THR 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 34 ARG Chi-restraints excluded: chain B residue 63 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 133 PHE Chi-restraints excluded: chain B residue 159 VAL 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 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU 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 505 HIS Chi-restraints excluded: chain B residue 517 LEU 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 650 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 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 277 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 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 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 615 VAL Chi-restraints excluded: chain C residue 729 VAL 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 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS 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 1038 LYS 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 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 75 LEU 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 189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 221 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 784 GLN B 317 ASN B 542 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.184260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135224 restraints weight = 55006.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139466 restraints weight = 22365.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142006 restraints weight = 11953.628| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 31186 Z= 0.290 Angle : 0.705 14.060 42535 Z= 0.358 Chirality : 0.048 0.235 4863 Planarity : 0.005 0.067 5471 Dihedral : 6.268 56.291 4331 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.80 % Allowed : 19.76 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3888 helix: 0.29 (0.20), residues: 662 sheet: -1.63 (0.17), residues: 809 loop : -2.42 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.010 0.001 HIS B1064 PHE 0.037 0.002 PHE A 190 TYR 0.028 0.002 TYR C 91 ARG 0.009 0.001 ARG C1019 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 832) hydrogen bonds : angle 5.56016 ( 2268) SS BOND : bond 0.00437 ( 47) SS BOND : angle 2.03354 ( 94) covalent geometry : bond 0.00641 (31139) covalent geometry : angle 0.69889 (42441) *********************** 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 807 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 644 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6369 (tttp) REVERT: A 117 LEU cc_start: 0.8696 (tp) cc_final: 0.8362 (tt) REVERT: A 189 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 193 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (ptpp) REVERT: A 204 LYS cc_start: 0.8435 (tttt) cc_final: 0.8012 (tppt) REVERT: A 233 ILE cc_start: 0.3718 (OUTLIER) cc_final: 0.3461 (mm) REVERT: A 276 LEU cc_start: 0.8425 (tp) cc_final: 0.7890 (tt) REVERT: A 280 ASN cc_start: 0.7279 (t0) cc_final: 0.6844 (t0) REVERT: A 307 THR cc_start: 0.7673 (m) cc_final: 0.7280 (p) REVERT: A 314 GLN cc_start: 0.7470 (tp40) cc_final: 0.7150 (tt0) REVERT: A 334 ASN cc_start: 0.7379 (t0) cc_final: 0.7019 (t0) REVERT: A 342 PHE cc_start: 0.7573 (m-80) cc_final: 0.7302 (m-80) REVERT: A 357 ARG cc_start: 0.6443 (ptm-80) cc_final: 0.6058 (tmt170) REVERT: A 358 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7356 (pt) REVERT: A 574 ASP cc_start: 0.7688 (p0) cc_final: 0.7479 (p0) REVERT: A 751 ASN cc_start: 0.7775 (m-40) cc_final: 0.7380 (m-40) REVERT: A 752 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8318 (mt) REVERT: A 755 GLN cc_start: 0.7589 (mp-120) cc_final: 0.7332 (mp-120) REVERT: A 776 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7909 (tmmt) REVERT: A 790 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7664 (mtpt) REVERT: A 795 LYS cc_start: 0.8706 (mptt) cc_final: 0.8341 (mptt) REVERT: A 825 LYS cc_start: 0.8346 (mtpm) cc_final: 0.8077 (mttm) REVERT: A 855 PHE cc_start: 0.8597 (m-80) cc_final: 0.8304 (m-80) REVERT: A 878 LEU cc_start: 0.8525 (mt) cc_final: 0.8245 (mp) REVERT: A 922 LEU cc_start: 0.8853 (tp) cc_final: 0.8543 (tt) REVERT: A 933 