Starting phenix.real_space_refine on Wed Jun 25 20:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvq_32857/06_2025/7wvq_32857.cif" } resolution = 4.04 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= 0.003 sd= 0.034 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 143 5.16 5 C 18895 2.51 5 N 4913 2.21 5 O 5576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29527 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 17.50, per 1000 atoms: 0.59 Number of scatterers: 29527 At special positions: 0 Unit cell: (148.648, 146.462, 238.274, 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 143 16.00 O 5576 8.00 N 4913 7.00 C 18895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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=2.04 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.04 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 A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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: 7.07 Conformation dependent library (CDL) restraints added in 3.8 seconds 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 61 sheets defined 25.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 746 through 752 removed outlier: 3.958A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 752' Processing helix chain 'D' and resid 753 through 757 removed outlier: 3.634A pdb=" N TYR D 756 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 772 Processing helix chain 'D' and resid 776 through 783 removed outlier: 4.040A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 removed outlier: 3.861A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 825 " --> pdb=" O LEU D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 883 removed outlier: 3.950A pdb=" N ALA D 876 " --> pdb=" O GLN D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.870A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 908 " --> pdb=" O TYR D 904 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.540A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 941 removed outlier: 4.067A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 930 " --> pdb=" O GLN D 926 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 931 " --> pdb=" O PHE D 927 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 940 " --> pdb=" O ASP D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 946 removed outlier: 3.515A pdb=" N LEU D 945 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 946 " --> pdb=" O SER D 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 946' Processing helix chain 'D' and resid 949 through 961 removed outlier: 3.516A pdb=" N ASN D 953 " --> pdb=" O GLN D 949 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 984 removed outlier: 4.030A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 983 " --> pdb=" O ASP D 979 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 984 " --> pdb=" O ILE D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1031 removed outlier: 3.870A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 998 " --> pdb=" O ASP D 994 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D1003 " --> pdb=" O GLY D 999 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D1006 " --> pdb=" O GLN D1002 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D1009 " --> pdb=" O GLN D1005 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D1010 " --> pdb=" O THR D1006 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D1022 " --> pdb=" O ILE D1018 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.570A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.766A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.858A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.570A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 removed outlier: 4.260A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.834A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.939A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 919' Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.755A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.553A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS C 954 " --> pdb=" O ASP C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 977 through 982 removed outlier: 4.202A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 982' Processing helix chain 'C' and resid 985 through 994 removed outlier: 3.924A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1032 removed outlier: 3.704A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 4.461A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.531A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.022A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.165A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 768 removed outlier: 3.735A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.795A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.883A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.934A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.878A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.567A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 965 removed outlier: 3.628A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.766A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.965A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.874A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 52 " --> pdb=" O TRP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.725A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.858A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.734A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.694A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.851A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.667A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.034A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.870A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 4.220A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 194' Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.648A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 3.887A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.984A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 267 " --> pdb=" O ALA A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.640A pdb=" N THR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.659A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.985A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.160A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 331' Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.795A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.753A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.540A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.527A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.543A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.650A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.273A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 4.117A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.040A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 4.029A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.904A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 533 removed outlier: 4.143A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.549A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.531A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.724A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.866A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 202 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN D 188 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 96 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.806A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.041A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.041A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 130 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 132 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.629A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 325 through 327 removed outlier: 5.940A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 576 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY D 566 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE D 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.982A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.982A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.605A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 448 through 454 removed outlier: 7.347A pdb=" N TYR D 451 " --> pdb=" O TYR D 495 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 495 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.671A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.784A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 693 " --> pdb=" O SER D 673 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.083A pdb=" N ALA D 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'D' and resid 718 through 723 removed outlier: 3.803A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D1066 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D1060 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU D 727 " --> pdb=" O VAL D1060 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 718 through 723 removed outlier: 3.803A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D1066 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D1061 " --> pdb=" O GLN D1054 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.471A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 735 " --> pdb=" O THR D 859 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR D 859 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 788 through 790 removed outlier: 5.856A pdb=" N ILE D 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 3.566A pdb=" N SER D1123 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1094 through 1097 removed outlier: 3.803A pdb=" N PHE D1103 " --> pdb=" O VAL D1096 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.792A pdb=" N THR C 22 " --> pdb=" O PHE C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.137A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.538A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.975A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.975A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 89 through 94 removed outlier: 3.561A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.328A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.842A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.925A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.925A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD7, first strand: chain 'C' and resid 448 through 454 removed outlier: 7.331A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.651A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 566 through 567 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.616A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.785A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 724 removed outlier: 3.749A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 727 through 728 removed outlier: 4.673A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.502A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.895A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.874A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C1103 " --> pdb=" O VAL C1096 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.053A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.084A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.436A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.649A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AF4, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.451A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.662A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 376 through 378 removed outlier: 4.150A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 511 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 376 through 378 removed outlier: 4.150A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 511 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.541A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.639A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.813A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.613A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 861 " --> pdb=" O LYS B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AG6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.399A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 738 hydrogen bonds defined for protein. 2055 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: 14.05 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4893 1.31 - 1.44: 8417 1.44 - 1.57: 16733 1.57 - 1.71: 0 1.71 - 1.84: 194 Bond restraints: 30237 Sorted by residual: bond pdb=" C ASP A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.334 1.516 -0.183 2.34e-02 1.83e+03 6.09e+01 bond pdb=" CA SER B1003 " pdb=" C SER B1003 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.29e-02 6.01e+03 5.45e+01 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.337 1.417 -0.081 1.11e-02 8.12e+03 5.29e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.22e+01 bond pdb=" CA ILE B 997 " pdb=" C ILE B 997 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.27e-02 6.20e+03 4.94e+01 ... (remaining 30232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 40728 4.28 - 8.56: 336 8.56 - 12.84: 40 12.84 - 17.12: 2 17.12 - 21.40: 2 Bond angle restraints: 41108 Sorted by residual: angle pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" O GLY B 526 " ideal model delta sigma weight residual 121.52 139.66 -18.14 1.43e+00 4.89e-01 1.61e+02 angle pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" C GLN B 957 " ideal model delta sigma weight residual 111.28 98.04 13.24 1.09e+00 8.42e-01 1.48e+02 angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 133.74 -21.40 2.04e+00 2.40e-01 1.10e+02 angle pdb=" N ASP B 389 " pdb=" CA ASP B 389 " pdb=" C ASP B 389 " ideal model delta sigma weight residual 111.07 121.32 -10.25 1.07e+00 8.73e-01 9.17e+01 angle pdb=" N GLN C1002 " pdb=" CA GLN C1002 " pdb=" C GLN C1002 " ideal model delta sigma weight residual 112.38 100.82 11.56 1.22e+00 6.72e-01 8.98e+01 ... (remaining 41103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 17244 16.01 - 32.01: 611 32.01 - 48.02: 140 48.02 - 64.03: 26 64.03 - 80.04: 16 Dihedral angle restraints: 18037 sinusoidal: 7121 harmonic: 10916 Sorted by residual: dihedral pdb=" C CYS B 525 " pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual -122.60 -140.16 17.56 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual 122.80 137.77 -14.97 0 2.50e+00 1.60e-01 3.58e+01 dihedral pdb=" CA PRO A 389 " pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 4429 0.132 - 0.265: 138 0.265 - 0.397: 17 0.397 - 0.529: 5 0.529 - 0.662: 3 Chirality restraints: 4592 Sorted by residual: chirality pdb=" CA CYS B 525 " pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CB CYS B 525 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ILE C 993 " pdb=" N ILE C 993 " pdb=" C ILE C 993 " pdb=" CB ILE C 993 " both_signs ideal model delta sigma weight residual False 2.43 1.85 0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" CA LEU B 966 " pdb=" N LEU B 966 " pdb=" C LEU B 966 " pdb=" CB LEU B 966 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 4589 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 964 " 0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C LYS B 964 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS B 964 " 0.033 2.00e-02 2.50e+03 pdb=" N GLN B 965 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO B 987 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 390 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 390 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 390 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS B 391 " -0.027 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9394 2.85 - 3.36: 22516 3.36 - 3.88: 47426 3.88 - 4.39: 49107 4.39 - 4.90: 86838 Nonbonded interactions: 215281 Sorted by model distance: nonbonded pdb=" O GLY B 526 " pdb=" CA PRO B 527 " model vdw 2.339 2.776 nonbonded pdb=" OG SER C 816 " pdb=" OE1 GLU C 819 " model vdw 2.349 3.040 nonbonded pdb=" N GLN B 957 " pdb=" N ALA B 958 " model vdw 2.356 2.560 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.367 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.371 3.040 ... (remaining 215276 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 'B' selection = chain 'C' selection = chain 'D' } 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: 2.780 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: 0.040 Extract box with map and model: 1.080 Check model and map are aligned: 0.220 Set scattering table: 0.240 Process input model: 68.250 Find NCS groups from input model: 0.870 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 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 : 0.007 0.183 30279 Z= 0.422 Angle : 1.051 21.404 41192 Z= 0.628 Chirality : 0.065 0.662 4592 Planarity : 0.008 0.122 5321 Dihedral : 9.787 80.037 10877 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.20 % Favored : 94.61 % Rotamer: Outliers : 0.46 % Allowed : 1.10 % Favored : 98.45 % Cbeta Deviations : 0.17 % 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: -3.46 (0.11), residues: 3691 helix: -4.60 (0.09), residues: 801 sheet: -0.63 (0.22), residues: 366 loop : -1.84 (0.10), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 461 HIS 0.012 0.001 HIS A 265 PHE 0.025 0.003 PHE D 275 TYR 0.030 0.002 TYR D 873 ARG 0.006 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.32237 ( 712) hydrogen bonds : angle 11.57925 ( 2055) SS BOND : bond 0.00445 ( 42) SS BOND : angle 1.46757 ( 84) covalent geometry : bond 0.00742 (30237) covalent geometry : angle 1.05012 (41108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 617 time to evaluate : 2.812 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: D 44 ARG cc_start: 0.6993 (ptp90) cc_final: 0.6740 (ptp90) REVERT: D 135 PHE cc_start: 0.5293 (m-10) cc_final: 0.4777 (m-10) REVERT: D 177 MET cc_start: 0.2371 (ptp) cc_final: 0.2154 (ptm) REVERT: D 223 LEU cc_start: 0.8853 (mp) cc_final: 0.8397 (mm) REVERT: D 298 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7161 (mt-10) REVERT: D 591 SER cc_start: 0.7868 (t) cc_final: 0.7511 (t) REVERT: D 955 ASN cc_start: 0.7573 (m-40) cc_final: 0.7346 (m-40) REVERT: D 960 ASN cc_start: 0.7710 (m110) cc_final: 0.7290 (m110) REVERT: D 1000 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7217 (mmt180) REVERT: D 1004 LEU cc_start: 0.8930 (mt) cc_final: 0.8666 (mm) REVERT: D 1012 LEU cc_start: 0.9260 (mt) cc_final: 0.9058 (mm) REVERT: C 164 ASN cc_start: 0.6588 (p0) cc_final: 0.6374 (p0) REVERT: C 189 LEU cc_start: 0.7046 (tp) cc_final: 0.6823 (tp) REVERT: C 192 PHE cc_start: 0.7425 (m-80) cc_final: 0.6877 (t80) REVERT: C 287 ASP cc_start: 0.8223 (t0) cc_final: 0.7911 (p0) REVERT: C 293 LEU cc_start: 0.7790 (tp) cc_final: 0.7173 (tp) REVERT: C 294 ASP cc_start: 0.8029 (m-30) cc_final: 0.7417 (m-30) REVERT: C 314 GLN cc_start: 0.7910 (tt0) cc_final: 0.7517 (tm-30) REVERT: C 651 ILE cc_start: 0.5810 (mt) cc_final: 0.5527 (mt) REVERT: C 726 ILE cc_start: 0.6803 (mp) cc_final: 0.6441 (mp) REVERT: C 740 MET cc_start: 0.5327 (tpt) cc_final: 0.4734 (tpp) REVERT: C 752 LEU cc_start: 0.8727 (mp) cc_final: 0.8469 (mp) REVERT: C 776 LYS cc_start: 0.8188 (tptt) cc_final: 0.7945 (tptt) REVERT: C 797 PHE cc_start: 0.4292 (m-80) cc_final: 0.3614 (m-80) REVERT: C 902 MET cc_start: 0.6837 (mtm) cc_final: 0.6452 (mtm) REVERT: C 928 ASN cc_start: 0.7782 (m110) cc_final: 0.7537 (m110) REVERT: C 951 VAL cc_start: 0.8492 (m) cc_final: 0.8154 (p) REVERT: C 969 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8693 (mmmt) REVERT: C 976 VAL cc_start: 0.5190 (t) cc_final: 0.4786 (t) REVERT: C 996 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 998 THR cc_start: 0.8433 (m) cc_final: 0.7676 (p) REVERT: C 1002 GLN cc_start: 0.8491 (mt0) cc_final: 0.8105 (mt0) REVERT: C 1017 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7426 (tp30) REVERT: C 1062 PHE cc_start: 0.6804 (m-10) cc_final: 0.6498 (m-80) REVERT: C 1108 ASN cc_start: 0.6226 (m110) cc_final: 0.5886 (m110) REVERT: B 177 MET cc_start: -0.3365 (tpt) cc_final: -0.4477 (mmt) REVERT: B 238 PHE cc_start: 0.8528 (p90) cc_final: 0.7992 (p90) REVERT: B 514 SER cc_start: 0.6152 (t) cc_final: 0.5584 (p) REVERT: B 532 ASN cc_start: 0.7505 (t0) cc_final: 0.7252 (t0) REVERT: B 584 ILE cc_start: 0.7035 (pt) cc_final: 0.6642 (mm) REVERT: B 725 GLU cc_start: 0.6620 (pt0) cc_final: 0.6173 (pt0) REVERT: B 731 MET cc_start: 0.6947 (ptm) cc_final: 0.6473 (ptm) REVERT: B 780 GLU cc_start: 0.7724 (tp30) cc_final: 0.7308 (tp30) REVERT: B 819 GLU cc_start: 0.7742 (pt0) cc_final: 0.6982 (mp0) REVERT: B 820 ASP cc_start: 0.8153 (t70) cc_final: 0.7910 (t70) REVERT: B 936 ASP cc_start: 0.7544 (t0) cc_final: 0.7342 (m-30) REVERT: B 957 GLN cc_start: 0.9267 (tt0) cc_final: 0.9018 (tp40) REVERT: B 966 LEU cc_start: 0.7847 (mp) cc_final: 0.7634 (mp) REVERT: B 1000 ARG cc_start: 0.8526 (ttt90) cc_final: 0.7762 (ttt90) REVERT: A 341 LYS cc_start: 0.8205 (tptt) cc_final: 0.7820 (tptt) REVERT: A 351 LEU cc_start: 0.5895 (mt) cc_final: 0.5402 (tp) REVERT: A 474 MET cc_start: -0.1080 (mmp) cc_final: -0.3471 (tpt) outliers start: 15 outliers final: 6 residues processed: 626 average time/residue: 0.4174 time to fit residues: 408.1328 Evaluate side-chains 455 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 448 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 156 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 290 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 176 optimal weight: 0.0570 chunk 216 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 ASN D 564 GLN D 690 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN D1088 HIS D1108 ASN C 173 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 872 GLN C 935 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1010 GLN C1088 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 394 ASN B 955 ASN B1023 ASN A 24 GLN A 81 GLN A 96 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.205411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.169067 restraints weight = 103112.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.172550 restraints weight = 72971.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.175141 restraints weight = 54900.229| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30279 Z= 0.116 Angle : 0.604 10.327 41192 Z= 0.314 Chirality : 0.044 0.165 4592 Planarity : 0.006 0.091 5321 Dihedral : 5.124 23.137 4011 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.11), residues: 3691 helix: -3.06 (0.13), residues: 826 sheet: -0.13 (0.22), residues: 411 loop : -1.62 (0.10), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 461 HIS 0.010 0.001 HIS A 378 PHE 0.020 0.001 PHE C 823 TYR 0.017 0.001 TYR D 873 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.05506 ( 712) hydrogen bonds : angle 6.69685 ( 2055) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.23690 ( 84) covalent geometry : bond 0.00233 (30237) covalent geometry : angle 0.60248 (41108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 531 time to evaluate : 3.323 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: D 135 PHE cc_start: 0.5838 (m-10) cc_final: 0.5238 (m-10) REVERT: D 153 MET cc_start: 0.2029 (ppp) cc_final: 0.1581 (ppp) REVERT: D 177 MET cc_start: 0.2393 (ptp) cc_final: 0.1852 (ptm) REVERT: D 223 LEU cc_start: 0.8785 (mp) cc_final: 0.8381 (mp) REVERT: D 279 TYR cc_start: 0.7573 (m-80) cc_final: 0.7187 (m-80) REVERT: D 298 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7366 (mt-10) REVERT: D 299 THR cc_start: 0.8294 (m) cc_final: 0.8075 (p) REVERT: D 300 LYS cc_start: 0.8342 (mttt) cc_final: 0.7631 (mttt) REVERT: D 571 ASP cc_start: 0.5963 (m-30) cc_final: 0.5711 (m-30) REVERT: D 654 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6685 (mm-30) REVERT: D 695 TYR cc_start: 0.7800 (p90) cc_final: 0.7549 (p90) REVERT: D 802 PHE cc_start: 0.6121 (m-10) cc_final: 0.5820 (m-10) REVERT: D 878 LEU cc_start: 0.9006 (mt) cc_final: 0.8802 (mt) REVERT: D 895 GLN cc_start: 0.3916 (tt0) cc_final: 0.2757 (pt0) REVERT: D 960 ASN cc_start: 0.8036 (m110) cc_final: 0.7618 (m110) REVERT: D 1000 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7529 (mmt180) REVERT: D 1012 LEU cc_start: 0.9216 (mt) cc_final: 0.8985 (mt) REVERT: C 51 THR cc_start: 0.8199 (p) cc_final: 0.7893 (m) REVERT: C 275 PHE cc_start: 0.7891 (t80) cc_final: 0.7652 (t80) REVERT: C 287 ASP cc_start: 0.8191 (t0) cc_final: 0.7677 (p0) REVERT: C 294 ASP cc_start: 0.7912 (m-30) cc_final: 0.7638 (m-30) REVERT: C 314 GLN cc_start: 0.8063 (tt0) cc_final: 0.7666 (tm-30) REVERT: C 651 ILE cc_start: 0.6184 (mt) cc_final: 0.5842 (mt) REVERT: C 740 MET cc_start: 0.5728 (tpt) cc_final: 0.5202 (tpp) REVERT: C 752 LEU cc_start: 0.8718 (mp) cc_final: 0.8287 (mp) REVERT: C 776 LYS cc_start: 0.8224 (tptt) cc_final: 0.7470 (tptt) REVERT: C 902 MET cc_start: 0.7191 (mtm) cc_final: 0.6823 (mtm) REVERT: C 955 ASN cc_start: 0.8742 (m-40) cc_final: 0.8542 (m-40) REVERT: C 969 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8757 (mmmt) REVERT: C 992 GLN cc_start: 0.8274 (mm110) cc_final: 0.7831 (mm110) REVERT: C 998 THR cc_start: 0.8292 (m) cc_final: 0.7514 (p) REVERT: C 1002 GLN cc_start: 0.8160 (mt0) cc_final: 0.7835 (mt0) REVERT: C 1005 GLN cc_start: 0.8208 (mt0) cc_final: 0.7893 (mt0) REVERT: C 1010 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7291 (tp40) REVERT: C 1013 ILE cc_start: 0.8560 (pt) cc_final: 0.8310 (pt) REVERT: C 1023 ASN cc_start: 0.7215 (m-40) cc_final: 0.7005 (m110) REVERT: C 1028 LYS cc_start: 0.7089 (mtmm) cc_final: 0.6805 (mtmm) REVERT: C 1062 PHE cc_start: 0.6968 (m-10) cc_final: 0.6693 (m-80) REVERT: C 1108 ASN cc_start: 0.6064 (m110) cc_final: 0.5723 (m110) REVERT: B 177 MET cc_start: -0.4169 (tpt) cc_final: -0.4991 (mmt) REVERT: B 238 PHE cc_start: 0.8405 (p90) cc_final: 0.8140 (p90) REVERT: B 303 LEU cc_start: 0.8948 (tt) cc_final: 0.8731 (tp) REVERT: B 509 ARG cc_start: 0.5615 (ttp80) cc_final: 0.5187 (tmt-80) REVERT: B 532 ASN cc_start: 0.7443 (t0) cc_final: 0.7208 (t0) REVERT: B 565 PHE cc_start: 0.6976 (p90) cc_final: 0.6200 (p90) REVERT: B 775 ASP cc_start: 0.8476 (m-30) cc_final: 0.8191 (m-30) REVERT: B 780 GLU cc_start: 0.8060 (tp30) cc_final: 0.7637 (tp30) REVERT: B 820 ASP cc_start: 0.8436 (t70) cc_final: 0.8217 (t70) REVERT: B 936 ASP cc_start: 0.7706 (t0) cc_final: 0.7449 (m-30) REVERT: B 957 GLN cc_start: 0.8708 (tt0) cc_final: 0.8403 (tp40) REVERT: B 1002 GLN cc_start: 0.8677 (tt0) cc_final: 0.8476 (tt0) REVERT: A 123 MET cc_start: -0.5360 (mmm) cc_final: -0.6002 (mmt) REVERT: A 341 LYS cc_start: 0.8314 (tptt) cc_final: 0.8048 (tptt) REVERT: A 474 MET cc_start: 0.2027 (mmp) cc_final: -0.0942 (tpt) REVERT: A 480 MET cc_start: 0.5367 (ptt) cc_final: 0.4806 (ptt) REVERT: A 579 MET cc_start: 0.5873 (tpp) cc_final: 0.5508 (mmm) outliers start: 2 outliers final: 0 residues processed: 531 average time/residue: 0.4402 time to fit residues: 376.7893 Evaluate side-chains 447 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 322 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 353 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS D 234 ASN D 394 ASN ** D 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1088 HIS C 49 HIS C 928 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS C1119 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 460 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1054 GLN B1058 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN A 330 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.190902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.152639 restraints weight = 102063.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.155844 restraints weight = 72342.