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8275 (mtmm) REVERT: A 935 GLN cc_start: 0.8397 (tt0) cc_final: 0.8098 (tt0) REVERT: A 950 ASP cc_start: 0.7138 (t0) cc_final: 0.6744 (t0) REVERT: A 957 GLN cc_start: 0.7491 (pt0) cc_final: 0.7115 (pm20) REVERT: A 964 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7853 (mtmt) REVERT: A 975 SER cc_start: 0.8656 (m) cc_final: 0.8045 (t) REVERT: A 976 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 979 ASP cc_start: 0.7609 (m-30) cc_final: 0.7377 (m-30) REVERT: A 981 PHE cc_start: 0.7761 (m-10) cc_final: 0.7555 (m-10) REVERT: A 1017 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 1019 ARG cc_start: 0.7338 (ttm110) cc_final: 0.7076 (ttp80) REVERT: A 1058 HIS cc_start: 0.8071 (m-70) cc_final: 0.7782 (m-70) REVERT: A 1073 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7836 (tttm) REVERT: A 1110 TYR cc_start: 0.8194 (t80) cc_final: 0.7625 (t80) REVERT: B 34 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7680 (mtt-85) REVERT: B 63 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 83 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (p) REVERT: B 193 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7633 (ttmt) REVERT: B 307 THR cc_start: 0.8059 (m) cc_final: 0.7596 (p) REVERT: B 308 VAL cc_start: 0.8490 (t) cc_final: 0.8286 (m) REVERT: B 338 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6314 (t80) REVERT: B 353 TRP cc_start: 0.6856 (m-10) cc_final: 0.6065 (m-10) REVERT: B 355 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8285 (tpt-90) REVERT: B 356 LYS cc_start: 0.8640 (tmmt) cc_final: 0.8274 (tmmt) REVERT: B 398 ASP cc_start: 0.6520 (t70) cc_final: 0.5733 (t0) REVERT: B 402 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6588 (tt) REVERT: B 528 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8354 (mmtt) REVERT: B 563 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6589 (mm-40) REVERT: B 568 ASP cc_start: 0.6538 (p0) cc_final: 0.6210 (p0) REVERT: B 619 GLU cc_start: 0.6639 (tt0) cc_final: 0.6433 (tt0) REVERT: B 650 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8158 (tp) REVERT: B 703 ASN cc_start: 0.8535 (t0) cc_final: 0.8287 (t0) REVERT: B 714 ILE cc_start: 0.8107 (mp) cc_final: 0.7841 (mm) REVERT: B 750 SER cc_start: 0.8310 (m) cc_final: 0.7896 (p) REVERT: B 759 PHE cc_start: 0.7330 (t80) cc_final: 0.6863 (t80) REVERT: B 765 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7275 (ttp80) REVERT: B 776 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8168 (ttmt) REVERT: B 795 LYS cc_start: 0.7877 (mttt) cc_final: 0.7664 (mttp) REVERT: B 820 ASP cc_start: 0.7568 (t70) cc_final: 0.7296 (t0) REVERT: B 825 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7850 (mtpp) REVERT: B 868 GLU cc_start: 0.7170 (tp30) cc_final: 0.6758 (tp30) REVERT: B 954 HIS cc_start: 0.7359 (m170) cc_final: 0.6975 (m90) REVERT: B 957 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7435 (tp40) REVERT: B 961 THR cc_start: 0.8284 (p) cc_final: 0.8061 (t) REVERT: B 1003 SER cc_start: 0.8560 (m) cc_final: 0.8051 (t) REVERT: B 1014 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7265 (ttm110) REVERT: B 1073 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7407 (ttmm) REVERT: B 1118 ASP cc_start: 0.7465 (t70) cc_final: 0.6997 (t0) REVERT: B 1127 ASP cc_start: 0.7640 (t0) cc_final: 0.7321 (t0) REVERT: B 1141 LEU cc_start: 0.8226 (tt) cc_final: 0.7970 (tt) REVERT: C 96 GLU cc_start: 0.6583 (pt0) cc_final: 0.6208 (pt0) REVERT: C 99 ASN cc_start: 0.7642 (t0) cc_final: 0.7151 (t0) REVERT: C 106 PHE cc_start: 0.8061 (m-80) cc_final: 0.7814 (m-10) REVERT: C 120 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (p) REVERT: C 121 ASN cc_start: 0.8069 (p0) cc_final: 0.7693 (p0) REVERT: C 129 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6892 (tppt) REVERT: C 164 ASN cc_start: 0.7910 (t0) cc_final: 0.7664 (t0) REVERT: C 189 GLU cc_start: 0.7654 (pt0) cc_final: 0.7002 (tt0) REVERT: C 228 ASP cc_start: 0.7354 (t70) cc_final: 0.7072 (t0) REVERT: C 237 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7378 (mtp-110) REVERT: C 275 PHE cc_start: 0.8151 (m-80) cc_final: 0.7582 (m-10) REVERT: C 281 GLU cc_start: 0.6934 (pp20) cc_final: 0.6412 (pp20) REVERT: C 297 SER cc_start: 0.7721 (m) cc_final: 0.7292 (p) REVERT: C 356 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8022 (ttpp) REVERT: C 357 ARG cc_start: 0.7122 (ptp-170) cc_final: 0.6869 (ptp-170) REVERT: C 387 LEU cc_start: 0.8499 (tp) cc_final: 0.8213 (tt) REVERT: C 408 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6965 (ppp-140) REVERT: C 508 TYR cc_start: 0.6822 (m-80) cc_final: 0.5743 (m-80) REVERT: C 558 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7565 (mmtp) REVERT: C 574 ASP cc_start: 0.7489 (t70) cc_final: 0.6474 (t0) REVERT: C 578 ASP cc_start: 0.6675 (t0) cc_final: 0.6327 (t70) REVERT: C 588 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 599 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8425 (p) REVERT: C 602 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8039 (p) REVERT: C 655 TYR cc_start: 0.7505 (t80) cc_final: 0.7058 (t80) REVERT: C 723 THR cc_start: 0.8405 (t) cc_final: 0.8165 (p) REVERT: C 725 GLU cc_start: 0.7272 (tt0) cc_final: 0.7005 (tt0) REVERT: C 765 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7744 (ttp-110) REVERT: C 776 LYS cc_start: 0.8368 (ttpm) cc_final: 0.8123 (ttpp) REVERT: C 790 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7944 (ttmm) REVERT: C 795 LYS cc_start: 0.8753 (mttt) cc_final: 0.8446 (mttm) REVERT: C 810 SER cc_start: 0.8747 (m) cc_final: 0.7927 (p) REVERT: C 854 LYS cc_start: 0.8019 (tmmt) cc_final: 0.7806 (tptp) REVERT: C 858 LEU cc_start: 0.8551 (mm) cc_final: 0.8258 (mp) REVERT: C 868 GLU cc_start: 0.6923 (tp30) cc_final: 0.6657 (tp30) REVERT: C 886 TRP cc_start: 0.8400 (OUTLIER) cc_final: 0.7964 (p90) REVERT: C 933 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8103 (ttmm) REVERT: C 957 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 980 ILE cc_start: 0.8715 (mt) cc_final: 0.8398 (mm) REVERT: C 981 PHE cc_start: 0.8026 (m-80) cc_final: 0.7683 (m-80) REVERT: C 1014 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7524 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8042 (mmmt) REVERT: D 182 LEU cc_start: 0.4369 (mt) cc_final: 0.4100 (tp) REVERT: E 47 LYS cc_start: 0.3401 (OUTLIER) cc_final: 0.2110 (ttmm) REVERT: E 194 TYR cc_start: 0.3107 (OUTLIER) cc_final: 0.1623 (m-80) REVERT: F 182 LEU cc_start: 0.7804 (tp) cc_final: 0.7121 (tt) outliers start: 163 outliers final: 123 residues processed: 750 average time/residue: 0.5240 time to fit residues: 629.7149 Evaluate side-chains 782 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 637 time to evaluate : 5.119 ------------------------------------------------------------------------------- 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 113 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 LYS 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 390 LEU 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 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 868 GLU 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 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1076 THR 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 34 ARG Chi-restraints excluded: chain B residue 63 THR 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 189 GLU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 196 ASP 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 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN 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 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 539 VAL 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 650 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1001 LEU 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 120 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 277 LEU Chi-restraints excluded: chain C residue 286 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 585 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 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS 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 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 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 217 ARG Chi-restraints excluded: chain G residue 75 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 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 354 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 331 optimal weight: 0.7980 chunk 170 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 389 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 377 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 317 ASN B 542 ASN B 710 ASN B1005 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.188954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137962 restraints weight = 56311.