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.158260 restraints weight = 54774.002| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 30279 Z= 0.234 Angle : 0.772 13.199 41192 Z= 0.402 Chirality : 0.049 0.207 4592 Planarity : 0.006 0.080 5321 Dihedral : 5.419 23.401 4011 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 3691 helix: -1.74 (0.15), residues: 852 sheet: -0.45 (0.21), residues: 477 loop : -1.40 (0.11), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP A 461 HIS 0.013 0.002 HIS A 378 PHE 0.029 0.003 PHE C 906 TYR 0.026 0.002 TYR C 160 ARG 0.012 0.001 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 712) hydrogen bonds : angle 6.01555 ( 2055) SS BOND : bond 0.00522 ( 42) SS BOND : angle 1.64382 ( 84) covalent geometry : bond 0.00494 (30237) covalent geometry : angle 0.76895 (41108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 528 time to evaluate : 2.968 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: D 100 ILE cc_start: 0.8269 (mm) cc_final: 0.8014 (mm) REVERT: D 135 PHE cc_start: 0.6456 (m-10) cc_final: 0.5727 (m-80) REVERT: D 153 MET cc_start: 0.2918 (ppp) cc_final: 0.2030 (ppp) REVERT: D 177 MET cc_start: 0.2360 (ptp) cc_final: 0.1456 (ptm) REVERT: D 201 PHE cc_start: 0.6830 (m-10) cc_final: 0.6629 (m-10) REVERT: D 223 LEU cc_start: 0.8884 (mp) cc_final: 0.8320 (tp) REVERT: D 298 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 299 THR cc_start: 0.8886 (m) cc_final: 0.8656 (p) REVERT: D 571 ASP cc_start: 0.7607 (m-30) cc_final: 0.7321 (m-30) REVERT: D 655 TYR cc_start: 0.7014 (t80) cc_final: 0.6478 (t80) REVERT: D 740 MET cc_start: 0.8073 (tpt) cc_final: 0.7764 (tpp) REVERT: D 756 TYR cc_start: 0.7275 (m-80) cc_final: 0.7002 (m-80) REVERT: D 763 LEU cc_start: 0.8530 (mt) cc_final: 0.8266 (mt) REVERT: D 768 THR cc_start: 0.7859 (p) cc_final: 0.7630 (p) REVERT: D 779 GLN cc_start: 0.7807 (tp40) cc_final: 0.6997 (tm-30) REVERT: D 860 VAL cc_start: 0.8917 (t) cc_final: 0.8648 (p) REVERT: D 902 MET cc_start: 0.7022 (mmp) cc_final: 0.6606 (ttt) REVERT: D 954 HIS cc_start: 0.8547 (m170) cc_final: 0.8211 (m170) REVERT: D 960 ASN cc_start: 0.8307 (m110) cc_final: 0.7987 (m110) REVERT: D 1000 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7931 (mtt90) REVERT: D 1010 GLN cc_start: 0.8270 (pt0) cc_final: 0.7772 (pt0) REVERT: D 1012 LEU cc_start: 0.9235 (mt) cc_final: 0.9019 (mt) REVERT: D 1013 ILE cc_start: 0.8911 (pt) cc_final: 0.8679 (pt) REVERT: D 1017 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 57 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.7919 (Cg_endo) REVERT: C 192 PHE cc_start: 0.7235 (t80) cc_final: 0.6921 (t80) REVERT: C 237 ARG cc_start: 0.7597 (tpt170) cc_final: 0.6530 (tpt170) REVERT: C 270 LEU cc_start: 0.8323 (mt) cc_final: 0.8112 (mt) REVERT: C 275 PHE cc_start: 0.8205 (t80) cc_final: 0.7976 (t80) REVERT: C 290 ASP cc_start: 0.8351 (t0) cc_final: 0.8001 (t70) REVERT: C 294 ASP cc_start: 0.7807 (m-30) cc_final: 0.7585 (m-30) REVERT: C 314 GLN cc_start: 0.8190 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 651 ILE cc_start: 0.6244 (mt) cc_final: 0.5958 (pt) REVERT: C 731 MET cc_start: 0.8321 (pmm) cc_final: 0.7844 (pmm) REVERT: C 740 MET cc_start: 0.7138 (tpt) cc_final: 0.5815 (tpt) REVERT: C 752 LEU cc_start: 0.9095 (mp) cc_final: 0.8638 (mp) REVERT: C 753 LEU cc_start: 0.8585 (mt) cc_final: 0.8113 (mt) REVERT: C 775 ASP cc_start: 0.8607 (m-30) cc_final: 0.8312 (m-30) REVERT: C 776 LYS cc_start: 0.8702 (tptt) cc_final: 0.8081 (tptt) REVERT: C 860 VAL cc_start: 0.8437 (t) cc_final: 0.8119 (p) REVERT: C 873 TYR cc_start: 0.7507 (m-80) cc_final: 0.7246 (m-80) REVERT: C 902 MET cc_start: 0.7043 (mtm) cc_final: 0.6672 (mtm) REVERT: C 914 ASN cc_start: 0.6797 (t0) cc_final: 0.6596 (t0) REVERT: C 992 GLN cc_start: 0.8440 (mm110) cc_final: 0.8148 (mm110) REVERT: C 998 THR cc_start: 0.8694 (m) cc_final: 0.7812 (p) REVERT: C 1002 GLN cc_start: 0.8508 (mt0) cc_final: 0.8003 (mt0) REVERT: C 1005 GLN cc_start: 0.8408 (mt0) cc_final: 0.8097 (mt0) REVERT: C 1010 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7950 (tp-100) REVERT: C 1017 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 1023 ASN cc_start: 0.7571 (m-40) cc_final: 0.7326 (m-40) REVERT: B 56 LEU cc_start: 0.7830 (tp) cc_final: 0.7534 (tp) REVERT: B 153 MET cc_start: -0.0210 (pmm) cc_final: -0.0573 (ptp) REVERT: B 177 MET cc_start: -0.4378 (tpt) cc_final: -0.4939 (mmm) REVERT: B 314 GLN cc_start: 0.8302 (tt0) cc_final: 0.7782 (tm-30) REVERT: B 532 ASN cc_start: 0.8025 (t0) cc_final: 0.7764 (t0) REVERT: B 731 MET cc_start: 0.8077 (ppp) cc_final: 0.7794 (tmm) REVERT: B 740 MET cc_start: 0.7405 (mmp) cc_final: 0.7003 (mmp) REVERT: B 752 LEU cc_start: 0.8590 (mp) cc_final: 0.8318 (tp) REVERT: B 775 ASP cc_start: 0.8665 (m-30) cc_final: 0.8326 (m-30) REVERT: B 780 GLU cc_start: 0.8132 (tp30) cc_final: 0.7521 (tp30) REVERT: B 820 ASP cc_start: 0.8378 (t70) cc_final: 0.7846 (t70) REVERT: B 824 ASN cc_start: 0.8242 (m-40) cc_final: 0.8034 (m-40) REVERT: B 936 ASP cc_start: 0.7780 (t0) cc_final: 0.7574 (m-30) REVERT: B 957 GLN cc_start: 0.8662 (tt0) cc_final: 0.8461 (tp40) REVERT: B 985 ASP cc_start: 0.8260 (t0) cc_final: 0.7423 (t0) REVERT: B 996 LEU cc_start: 0.8829 (mt) cc_final: 0.8619 (mt) REVERT: B 1000 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: B 1007 TYR cc_start: 0.8798 (t80) cc_final: 0.8527 (t80) REVERT: B 1017 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 1038 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7220 (mppt) REVERT: B 1050 MET cc_start: 0.5944 (mmt) cc_final: 0.5689 (mmt) REVERT: B 1081 ILE cc_start: 0.8154 (mm) cc_final: 0.7789 (tp) REVERT: B 1089 PHE cc_start: 0.7387 (m-80) cc_final: 0.7005 (m-80) REVERT: A 48 TRP cc_start: 0.6871 (t60) cc_final: 0.6430 (t60) REVERT: A 123 MET cc_start: -0.3223 (mmm) cc_final: -0.4885 (tpp) REVERT: A 341 LYS cc_start: 0.8334 (tptt) cc_final: 0.8102 (tptt) REVERT: A 360 MET cc_start: -0.0602 (ptt) cc_final: -0.0873 (mtm) outliers start: 8 outliers final: 2 residues processed: 533 average time/residue: 0.3922 time to fit residues: 335.8785 Evaluate side-chains 456 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 353 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 219 optimal weight: 7.9990 chunk 366 optimal weight: 0.1980 chunk 298 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 218 GLN D 606 ASN D 779 GLN D 895 GLN D 957 GLN D1011 GLN D1088 HIS C 49 HIS C 422 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 928 ASN C1064 HIS C1106 GLN B 137 ASN B 460 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 522 GLN ** 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 = 0.4858 r_free = 0.4858 target = 0.191011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.152828 restraints weight = 102122.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.156099 restraints weight = 71496.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.158545 restraints weight = 53537.614| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30279 Z= 0.155 Angle : 0.604 12.206 41192 Z= 0.309 Chirality : 0.045 0.230 4592 Planarity : 0.005 0.129 5321 Dihedral : 4.916 22.333 4011 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.12), residues: 3691 helix: -0.96 (0.17), residues: 823 sheet: -0.43 (0.22), residues: 486 loop : -1.26 (0.11), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 461 HIS 0.010 0.001 HIS A 378 PHE 0.024 0.002 PHE D1052 TYR 0.028 0.002 TYR D 612 ARG 0.010 0.001 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 712) hydrogen bonds : angle 5.48125 ( 2055) SS BOND : bond 0.01155 ( 42) SS BOND : angle 1.07152 ( 84) covalent geometry : bond 0.00319 (30237) covalent geometry : angle 0.60315 (41108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 512 time to evaluate : 2.841 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: D 100 ILE cc_start: 0.7984 (mm) cc_final: 0.7729 (mm) REVERT: D 135 PHE cc_start: 0.6479 (m-10) cc_final: 0.5154 (m-80) REVERT: D 153 MET cc_start: 0.3249 (ppp) cc_final: 0.2357 (ppp) REVERT: D 177 MET cc_start: 0.2534 (ptp) cc_final: 0.1699 (ptm) REVERT: D 201 PHE cc_start: 0.7246 (m-10) cc_final: 0.7045 (m-10) REVERT: D 204 TYR cc_start: 0.6821 (m-80) cc_final: 0.6617 (m-80) REVERT: D 223 LEU cc_start: 0.9000 (mp) cc_final: 0.8665 (mp) REVERT: D 299 THR cc_start: 0.8937 (m) cc_final: 0.8519 (p) REVERT: D 571 ASP cc_start: 0.7552 (m-30) cc_final: 0.7193 (m-30) REVERT: D 606 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7562 (t0) REVERT: D 612 TYR cc_start: 0.4638 (t80) cc_final: 0.4315 (t80) REVERT: D 740 MET cc_start: 0.7931 (tpt) cc_final: 0.7708 (tpt) REVERT: D 756 TYR cc_start: 0.7324 (m-80) cc_final: 0.7008 (m-80) REVERT: D 779 GLN cc_start: 0.7658 (tp-100) cc_final: 0.6986 (tm-30) REVERT: D 802 PHE cc_start: 0.7883 (m-10) cc_final: 0.7496 (m-10) REVERT: D 822 LEU cc_start: 0.8639 (mt) cc_final: 0.8426 (mt) REVERT: D 860 VAL cc_start: 0.9045 (t) cc_final: 0.8797 (p) REVERT: D 954 HIS cc_start: 0.8521 (m170) cc_final: 0.8218 (m170) REVERT: D 960 ASN cc_start: 0.8319 (m110) cc_final: 0.7982 (m110) REVERT: D 1000 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7872 (mtt90) REVERT: D 1001 LEU cc_start: 0.9046 (mm) cc_final: 0.8838 (mm) REVERT: D 1010 GLN cc_start: 0.8250 (pt0) cc_final: 0.7816 (pt0) REVERT: D 1012 LEU cc_start: 0.9262 (mt) cc_final: 0.9011 (mt) REVERT: D 1013 ILE cc_start: 0.8880 (pt) cc_final: 0.8678 (pt) REVERT: D 1017 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8288 (mt-10) REVERT: D 1023 ASN cc_start: 0.7519 (m-40) cc_final: 0.6934 (m-40) REVERT: D 1106 GLN cc_start: 0.8397 (pt0) cc_final: 0.8068 (pt0) REVERT: C 237 ARG cc_start: 0.7801 (tpm170) cc_final: 0.7597 (tpp-160) REVERT: C 270 LEU cc_start: 0.8283 (mt) cc_final: 0.8062 (mt) REVERT: C 287 ASP cc_start: 0.8471 (t70) cc_final: 0.8112 (t70) REVERT: C 290 ASP cc_start: 0.8207 (t0) cc_final: 0.7758 (t70) REVERT: C 294 ASP cc_start: 0.7874 (m-30) cc_final: 0.7666 (m-30) REVERT: C 314 GLN cc_start: 0.8059 (tt0) cc_final: 0.7684 (tm-30) REVERT: C 651 ILE cc_start: 0.6236 (mt) cc_final: 0.5927 (pt) REVERT: C 731 MET cc_start: 0.8348 (pmm) cc_final: 0.7071 (ppp) REVERT: C 740 MET cc_start: 0.6837 (tpt) cc_final: 0.6606 (mmm) REVERT: C 752 LEU cc_start: 0.9186 (mp) cc_final: 0.8689 (mp) REVERT: C 753 LEU cc_start: 0.8628 (mt) cc_final: 0.8369 (mt) REVERT: C 775 ASP cc_start: 0.8525 (m-30) cc_final: 0.8282 (m-30) REVERT: C 776 LYS cc_start: 0.8689 (tptt) cc_final: 0.8054 (tptt) REVERT: C 784 GLN cc_start: 0.8711 (pm20) cc_final: 0.8499 (pm20) REVERT: C 860 VAL cc_start: 0.8529 (t) cc_final: 0.8155 (p) REVERT: C 869 MET cc_start: 0.8092 (ptm) cc_final: 0.7729 (ptm) REVERT: C 873 TYR cc_start: 0.7540 (m-80) cc_final: 0.7152 (m-80) REVERT: C 902 MET cc_start: 0.7259 (mtm) cc_final: 0.6902 (mtm) REVERT: C 960 ASN cc_start: 0.8715 (m110) cc_final: 0.8501 (m110) REVERT: C 969 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8848 (mmmt) REVERT: C 992 GLN cc_start: 0.8403 (mm110) cc_final: 0.8075 (mm110) REVERT: C 998 THR cc_start: 0.8758 (m) cc_final: 0.8069 (p) REVERT: C 1002 GLN cc_start: 0.8576 (mt0) cc_final: 0.8053 (mt0) REVERT: C 1010 GLN cc_start: 0.8380 (tp-100) cc_final: 0.7631 (tp40) REVERT: C 1013 ILE cc_start: 0.9029 (pt) cc_final: 0.8705 (pt) REVERT: C 1017 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8424 (mt-10) REVERT: C 1023 ASN cc_start: 0.7756 (m-40) cc_final: 0.7424 (m110) REVERT: B 56 LEU cc_start: 0.7662 (tp) cc_final: 0.7352 (tp) REVERT: B 177 MET cc_start: -0.4203 (tpt) cc_final: -0.4672 (mmm) REVERT: B 303 LEU cc_start: 0.8958 (tt) cc_final: 0.8734 (tt) REVERT: B 314 GLN cc_start: 0.8246 (tt0) cc_final: 0.7688 (tm-30) REVERT: B 565 PHE cc_start: 0.7422 (p90) cc_final: 0.7004 (p90) REVERT: B 731 MET cc_start: 0.8155 (ppp) cc_final: 0.7884 (tmm) REVERT: B 740 MET cc_start: 0.7126 (mmp) cc_final: 0.6752 (mmp) REVERT: B 772 VAL cc_start: 0.8913 (m) cc_final: 0.8602 (m) REVERT: B 775 ASP cc_start: 0.8564 (m-30) cc_final: 0.8018 (m-30) REVERT: B 820 ASP cc_start: 0.8407 (t70) cc_final: 0.7843 (t70) REVERT: B 824 ASN cc_start: 0.8241 (m-40) cc_final: 0.8025 (m-40) REVERT: B 861 LEU cc_start: 0.8442 (mm) cc_final: 0.7596 (tp) REVERT: B 936 ASP cc_start: 0.7853 (t0) cc_final: 0.7630 (m-30) REVERT: B 957 GLN cc_start: 0.8616 (tt0) cc_final: 0.8408 (tp40) REVERT: B 964 LYS cc_start: 0.8629 (tttt) cc_final: 0.8376 (tttt) REVERT: B 970 PHE cc_start: 0.6662 (m-80) cc_final: 0.6389 (m-80) REVERT: B 985 ASP cc_start: 0.8195 (t0) cc_final: 0.7640 (t0) REVERT: B 996 LEU cc_start: 0.8775 (mt) cc_final: 0.8516 (mt) REVERT: B 1000 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7635 (mmm-85) REVERT: B 1005 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 1006 THR cc_start: 0.8898 (p) cc_final: 0.8303 (p) REVERT: B 1017 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 1050 MET cc_start: 0.5723 (mmt) cc_final: 0.5161 (mmt) REVERT: B 1089 PHE cc_start: 0.7360 (m-80) cc_final: 0.7042 (m-80) REVERT: A 48 TRP cc_start: 0.6652 (t60) cc_final: 0.6258 (t60) REVERT: A 123 MET cc_start: -0.3406 (mmm) cc_final: -0.4675 (tpp) REVERT: A 474 MET cc_start: 0.3912 (mmp) cc_final: 0.0687 (tpt) REVERT: A 480 MET cc_start: 0.5352 (ptt) cc_final: 0.4972 (ptt) outliers start: 3 outliers final: 0 residues processed: 513 average time/residue: 0.4006 time to fit residues: 328.7063 Evaluate side-chains 445 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 112 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 74 optimal weight: 0.0010 chunk 315 optimal weight: 0.3980 chunk 358 optimal weight: 1.9990 chunk 367 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 283 optimal weight: 0.0870 chunk 278 optimal weight: 0.5980 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN D 370 ASN D1011 GLN D1088 HIS C 928 ASN C1106 GLN B 52 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** 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 = 0.4888 r_free = 0.4888 target = 0.193756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.156403 restraints weight = 102408.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.159589 restraints weight = 71600.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.162124 restraints weight = 53602.067| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30279 Z= 0.094 Angle : 0.550 11.902 41192 Z= 0.276 Chirality : 0.044 0.212 4592 Planarity : 0.005 0.072 5321 Dihedral : 4.491 22.858 4011 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3691 helix: -0.55 (0.18), residues: 829 sheet: -0.30 (0.21), residues: 503 loop : -1.17 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1102 HIS 0.009 0.001 HIS A 378 PHE 0.019 0.001 PHE D1062 TYR 0.022 0.001 TYR A 385 ARG 0.008 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 712) hydrogen bonds : angle 5.06361 ( 2055) SS BOND : bond 0.00238 ( 42) SS BOND : angle 1.56965 ( 84) covalent geometry : bond 0.00206 (30237) covalent geometry : angle 0.54614 (41108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 2.957 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: D 100 ILE cc_start: 0.7758 (mm) cc_final: 0.7512 (mm) REVERT: D 135 PHE cc_start: 0.6131 (m-10) cc_final: 0.4795 (m-80) REVERT: D 153 MET cc_start: 0.3136 (ppp) cc_final: 0.2262 (ppp) REVERT: D 177 MET cc_start: 0.2412 (ptp) cc_final: 0.1683 (ptm) REVERT: D 223 LEU cc_start: 0.8960 (mp) cc_final: 0.8625 (mp) REVERT: D 279 TYR cc_start: 0.8618 (m-80) cc_final: 0.8309 (m-80) REVERT: D 299 THR cc_start: 0.8788 (m) cc_final: 0.8471 (p) REVERT: D 571 ASP cc_start: 0.7431 (m-30) cc_final: 0.7085 (m-30) REVERT: D 612 TYR cc_start: 0.4790 (t80) cc_final: 0.4578 (t80) REVERT: D 655 TYR cc_start: 0.7152 (t80) cc_final: 0.6610 (t80) REVERT: D 756 TYR cc_start: 0.7179 (m-80) cc_final: 0.6878 (m-80) REVERT: D 764 LYS cc_start: 0.8890 (mptt) cc_final: 0.8685 (mmtt) REVERT: D 779 GLN cc_start: 0.7512 (tp-100) cc_final: 0.6969 (tm-30) REVERT: D 822 LEU cc_start: 0.8466 (mt) cc_final: 0.8248 (mt) REVERT: D 860 VAL cc_start: 0.9032 (t) cc_final: 0.8775 (p) REVERT: D 878 LEU cc_start: 0.9047 (mt) cc_final: 0.8835 (mt) REVERT: D 900 MET cc_start: 0.4882 (mpp) cc_final: 0.4500 (mpp) REVERT: D 954 HIS cc_start: 0.8362 (m170) cc_final: 0.8091 (m170) REVERT: D 960 ASN cc_start: 0.8127 (m110) cc_final: 0.7739 (m110) REVERT: D 1000 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7545 (mtt90) REVERT: D 1012 LEU cc_start: 0.9154 (mt) cc_final: 0.8855 (mt) REVERT: D 1013 ILE cc_start: 0.8686 (pt) cc_final: 0.8475 (pt) REVERT: D 1017 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 1023 ASN cc_start: 0.7424 (m-40) cc_final: 0.6715 (m-40) REVERT: D 1106 GLN cc_start: 0.8100 (pt0) cc_final: 0.7833 (pt0) REVERT: C 237 ARG cc_start: 0.8053 (tpm170) cc_final: 0.7742 (tpp-160) REVERT: C 270 LEU cc_start: 0.8175 (mt) cc_final: 0.7973 (mt) REVERT: C 287 ASP cc_start: 0.8432 (t70) cc_final: 0.8000 (t0) REVERT: C 290 ASP cc_start: 0.8092 (t0) cc_final: 0.7488 (t70) REVERT: C 294 ASP cc_start: 0.7772 (m-30) cc_final: 0.7551 (m-30) REVERT: C 314 GLN cc_start: 0.7907 (tt0) cc_final: 0.7555 (tm-30) REVERT: C 651 ILE cc_start: 0.6237 (mt) cc_final: 0.5930 (pt) REVERT: C 727 LEU cc_start: 0.8072 (mt) cc_final: 0.7782 (mt) REVERT: C 731 MET cc_start: 0.8123 (pmm) cc_final: 0.6996 (ppp) REVERT: C 740 MET cc_start: 0.6568 (tpt) cc_final: 0.5317 (tpt) REVERT: C 752 LEU cc_start: 0.9078 (mp) cc_final: 0.8807 (mp) REVERT: C 753 LEU cc_start: 0.8548 (mt) cc_final: 0.8297 (mt) REVERT: C 770 ILE cc_start: 0.9080 (mp) cc_final: 0.8866 (mp) REVERT: C 776 LYS cc_start: 0.8548 (tptt) cc_final: 0.7906 (tptt) REVERT: C 860 VAL cc_start: 0.8491 (t) cc_final: 0.8076 (p) REVERT: C 866 THR cc_start: 0.8015 (p) cc_final: 0.7767 (t) REVERT: C 869 MET cc_start: 0.7917 (ptm) cc_final: 0.7550 (ptm) REVERT: C 873 TYR cc_start: 0.7269 (m-80) cc_final: 0.7013 (m-80) REVERT: C 902 MET cc_start: 0.7006 (mtm) cc_final: 0.6700 (mtm) REVERT: C 955 ASN cc_start: 0.8651 (m-40) cc_final: 0.8404 (m-40) REVERT: C 969 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8838 (mmmt) REVERT: C 992 GLN cc_start: 0.8181 (mm110) cc_final: 0.7850 (mm110) REVERT: C 998 THR cc_start: 0.8558 (m) cc_final: 0.7668 (p) REVERT: C 1002 GLN cc_start: 0.8509 (mt0) cc_final: 0.7954 (mt0) REVERT: C 1010 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7742 (tp-100) REVERT: C 1013 ILE cc_start: 0.8890 (pt) cc_final: 0.8616 (pt) REVERT: C 1017 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8272 (mt-10) REVERT: C 1023 ASN cc_start: 0.7600 (m-40) cc_final: 0.7327 (m110) REVERT: C 1062 PHE cc_start: 0.7530 (m-80) cc_final: 0.7115 (t80) REVERT: B 56 LEU cc_start: 0.7507 (tp) cc_final: 0.7200 (tp) REVERT: B 177 MET cc_start: -0.4184 (tpt) cc_final: -0.4625 (mmm) REVERT: B 314 GLN cc_start: 0.8166 (tt0) cc_final: 0.7679 (tm-30) REVERT: B 565 PHE cc_start: 0.7458 (p90) cc_final: 0.7142 (p90) REVERT: B 731 MET cc_start: 0.8108 (ppp) cc_final: 0.7793 (tmm) REVERT: B 740 MET cc_start: 0.7009 (mmp) cc_final: 0.6743 (mmp) REVERT: B 772 VAL cc_start: 0.8848 (m) cc_final: 0.8508 (m) REVERT: B 775 ASP cc_start: 0.8359 (m-30) cc_final: 0.7893 (m-30) REVERT: B 780 GLU cc_start: 0.8150 (tp30) cc_final: 0.7492 (tp30) REVERT: B 820 ASP cc_start: 0.8314 (t70) cc_final: 0.8091 (t70) REVERT: B 861 LEU cc_start: 0.8296 (mm) cc_final: 0.7572 (tp) REVERT: B 964 LYS cc_start: 0.8516 (tttt) cc_final: 0.8310 (tttt) REVERT: B 985 ASP cc_start: 0.8263 (t0) cc_final: 0.7723 (t0) REVERT: B 1005 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 1050 MET cc_start: 0.5257 (mmt) cc_final: 0.4857 (mmt) REVERT: B 1089 PHE cc_start: 0.7205 (m-80) cc_final: 0.6899 (m-80) REVERT: B 1107 ARG cc_start: 0.8042 (ttp80) cc_final: 0.6584 (mpt180) REVERT: A 48 TRP cc_start: 0.6444 (t60) cc_final: 0.6047 (t60) REVERT: A 123 MET cc_start: -0.3866 (mmm) cc_final: -0.4795 (tpp) REVERT: A 297 MET cc_start: -0.2569 (ptp) cc_final: -0.2858 (ptp) REVERT: A 306 ARG cc_start: 0.6931 (ttt90) cc_final: 0.6616 (mmp-170) REVERT: A 366 MET cc_start: 0.6979 (tpt) cc_final: 0.5862 (ppp) REVERT: A 474 MET cc_start: 0.3195 (mmp) cc_final: 0.0204 (tpt) REVERT: A 480 MET cc_start: 0.5263 (ptt) cc_final: 0.4806 (ptt) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.4037 time to fit residues: 331.1491 Evaluate side-chains 448 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 163 optimal weight: 0.4980 chunk 284 optimal weight: 0.4980 chunk 286 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 211 optimal weight: 0.0010 chunk 227 optimal weight: 0.4980 chunk 351 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 357 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN D1088 HIS C 49 HIS C 928 ASN B1106 GLN A 241 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.192957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.155468 restraints weight = 101536.