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142454 restraints weight = 26633.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142543 restraints weight = 16623.637| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31186 Z= 0.128 Angle : 0.634 12.520 42535 Z= 0.316 Chirality : 0.045 0.203 4863 Planarity : 0.005 0.072 5471 Dihedral : 6.073 58.715 4331 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.09 % Allowed : 21.03 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 3888 helix: 0.63 (0.20), residues: 667 sheet: -1.35 (0.17), residues: 823 loop : -2.36 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS B1048 PHE 0.053 0.001 PHE C 168 TYR 0.026 0.001 TYR A 265 ARG 0.008 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 832) hydrogen bonds : angle 5.31120 ( 2268) SS BOND : bond 0.00294 ( 47) SS BOND : angle 1.64657 ( 94) covalent geometry : bond 0.00291 (31139) covalent geometry : angle 0.63024 (42441) ********************** 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 769 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 630 time to evaluate : 7.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6722 (ttm110) cc_final: 0.6146 (ttm110) REVERT: A 113 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6291 (tttp) REVERT: A 117 LEU cc_start: 0.8320 (tp) cc_final: 0.7899 (tt) REVERT: A 193 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7459 (ptpp) REVERT: A 233 ILE cc_start: 0.3804 (OUTLIER) cc_final: 0.3469 (mm) REVERT: A 269 TYR cc_start: 0.7327 (m-10) cc_final: 0.6405 (m-80) REVERT: A 276 LEU cc_start: 0.8372 (tp) cc_final: 0.7843 (tt) REVERT: A 280 ASN cc_start: 0.7233 (t0) cc_final: 0.6734 (t0) REVERT: A 314 GLN cc_start: 0.7433 (tp40) cc_final: 0.7112 (tt0) REVERT: A 334 ASN cc_start: 0.7241 (t0) cc_final: 0.6835 (t0) REVERT: A 342 PHE cc_start: 0.7795 (m-80) cc_final: 0.7400 (m-80) REVERT: A 357 ARG cc_start: 0.6346 (ptm-80) cc_final: 0.5701 (tmt170) REVERT: A 542 ASN cc_start: 0.8349 (t0) cc_final: 0.7992 (t0) REVERT: A 565 PHE cc_start: 0.7708 (m-10) cc_final: 0.7347 (m-10) REVERT: A 751 ASN cc_start: 0.7522 (m-40) cc_final: 0.7142 (m-40) REVERT: A 752 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 755 GLN cc_start: 0.7432 (mp-120) cc_final: 0.7113 (mp-120) REVERT: A 765 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7027 (mtm180) REVERT: A 776 LYS cc_start: 0.8259 (tmmt) cc_final: 0.7868 (tmmt) REVERT: A 790 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7644 (mtpt) REVERT: A 795 LYS cc_start: 0.8659 (mptt) cc_final: 0.8318 (mptt) REVERT: A 825 LYS cc_start: 0.8356 (mtpm) cc_final: 0.8082 (mttm) REVERT: A 855 PHE cc_start: 0.8516 (m-80) cc_final: 0.8275 (m-80) REVERT: A 922 LEU cc_start: 0.8697 (tp) cc_final: 0.8416 (tt) REVERT: A 933 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8187 (mtmm) REVERT: A 935 GLN cc_start: 0.8325 (tt0) cc_final: 0.8047 (tt0) REVERT: A 950 ASP cc_start: 0.7150 (t0) cc_final: 0.6711 (t0) REVERT: A 957 GLN cc_start: 0.7460 (pt0) cc_final: 0.7058 (pm20) REVERT: A 964 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7780 (mtmt) REVERT: A 975 SER cc_start: 0.8627 (m) cc_final: 0.8025 (t) REVERT: A 976 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 979 ASP cc_start: 0.7624 (m-30) cc_final: 0.7221 (m-30) REVERT: A 980 ILE cc_start: 0.8686 (mt) cc_final: 0.8391 (tt) REVERT: A 981 PHE cc_start: 0.7777 (m-10) cc_final: 0.7561 (m-10) REVERT: A 1017 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6789 (tm-30) REVERT: A 1031 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6637 (mp0) REVERT: A 1110 TYR cc_start: 0.8199 (t80) cc_final: 0.7641 (t80) REVERT: B 34 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7716 (mtt-85) REVERT: B 63 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 91 TYR cc_start: 0.7419 (t80) cc_final: 0.6953 (t80) REVERT: B 102 ARG cc_start: 0.6787 (mtp-110) cc_final: 0.6356 (mtp-110) REVERT: B 193 