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.158783 restraints weight = 70380.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.161294 restraints weight = 52174.525| |-----------------------------------------------------------------------------| r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30279 Z= 0.092 Angle : 0.536 11.884 41192 Z= 0.267 Chirality : 0.043 0.241 4592 Planarity : 0.004 0.072 5321 Dihedral : 4.292 22.665 4011 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3691 helix: -0.23 (0.18), residues: 839 sheet: -0.25 (0.21), residues: 513 loop : -1.08 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.001 TRP A 461 HIS 0.008 0.001 HIS A 378 PHE 0.020 0.001 PHE A 308 TYR 0.022 0.001 TYR C1007 ARG 0.007 0.000 ARG D1091 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 712) hydrogen bonds : angle 4.88224 ( 2055) SS BOND : bond 0.00186 ( 42) SS BOND : angle 1.26164 ( 84) covalent geometry : bond 0.00201 (30237) covalent geometry : angle 0.53320 (41108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ILE cc_start: 0.7795 (mm) cc_final: 0.7552 (mm) REVERT: D 128 ILE cc_start: 0.6895 (mp) cc_final: 0.6292 (mp) REVERT: D 135 PHE cc_start: 0.6309 (m-10) cc_final: 0.5721 (m-80) REVERT: D 153 MET cc_start: 0.3214 (ppp) cc_final: 0.2361 (ppp) REVERT: D 177 MET cc_start: 0.2522 (ptp) cc_final: 0.0853 (ptm) REVERT: D 223 LEU cc_start: 0.8975 (mp) cc_final: 0.8643 (mp) REVERT: D 279 TYR cc_start: 0.8703 (m-80) cc_final: 0.8313 (m-80) REVERT: D 299 THR cc_start: 0.8805 (m) cc_final: 0.8544 (p) REVERT: D 571 ASP cc_start: 0.7414 (m-30) cc_final: 0.7092 (m-30) REVERT: D 655 TYR cc_start: 0.6997 (t80) cc_final: 0.6616 (t80) REVERT: D 740 MET cc_start: 0.7725 (tpt) cc_final: 0.7522 (tpt) REVERT: D 756 TYR cc_start: 0.7251 (m-80) cc_final: 0.6943 (m-80) REVERT: D 764 LYS cc_start: 0.9006 (mptt) cc_final: 0.8758 (mmtt) REVERT: D 779 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7138 (tm-30) REVERT: D 802 PHE cc_start: 0.7306 (m-10) cc_final: 0.7063 (m-10) REVERT: D 822 LEU cc_start: 0.8485 (mt) cc_final: 0.8272 (mt) REVERT: D 860 VAL cc_start: 0.9087 (t) cc_final: 0.8809 (p) REVERT: D 878 LEU cc_start: 0.9020 (mt) cc_final: 0.8800 (mt) REVERT: D 900 MET cc_start: 0.4736 (mpp) cc_final: 0.4293 (mpp) REVERT: D 960 ASN cc_start: 0.8144 (m110) cc_final: 0.7730 (m110) REVERT: D 1000 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7718 (mtt90) REVERT: D 1001 LEU cc_start: 0.9012 (mm) cc_final: 0.8788 (mm) REVERT: D 1010 GLN cc_start: 0.8201 (pt0) cc_final: 0.7795 (pt0) REVERT: D 1012 LEU cc_start: 0.9140 (mt) cc_final: 0.8850 (mt) REVERT: D 1013 ILE cc_start: 0.8760 (pt) cc_final: 0.8515 (pt) REVERT: D 1017 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 1023 ASN cc_start: 0.7373 (m-40) cc_final: 0.6742 (m-40) REVERT: D 1106 GLN cc_start: 0.8217 (pt0) cc_final: 0.7914 (pt0) REVERT: D 1125 ASN cc_start: 0.6361 (p0) cc_final: 0.5930 (p0) REVERT: C 237 ARG cc_start: 0.8011 (tpm170) cc_final: 0.7699 (tpp-160) REVERT: C 287 ASP cc_start: 0.8433 (t70) cc_final: 0.7973 (t0) REVERT: C 290 ASP cc_start: 0.8002 (t0) cc_final: 0.7701 (t0) REVERT: C 294 ASP cc_start: 0.7771 (m-30) cc_final: 0.7539 (m-30) REVERT: C 651 ILE cc_start: 0.6247 (mt) cc_final: 0.5968 (pt) REVERT: C 740 MET cc_start: 0.6779 (tpt) cc_final: 0.5866 (tpt) REVERT: C 747 THR cc_start: 0.8610 (m) cc_final: 0.8323 (t) REVERT: C 752 LEU cc_start: 0.9154 (mp) cc_final: 0.8891 (mp) REVERT: C 753 LEU cc_start: 0.8562 (mt) cc_final: 0.8226 (mt) REVERT: C 775 ASP cc_start: 0.8079 (m-30) cc_final: 0.7780 (m-30) REVERT: C 776 LYS cc_start: 0.8438 (tptt) cc_final: 0.7826 (tptt) REVERT: C 784 GLN cc_start: 0.8676 (pm20) cc_final: 0.8441 (pm20) REVERT: C 820 ASP cc_start: 0.7918 (t0) cc_final: 0.7699 (t0) REVERT: C 860 VAL cc_start: 0.8494 (t) cc_final: 0.8093 (p) REVERT: C 873 TYR cc_start: 0.7210 (m-80) cc_final: 0.6988 (m-80) REVERT: C 902 MET cc_start: 0.7070 (mtm) cc_final: 0.6772 (mtm) REVERT: C 928 ASN cc_start: 0.8187 (m-40) cc_final: 0.7901 (m110) REVERT: C 955 ASN cc_start: 0.8711 (m-40) cc_final: 0.8505 (m-40) REVERT: C 960 ASN cc_start: 0.8608 (m110) cc_final: 0.8394 (m110) REVERT: C 969 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8857 (mmmt) REVERT: C 992 GLN cc_start: 0.8231 (mm110) cc_final: 0.8024 (mp10) REVERT: C 998 THR cc_start: 0.8613 (m) cc_final: 0.7710 (p) REVERT: C 1002 GLN cc_start: 0.8491 (mt0) cc_final: 0.7971 (mt0) REVERT: C 1010 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7775 (tp-100) REVERT: C 1013 ILE cc_start: 0.8888 (pt) cc_final: 0.8581 (pt) REVERT: C 1017 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 1019 ARG cc_start: 0.8320 (mmm160) cc_final: 0.8112 (mmm160) REVERT: C 1023 ASN cc_start: 0.7667 (m-40) cc_final: 0.7394 (m110) REVERT: C 1062 PHE cc_start: 0.7541 (m-80) cc_final: 0.6981 (t80) REVERT: C 1109 PHE cc_start: 0.7809 (p90) cc_final: 0.7547 (p90) REVERT: B 56 LEU cc_start: 0.7579 (tp) cc_final: 0.7277 (tp) REVERT: B 177 MET cc_start: -0.3942 (tpt) cc_final: -0.4371 (mmm) REVERT: B 314 GLN cc_start: 0.8206 (tt0) cc_final: 0.7715 (tm-30) REVERT: B 386 LYS cc_start: 0.9000 (tptp) cc_final: 0.8686 (mtpt) REVERT: B 565 PHE cc_start: 0.7442 (p90) cc_final: 0.7077 (p90) REVERT: B 731 MET cc_start: 0.8169 (ppp) cc_final: 0.7809 (tmm) REVERT: B 775 ASP cc_start: 0.8318 (m-30) cc_final: 0.8056 (m-30) REVERT: B 861 LEU cc_start: 0.8340 (mm) cc_final: 0.7695 (tp) REVERT: B 964 LYS cc_start: 0.8611 (tttt) cc_final: 0.8307 (tttt) REVERT: B 985 ASP cc_start: 0.8284 (t0) cc_final: 0.7774 (t0) REVERT: B 1005 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 1006 THR cc_start: 0.8658 (p) cc_final: 0.7982 (p) REVERT: B 1019 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7947 (ptm160) REVERT: B 1050 MET cc_start: 0.5474 (mmt) cc_final: 0.5093 (mmt) REVERT: B 1089 PHE cc_start: 0.7295 (m-80) cc_final: 0.7056 (m-80) REVERT: B 1107 ARG cc_start: 0.7999 (ttp80) cc_final: 0.6590 (mpt180) REVERT: A 48 TRP cc_start: 0.6443 (t60) cc_final: 0.6029 (t60) REVERT: A 123 MET cc_start: -0.3674 (mmm) cc_final: -0.4688 (tpp) REVERT: A 297 MET cc_start: -0.2648 (ptp) cc_final: -0.2953 (ptp) REVERT: A 306 ARG cc_start: 0.6949 (ttt90) cc_final: 0.6643 (mmp-170) REVERT: A 366 MET cc_start: 0.6877 (tpt) cc_final: 0.5825 (ppp) REVERT: A 474 MET cc_start: 0.3428 (mmp) cc_final: 0.0058 (tpt) REVERT: A 480 MET cc_start: 0.5173 (ptt) cc_final: 0.4798 (ptt) outliers start: 1 outliers final: 0 residues processed: 501 average time/residue: 0.4434 time to fit residues: 359.5151 Evaluate side-chains 447 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 281 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 213 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN D 115 GLN D 370 ASN ** D 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 394 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN A 102 GLN A 277 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.182396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.145146 restraints weight = 98833.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.148340 restraints weight = 68527.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.150915 restraints weight = 50868.889| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 30279 Z= 0.224 Angle : 0.736 13.970 41192 Z= 0.382 Chirality : 0.048 0.271 4592 Planarity : 0.006 0.073 5321 Dihedral : 5.254 23.798 4011 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3691 helix: -0.62 (0.17), residues: 846 sheet: -0.63 (0.21), residues: 521 loop : -1.16 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 461 HIS 0.010 0.002 HIS A 378 PHE 0.026 0.002 PHE D 970 TYR 0.035 0.002 TYR A 385 ARG 0.012 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 712) hydrogen bonds : angle 5.72243 ( 2055) SS BOND : bond 0.00469 ( 42) SS BOND : angle 1.69731 ( 84) covalent geometry : bond 0.00473 (30237) covalent geometry : angle 0.73324 (41108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ILE cc_start: 0.8359 (mm) cc_final: 0.8067 (mm) REVERT: D 153 MET cc_start: 0.4325 (ppp) cc_final: 0.3374 (ppp) REVERT: D 223 LEU cc_start: 0.8978 (mp) cc_final: 0.8436 (tp) REVERT: D 279 TYR cc_start: 0.8982 (m-80) cc_final: 0.8534 (m-10) REVERT: D 571 ASP cc_start: 0.8091 (m-30) cc_final: 0.7890 (m-30) REVERT: D 612 TYR cc_start: 0.4869 (t80) cc_final: 0.4430 (t80) REVERT: D 740 MET cc_start: 0.8260 (tpt) cc_final: 0.7917 (tpt) REVERT: D 756 TYR cc_start: 0.7717 (m-80) cc_final: 0.7512 (m-80) REVERT: D 802 PHE cc_start: 0.8084 (m-10) cc_final: 0.7728 (m-10) REVERT: D 822 LEU cc_start: 0.8759 (mt) cc_final: 0.8541 (mt) REVERT: D 878 LEU cc_start: 