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7526 (ttmt) REVERT: B 223 LEU cc_start: 0.8028 (mp) cc_final: 0.7750 (mt) REVERT: B 307 THR cc_start: 0.8041 (m) cc_final: 0.7508 (p) REVERT: B 317 ASN cc_start: 0.7711 (m-40) cc_final: 0.7372 (m110) REVERT: B 338 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 355 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8100 (tpt-90) REVERT: B 356 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8083 (mmmm) REVERT: B 398 ASP cc_start: 0.6077 (t70) cc_final: 0.5269 (t0) REVERT: B 402 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6291 (tt) REVERT: B 528 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8267 (mmtt) REVERT: B 558 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7815 (mtmm) REVERT: B 563 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6698 (mm-40) REVERT: B 568 ASP cc_start: 0.6642 (p0) cc_final: 0.6295 (p0) REVERT: B 650 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 703 ASN cc_start: 0.8541 (t0) cc_final: 0.8302 (t0) REVERT: B 714 ILE cc_start: 0.7953 (mp) cc_final: 0.7742 (mm) REVERT: B 719 THR cc_start: 0.8051 (t) cc_final: 0.7820 (p) REVERT: B 750 SER cc_start: 0.8283 (m) cc_final: 0.7924 (p) REVERT: B 759 PHE cc_start: 0.7257 (t80) cc_final: 0.6893 (t80) REVERT: B 765 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7207 (ttp80) REVERT: B 776 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8111 (ttmt) REVERT: B 779 GLN cc_start: 0.8170 (tt0) cc_final: 0.7903 (tt0) REVERT: B 820 ASP cc_start: 0.7293 (t70) cc_final: 0.7048 (t0) REVERT: B 825 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7800 (mtpp) REVERT: B 868 GLU cc_start: 0.7181 (tp30) cc_final: 0.6780 (tp30) REVERT: B 954 HIS cc_start: 0.7378 (m170) cc_final: 0.6943 (m90) REVERT: B 957 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7322 (tp40) REVERT: B 961 THR cc_start: 0.8302 (p) cc_final: 0.7959 (t) REVERT: B 1003 SER cc_start: 0.8560 (m) cc_final: 0.7980 (t) REVERT: B 1005 GLN cc_start: 0.7750 (tp40) cc_final: 0.7535 (tp-100) REVERT: B 1014 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7268 (ttm110) REVERT: B 1019 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7309 (ttp80) REVERT: B 1073 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7345 (ttmm) REVERT: B 1118 ASP cc_start: 0.7418 (t70) cc_final: 0.6860 (t0) REVERT: B 1127 ASP cc_start: 0.7607 (t0) cc_final: 0.7324 (t0) REVERT: B 1141 LEU cc_start: 0.8371 (tt) cc_final: 0.8038 (tt) REVERT: C 96 GLU cc_start: 0.6770 (pt0) cc_final: 0.6264 (pt0) REVERT: C 99 ASN cc_start: 0.7636 (t0) cc_final: 0.7024 (t0) REVERT: C 106 PHE cc_start: 0.7831 (m-80) cc_final: 0.7490 (m-10) REVERT: C 120 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7621 (p) REVERT: C 121 ASN cc_start: 0.8129 (p0) cc_final: 0.7660 (p0) REVERT: C 164 ASN cc_start: 0.7624 (t0) cc_final: 0.7314 (t0) REVERT: C 189 GLU cc_start: 0.7732 (pt0) cc_final: 0.7345 (tt0) REVERT: C 228 ASP cc_start: 0.7339 (t70) cc_final: 0.6996 (t70) REVERT: C 275 PHE cc_start: 0.7994 (m-80) cc_final: 0.7456 (m-10) REVERT: C 281 GLU cc_start: 0.6895 (pp20) cc_final: 0.6336 (pp20) REVERT: C 297 SER cc_start: 0.7640 (m) cc_final: 0.7218 (p) REVERT: C 356 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7875 (ptmm) REVERT: C 408 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7426 (ppp-140) REVERT: C 508 TYR cc_start: 0.6741 (m-80) cc_final: 0.5669 (m-80) REVERT: C 558 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7431 (mmtp) REVERT: C 571 ASP cc_start: 0.6769 (t0) cc_final: 0.6471 (t0) REVERT: C 574 ASP cc_start: 0.7465 (t70) cc_final: 0.6420 (t0) REVERT: C 578 ASP cc_start: 0.6478 (t0) cc_final: 0.6020 (t70) REVERT: C 588 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 599 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 602 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (p) REVERT: C 719 THR cc_start: 0.7705 (t) cc_final: 0.7499 (p) REVERT: C 723 THR cc_start: 0.8412 (t) cc_final: 0.8186 (p) REVERT: C 725 GLU cc_start: 0.7261 (tt0) cc_final: 0.6950 (tt0) REVERT: C 765 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7623 (ttp-110) REVERT: C 776 LYS cc_start: 0.8337 (ttpm) cc_final: 0.8057 (ttpp) REVERT: C 790 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8044 (mtpt) REVERT: C 795 LYS cc_start: 0.8770 (mttt) cc_final: 0.8429 (mttm) REVERT: C 854 LYS cc_start: 0.7955 (tmmt) cc_final: 0.7687 (tptp) REVERT: C 858 LEU cc_start: 0.8448 (mm) cc_final: 0.8151 (mp) REVERT: C 868 GLU cc_start: 0.6940 (tp30) cc_final: 0.6684 (tp30) REVERT: C 886 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7860 (p90) REVERT: C 933 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8070 (ttmm) REVERT: C 957 GLN cc_start: 0.7466 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 980 ILE cc_start: 0.8622 (mt) cc_final: 0.8288 (mm) REVERT: C 981 PHE cc_start: 0.8142 (m-80) cc_final: 0.7788 (m-80) REVERT: C 1014 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7456 (ttm110) REVERT: C 1086 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7659 (mmmt) REVERT: D 182 LEU cc_start: 0.5299 (mt) cc_final: 0.4977 (tp) REVERT: E 47 LYS cc_start: 0.4076 (OUTLIER) cc_final: 0.2887 (ttmm) REVERT: E 194 TYR cc_start: 0.3761 (OUTLIER) cc_final: 0.2430 (m-80) REVERT: F 182 LEU cc_start: 0.8145 (tp) cc_final: 0.7580 (tt) outliers start: 139 outliers final: 110 residues processed: 726 average time/residue: 0.7685 time to fit residues: 903.1746 Evaluate side-chains 743 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 615 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG 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 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 376 THR Chi-restraints excluded: chain A residue 390 LEU 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 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR 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 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1076 THR 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 34 ARG Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS 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 206 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN 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 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 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1001 LEU 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 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR 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 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 547 LYS Chi-restraints excluded: chain C residue 585 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 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS 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 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 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 217 ARG Chi-restraints excluded: chain G residue 75 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 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 389 optimal weight: 20.0000 chunk 140 optimal weight: 0.0170 chunk 305 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 165 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 913 GLN B 542 ASN B 710 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.189357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138467 restraints weight = 56431.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142373 restraints weight = 26224.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143034 restraints weight = 16471.060| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4541 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= 0.128 Angle : 0.625 12.643 42535 Z= 0.310 Chirality : 0.045 0.191 4863 Planarity : 0.005 0.070 5471 Dihedral : 5.908 58.602 4328 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.83 % Allowed : 21.80 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3888 helix: 0.78 (0.21), residues: 668 sheet: -1.22 (0.18), residues: 827 loop : -2.30 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 37 HIS 0.005 0.001 HIS B1048 PHE 0.045 0.001 PHE C 168 TYR 0.025 0.001 TYR A 265 ARG 0.010 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 832) hydrogen bonds : angle 5.21265 ( 2268) SS BOND : bond 0.00346 ( 47) SS BOND : angle 1.65051 ( 94) covalent geometry : bond 0.00296 (31139) covalent geometry : angle 0.62042 (42441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16014.36 seconds wall clock time: 284 minutes 43.79 seconds (17083.79 seconds total)