0.9100 (mt) cc_final: 0.8874 (mt) REVERT: D 954 HIS cc_start: 0.8597 (m170) cc_final: 0.8303 (m170) REVERT: D 960 ASN cc_start: 0.8525 (m110) cc_final: 0.8170 (m110) REVERT: D 1000 ARG cc_start: 0.8477 (mtt180) cc_final: 0.8230 (mtt90) REVERT: D 1001 LEU cc_start: 0.9133 (mm) cc_final: 0.8666 (mm) REVERT: D 1005 GLN cc_start: 0.8502 (pt0) cc_final: 0.8035 (pt0) REVERT: D 1006 THR cc_start: 0.8671 (t) cc_final: 0.8398 (t) REVERT: D 1010 GLN cc_start: 0.8323 (pt0) cc_final: 0.8033 (pt0) REVERT: D 1012 LEU cc_start: 0.9254 (mt) cc_final: 0.8893 (mt) REVERT: D 1017 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8220 (mt-10) REVERT: D 1019 ARG cc_start: 0.8526 (tpt90) cc_final: 0.8243 (mmm160) REVERT: D 1023 ASN cc_start: 0.7858 (m-40) cc_final: 0.7403 (m-40) REVERT: D 1030 SER cc_start: 0.8426 (m) cc_final: 0.7937 (t) REVERT: D 1054 GLN cc_start: 0.6149 (mm-40) cc_final: 0.5837 (mm-40) REVERT: C 290 ASP cc_start: 0.8134 (t0) cc_final: 0.7793 (t0) REVERT: C 294 ASP cc_start: 0.7871 (m-30) cc_final: 0.7669 (m-30) REVERT: C 314 GLN cc_start: 0.8385 (pt0) cc_final: 0.8140 (tm-30) REVERT: C 651 ILE cc_start: 0.5959 (mt) cc_final: 0.5659 (pt) REVERT: C 740 MET cc_start: 0.7199 (tpt) cc_final: 0.6073 (tpt) REVERT: C 753 LEU cc_start: 0.8527 (mt) cc_final: 0.8197 (mt) REVERT: C 775 ASP cc_start: 0.8601 (m-30) cc_final: 0.8384 (m-30) REVERT: C 860 VAL cc_start: 0.8594 (t) cc_final: 0.8234 (p) REVERT: C 902 MET cc_start: 0.7418 (mtm) cc_final: 0.6989 (mtm) REVERT: C 950 ASP cc_start: 0.8521 (p0) cc_final: 0.7905 (p0) REVERT: C 960 ASN cc_start: 0.8772 (m110) cc_final: 0.8539 (m110) REVERT: C 992 GLN cc_start: 0.8587 (mm110) cc_final: 0.8328 (mm110) REVERT: C 998 THR cc_start: 0.8885 (m) cc_final: 0.8100 (m) REVERT: C 1002 GLN cc_start: 0.8720 (mt0) cc_final: 0.8269 (mt0) REVERT: C 1010 GLN cc_start: 0.8493 (tp-100) cc_final: 0.7771 (tp40) REVERT: C 1013 ILE cc_start: 0.9192 (pt) cc_final: 0.8977 (pt) REVERT: C 1017 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 1023 ASN cc_start: 0.8165 (m-40) cc_final: 0.7831 (m110) REVERT: C 1075 PHE cc_start: 0.7218 (m-10) cc_final: 0.6981 (m-10) REVERT: C 1109 PHE cc_start: 0.8351 (p90) cc_final: 0.7911 (p90) REVERT: B 56 LEU cc_start: 0.8163 (tp) cc_final: 0.7958 (tp) REVERT: B 64 TRP cc_start: 0.6504 (t-100) cc_final: 0.6174 (t-100) REVERT: B 273 ARG cc_start: 0.8230 (ptt180) cc_final: 0.7617 (ptt180) REVERT: B 280 ASN cc_start: 0.8585 (t0) cc_final: 0.8292 (t0) REVERT: B 303 LEU cc_start: 0.8941 (tt) cc_final: 0.8737 (tt) REVERT: B 313 TYR cc_start: 0.7729 (m-80) cc_final: 0.7388 (m-80) REVERT: B 314 GLN cc_start: 0.8392 (tt0) cc_final: 0.7760 (tm-30) REVERT: B 568 ASP cc_start: 0.8617 (t0) cc_final: 0.8334 (t0) REVERT: B 725 GLU cc_start: 0.7271 (pt0) cc_final: 0.6612 (pt0) REVERT: B 731 MET cc_start: 0.8186 (ppp) cc_final: 0.7864 (tmm) REVERT: B 738 CYS cc_start: 0.5989 (p) cc_final: 0.5024 (p) REVERT: B 763 LEU cc_start: 0.9211 (pp) cc_final: 0.8981 (pp) REVERT: B 764 LYS cc_start: 0.9118 (mmtp) cc_final: 0.8671 (mmtp) REVERT: B 775 ASP cc_start: 0.8604 (m-30) cc_final: 0.8288 (m-30) REVERT: B 802 PHE cc_start: 0.6069 (m-10) cc_final: 0.5868 (m-10) REVERT: B 935 GLN cc_start: 0.8144 (tp40) cc_final: 0.7813 (tm-30) REVERT: B 957 GLN cc_start: 0.8604 (tp40) cc_final: 0.8390 (tp40) REVERT: B 964 LYS cc_start: 0.8755 (tttt) cc_final: 0.8515 (tttt) REVERT: B 994 ASP cc_start: 0.8352 (m-30) cc_final: 0.8136 (m-30) REVERT: B 1005 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 1006 THR cc_start: 0.8957 (p) cc_final: 0.8337 (p) REVERT: B 1017 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 1081 ILE cc_start: 0.8401 (mm) cc_final: 0.8108 (tp) REVERT: B 1089 PHE cc_start: 0.6964 (m-80) cc_final: 0.6626 (m-80) REVERT: B 1107 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7065 (mpt180) REVERT: A 48 TRP cc_start: 0.6825 (t60) cc_final: 0.6582 (t60) REVERT: A 82 MET cc_start: 0.6286 (pmm) cc_final: 0.6055 (pmm) REVERT: A 123 MET cc_start: -0.3334 (mmm) cc_final: -0.4735 (tpp) REVERT: A 189 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 297 MET cc_start: -0.2631 (ptp) cc_final: -0.3049 (ptp) REVERT: A 323 MET cc_start: 0.5842 (ppp) cc_final: 0.3764 (pmm) REVERT: A 366 MET cc_start: 0.6981 (tpt) cc_final: 0.5868 (ppp) REVERT: A 474 MET cc_start: 0.4617 (mmp) cc_final: 0.1278 (tpt) REVERT: A 480 MET cc_start: 0.5320 (ptt) cc_final: 0.4942 (ptt) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4772 time to fit residues: 411.9061 Evaluate side-chains 466 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 90 optimal weight: 0.9990 chunk 368 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 chunk 43 optimal weight: 50.0000 chunk 272 optimal weight: 5.9990 chunk 240 optimal weight: 0.3980 chunk 226 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 88 optimal weight: 0.0470 chunk 313 optimal weight: 8.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1011 GLN D1088 HIS ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 616 ASN B 824 ASN B 955 ASN B1106 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.187956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.150364 restraints weight = 100405.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.153571 restraints weight = 69122.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.155912 restraints weight = 51094.266| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30279 Z= 0.110 Angle : 0.593 12.106 41192 Z= 0.299 Chirality : 0.045 0.187 4592 Planarity : 0.004 0.076 5321 Dihedral : 4.650 27.977 4011 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3691 helix: -0.36 (0.18), residues: 839 sheet: -0.43 (0.22), residues: 507 loop : -1.07 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 461 HIS 0.007 0.001 HIS A 378 PHE 0.018 0.001 PHE C1042 TYR 0.026 0.001 TYR D 313 ARG 0.012 0.001 ARG D1091 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 712) hydrogen bonds : angle 5.10169 ( 2055) SS BOND : bond 0.00636 ( 42) SS BOND : angle 1.56938 ( 84) covalent geometry : bond 0.00245 (30237) covalent geometry : angle 0.58974 (41108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 3.339 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: D 100 ILE cc_start: 0.8044 (mm) cc_final: 0.7762 (mm) REVERT: D 135 PHE cc_start: 0.6370 (m-80) cc_final: 0.5974 (m-80) REVERT: D 153 MET cc_start: 0.4449 (ppp) cc_final: 0.3542 (ppp) REVERT: D 177 MET cc_start: 0.3181 (ptp) cc_final: 0.2402 (ptm) REVERT: D 223 LEU cc_start: 0.8805 (mp) cc_final: 0.8321 (tp) REVERT: D 279 TYR cc_start: 0.8822 (m-80) cc_final: 0.8589 (m-10) REVERT: D 299 THR cc_start: 0.8974 (m) cc_final: 0.8585 (p) REVERT: D 309 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7572 (mp0) REVERT: D 612 TYR cc_start: 0.5120 (t80) cc_final: 0.4860 (t80) REVERT: D 760 CYS cc_start: 0.5396 (m) cc_final: 0.5119 (m) REVERT: D 764 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8633 (mmtt) REVERT: D 779 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7274 (tm-30) REVERT: D 822 LEU cc_start: 0.8596 (mt) cc_final: 0.8356 (mt) REVERT: D 874 THR cc_start: 0.8907 (p) cc_final: 0.8645 (p) REVERT: D 900 MET cc_start: 0.4999 (mpp) cc_final: 0.4763 (mpp) REVERT: D 954 HIS cc_start: 0.8421 (m170) cc_final: 0.8111 (m170) REVERT: D 960 ASN cc_start: 0.8281 (m110) cc_final: 0.7915 (m110) REVERT: D 1000 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7979 (mtt90) REVERT: D 1001 LEU cc_start: 0.8970 (mm) cc_final: 0.8751 (mm) REVERT: D 1006 THR cc_start: 0.8393 (t) cc_final: 0.8132 (t) REVERT: D 1010 GLN cc_start: 0.8207 (pt0) cc_final: 0.7850 (pt0) REVERT: D 1012 LEU cc_start: 0.9127 (mt) cc_final: 0.8765 (mt) REVERT: D 1013 ILE cc_start: 0.8801 (pt) cc_final: 0.8566 (pt) REVERT: D 1017 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 1019 ARG cc_start: 0.8408 (tpt90) cc_final: 0.8086 (mmm160) REVERT: D 1023 ASN cc_start: 0.7830 (m-40) cc_final: 0.7225 (m-40) REVERT: D 1030 SER cc_start: 0.8149 (m) cc_final: 0.7683 (p) REVERT: D 1054 GLN cc_start: 0.5851 (mm-40) cc_final: 0.5594 (mm-40) REVERT: D 1125 ASN cc_start: 0.6804 (p0) cc_final: 0.6208 (p0) REVERT: C 237 ARG cc_start: 0.8197 (tpm170) cc_final: 0.7234 (mmm160) REVERT: C 287 ASP cc_start: 0.8298 (t0) cc_final: 0.7996 (t0) REVERT: C 294 ASP cc_start: 0.7801 (m-30) cc_final: 0.7584 (m-30) REVERT: C 314 GLN cc_start: 0.8393 (pt0) cc_final: 0.7958 (tm-30) REVERT: C 651 ILE cc_start: 0.5983 (mt) cc_final: 0.5679 (pt) REVERT: C 740 MET cc_start: 0.6926 (tpt) cc_final: 0.6231 (tpp) REVERT: C 753 LEU cc_start: 0.8593 (mt) cc_final: 0.8213 (mt) REVERT: C 860 VAL cc_start: 0.8507 (t) cc_final: 0.8140 (p) REVERT: C 872 GLN cc_start: 0.8128 (pt0) cc_final: 0.7824 (pm20) REVERT: C 902 MET cc_start: 0.7220 (mtm) cc_final: 0.6792 (mtm) REVERT: C 950 ASP cc_start: 0.8359 (p0) cc_final: 0.8101 (p0) REVERT: C 951 VAL cc_start: 0.8971 (m) cc_final: 0.8627 (p) REVERT: C 955 ASN cc_start: 0.8702 (m-40) cc_final: 0.8491 (m-40) REVERT: C 960 ASN cc_start: 0.8756 (m110) cc_final: 0.8542 (m110) REVERT: C 1002 GLN cc_start: 0.8576 (mt0) cc_final: 0.8109 (mt0) REVERT: C 1010 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7554 (tp40) REVERT: C 1013 ILE cc_start: 0.9005 (pt) cc_final: 0.8720 (pt) REVERT: C 1017 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 1023 ASN cc_start: 0.7945 (m-40) cc_final: 0.7674 (m110) REVERT: C 1075 PHE cc_start: 0.7020 (m-10) cc_final: 0.6733 (m-10) REVERT: C 1109 PHE cc_start: 0.8162 (p90) cc_final: 0.7775 (p90) REVERT: B 56 LEU cc_start: 0.7934 (tp) cc_final: 0.7541 (tp) REVERT: B 202 LYS cc_start: 0.7883 (tptt) cc_final: 0.7110 (tppt) REVERT: B 273 ARG cc_start: 0.7567 (ptt180) cc_final: 0.7036 (ptt180) REVERT: B 275 PHE cc_start: 0.7220 (m-10) cc_final: 0.6537 (m-10) REVERT: B 278 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7850 (tptt) REVERT: B 280 ASN cc_start: 0.8482 (t0) cc_final: 0.8225 (t0) REVERT: B 303 LEU cc_start: 0.8929 (tt) cc_final: 0.8704 (tt) REVERT: B 313 TYR cc_start: 0.7583 (m-80) cc_final: 0.7295 (m-80) REVERT: B 314 GLN cc_start: 0.8366 (tt0) cc_final: 0.7673 (tm-30) REVERT: B 386 LYS cc_start: 0.9096 (tptp) cc_final: 0.8824 (mtpt) REVERT: B 565 PHE cc_start: 0.7567 (p90) cc_final: 0.7004 (p90) REVERT: B 731 MET cc_start: 0.8148 (ppp) cc_final: 0.7812 (tmm) REVERT: B 734 THR cc_start: 0.8697 (t) cc_final: 0.8455 (m) REVERT: B 738 CYS cc_start: 0.5433 (p) cc_final: 0.4541 (p) REVERT: B 763 LEU cc_start: 0.9153 (pp) cc_final: 0.8938 (pp) REVERT: B 764 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8633 (mmtp) REVERT: B 775 ASP cc_start: 0.8446 (m-30) cc_final: 0.7992 (m-30) REVERT: B 802 PHE cc_start: 0.5685 (m-10) cc_final: 0.5478 (m-10) REVERT: B 861 LEU cc_start: 0.8465 (mm) cc_final: 0.8114 (tp) REVERT: B 935 GLN cc_start: 0.8039 (tp40) cc_final: 0.7802 (tp40) REVERT: B 957 GLN cc_start: 0.8506 (tp40) cc_final: 0.8276 (tp40) REVERT: B 964 LYS cc_start: 0.8705 (tttt) cc_final: 0.8462 (tttt) REVERT: B 1005 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 1006 THR cc_start: 0.8724 (p) cc_final: 0.8074 (p) REVERT: B 1017 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 1019 ARG cc_start: 0.8514 (ptm160) cc_final: 0.7693 (ptp-110) REVERT: B 1089 PHE cc_start: 0.6901 (m-80) cc_final: 0.6394 (m-80) REVERT: B 1107 ARG cc_start: 0.8038 (ttp80) cc_final: 0.6948 (mpt180) REVERT: A 48 TRP cc_start: 0.6741 (t60) cc_final: 0.6376 (t60) REVERT: A 82 MET cc_start: 0.6178 (pmm) cc_final: 0.5937 (pmm) REVERT: A 123 MET cc_start: -0.2225 (mmm) cc_final: -0.3517 (tpp) REVERT: A 297 MET cc_start: -0.2413 (ptp) cc_final: -0.2963 (ptp) REVERT: A 366 MET cc_start: 0.7042 (tpt) cc_final: 0.5994 (ppp) REVERT: A 474 MET cc_start: 0.5126 (mmp) cc_final: 0.2119 (tpt) REVERT: A 480 MET cc_start: 0.5808 (ptt) cc_final: 0.5481 (ptt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.3987 time to fit residues: 330.0234 Evaluate side-chains 462 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 220 optimal weight: 0.5980 chunk 235 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 chunk 190 optimal weight: 0.0040 chunk 337 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 363 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1011 GLN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.184491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.147212 restraints weight = 98734.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.150420 restraints weight = 68069.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.152847 restraints weight = 50877.062| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30279 Z= 0.146 Angle : 0.614 11.815 41192 Z= 0.313 Chirality : 0.046 0.264 4592 Planarity : 0.005 0.071 5321 Dihedral : 4.724 25.425 4011 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3691 helix: -0.37 (0.18), residues: 838 sheet: -0.57 (0.21), residues: 521 loop : -1.05 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 461 HIS 0.007 0.001 HIS A 374 PHE 0.027 0.002 PHE C 927 TYR 0.023 0.001 TYR A 385 ARG 0.008 0.001 ARG D1091 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 712) hydrogen bonds : angle 5.24496 ( 2055) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.53567 ( 84) covalent geometry : bond 0.00316 (30237) covalent geometry : angle 0.61064 (41108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 3.125 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: D 135 PHE cc_start: 0.6361 (m-80) cc_final: 0.5916 (m-80) REVERT: D 153 MET cc_start: 0.4572 (ppp) cc_final: 0.3555 (ppp) REVERT: D 177 MET cc_start: 0.3334 (ptp) cc_final: 0.2766 (ptm) REVERT: D 223 LEU cc_start: 0.8791 (mp) cc_final: 0.8321 (tp) REVERT: D 279 TYR cc_start: 0.8899 (m-80) cc_final: 0.8566 (m-10) REVERT: D 299 THR cc_start: 0.8907 (m) cc_final: 0.8518 (p) REVERT: D 309 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7600 (mp0) REVERT: D 612 TYR cc_start: 0.5034 (t80) cc_final: 0.4801 (t80) REVERT: D 756 TYR cc_start: 0.7663 (m-10) cc_final: 0.7451 (m-80) REVERT: D 763 LEU cc_start: 0.8644 (mt) cc_final: 0.8393 (mt) REVERT: D 779 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7475 (tm-30) REVERT: D 802 PHE cc_start: 0.7845 (m-10) cc_final: 0.7499 (m-10) REVERT: D 822 LEU cc_start: 0.8678 (mt) cc_final: 0.8450 (mt) REVERT: D 860 VAL cc_start: 0.9137 (t) cc_final: 0.8928 (p) REVERT: D 874 THR cc_start: 0.8939 (p) cc_final: 0.8737 (p) REVERT: D 878 LEU cc_start: 0.8935 (mt) cc_final: 0.8728 (mt) REVERT: D 954 HIS cc_start: 0.8515 (m170) cc_final: 0.8210 (m170) REVERT: D 960 ASN cc_start: 0.8459 (m110) cc_final: 0.8077 (m110) REVERT: D 1000 ARG cc_start: 0.8372 (mtt180) cc_final: 0.8162 (mtt180) REVERT: D 1001 LEU cc_start: 0.9104 (mm) cc_final: 0.8770 (mm) REVERT: D 1005 GLN cc_start: 0.8318 (pt0) cc_final: 0.7851 (pt0) REVERT: D 1010 GLN cc_start: 0.8284 (pt0) cc_final: 0.7911 (pt0) REVERT: D 1012 LEU cc_start: 0.9186 (mt) cc_final: 0.8847 (mt) REVERT: D 1017 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 1019 ARG cc_start: 0.8471 (tpt90) cc_final: 0.8160 (tpt90) REVERT: D 1023 ASN cc_start: 0.8016 (m-40) cc_final: 0.7745 (m-40) REVERT: D 1028 LYS cc_start: 0.8445 (pttm) cc_final: 0.7515 (tttt) REVERT: D 1054 GLN cc_start: 0.5834 (mm-40) cc_final: 0.5563 (mm-40) REVERT: D 1125 ASN cc_start: 0.6736 (p0) cc_final: 0.6380 (p0) REVERT: C 287 ASP cc_start: 0.8396 (t0) cc_final: 0.7967 (t0) REVERT: C 294 ASP cc_start: 0.7829 (m-30) cc_final: 0.7597 (m-30) REVERT: C 314 GLN cc_start: 0.8405 (pt0) cc_final: 0.8078 (tm-30) REVERT: C 651 ILE cc_start: 0.5959 (mt) cc_final: 0.5699 (pt) REVERT: C 731 MET cc_start: 0.7968 (pmm) cc_final: 0.7178 (ppp) REVERT: C 733 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8095 (tmtt) REVERT: C 740 MET cc_start: 0.7483 (tpt) cc_final: 0.6308 (tpp) REVERT: C 753 LEU cc_start: 0.8614 (mt) cc_final: 0.8208 (mt) REVERT: C 860 VAL cc_start: 0.8580 (t) cc_final: 0.8225 (p) REVERT: C 861 LEU cc_start: 0.9133 (mm) cc_final: 0.8830 (mm) REVERT: C 902 MET cc_start: 0.7362 (mtm) cc_final: 0.6983 (mtm) REVERT: C 914 ASN cc_start: 0.7452 (t0) cc_final: 0.7243 (t0) REVERT: C 928 ASN cc_start: 0.8472 (m110) cc_final: 0.8269 (m-40) REVERT: C 935 GLN cc_start: 0.8139 (mp10) cc_final: 0.7938 (mp10) REVERT: C 950 ASP cc_start: 0.8363 (p0) cc_final: 0.7841 (p0) REVERT: C 951 VAL cc_start: 0.9033 (m) cc_final: 0.8638 (p) REVERT: C 954 HIS cc_start: 0.7880 (m90) cc_final: 0.7617 (m90) REVERT: C 955 ASN cc_start: 0.8841 (m-40) cc_final: 0.8558 (m-40) REVERT: C 998 THR cc_start: 0.8859 (m) cc_final: 0.8090 (m) REVERT: C 1002 GLN cc_start: 0.8648 (mt0) cc_final: 0.8260 (mt0) REVERT: C 1010 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7687 (tp40) REVERT: C 1013 ILE cc_start: 0.9111 (pt) cc_final: 0.8880 (pt) REVERT: C 1017 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 1023 ASN cc_start: 0.8062 (m-40) cc_final: 0.7820 (m110) REVERT: C 1062 PHE cc_start: 0.7718 (m-80) cc_final: 0.7374 (m-80) REVERT: C 1075 PHE cc_start: 0.6998 (m-10) cc_final: 0.6780 (m-10) REVERT: C 1109 PHE cc_start: 0.8231 (p90) cc_final: 0.7830 (p90) REVERT: B 49 HIS cc_start: 0.8164 (t-90) cc_final: 0.7964 (t-90) REVERT: B 56 LEU cc_start: 0.8047 (tp) cc_final: 0.7633 (tp) REVERT: B 189 LEU cc_start: 0.8674 (pp) cc_final: 0.8434 (mm) REVERT: B 202 LYS cc_start: 0.7937 (tptt) cc_final: 0.7170 (mttm) REVERT: B 273 ARG cc_start: 0.7883 (ptt180) cc_final: 0.7402 (ptt180) REVERT: B 275 PHE cc_start: 0.7352 (m-10) cc_final: 0.6560 (m-10) REVERT: B 278 LYS cc_start: 0.8419 (tmtt) cc_final: 0.8069 (tptt) REVERT: B 280 ASN cc_start: 0.8423 (t0) cc_final: 0.8205 (t0) REVERT: B 303 LEU cc_start: 0.8943 (tt) cc_final: 0.8713 (tt) REVERT: B 313 TYR cc_start: 0.7654 (m-80) cc_final: 0.7332 (m-80) REVERT: B 314 GLN cc_start: 0.8371 (tt0) cc_final: 0.7778 (tm-30) REVERT: B 386 LYS cc_start: 0.9068 (tptp) cc_final: 0.8794 (mtpt) REVERT: B 565 PHE cc_start: 0.7652 (p90) cc_final: 0.7211 (p90) REVERT: B 731 MET cc_start: 0.8241 (ppp) cc_final: 0.7866 (tmm) REVERT: B 738 CYS cc_start: 0.5548 (p) cc_final: 0.4620 (p) REVERT: B 752 LEU cc_start: 0.8681 (mp) cc_final: 0.8411 (mt) REVERT: B 763 LEU cc_start: 0.9179 (pp) cc_final: 0.8947 (pp) REVERT: B 764 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8665 (mmtp) REVERT: B 861 LEU cc_start: 0.8674 (mm) cc_final: 0.8287 (tp) REVERT: B 919 ASN cc_start: 0.7108 (p0) cc_final: 0.6747 (p0) REVERT: B 935 GLN cc_start: 0.8123 (tp40) cc_final: 0.7821 (tm-30) REVERT: B 949 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7631 (tp-100) REVERT: B 957 GLN cc_start: 0.8629 (tp40) cc_final: 0.8360 (tp-100) REVERT: B 964 LYS cc_start: 0.8863 (tttt) cc_final: 0.8604 (tttt) REVERT: B 984 LEU cc_start: 0.6517 (tp) cc_final: 0.6036 (tp) REVERT: B 985 ASP cc_start: 0.8829 (t0) cc_final: 0.8604 (t0) REVERT: B 992 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8217 (mm-40) REVERT: B 994 ASP cc_start: 0.8339 (m-30) cc_final: 0.8119 (m-30) REVERT: B 1005 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 1006 THR cc_start: 0.8829 (p) cc_final: 0.8169 (p) REVERT: B 1019 ARG cc_start: 0.8634 (ptm160) cc_final: 0.7875 (ptm160) REVERT: B 1089 PHE cc_start: 0.7003 (m-80) cc_final: 0.6294 (m-80) REVERT: B 1107 ARG cc_start: 0.8236 (ttp80) cc_final: 0.6886 (mpt180) REVERT: A 48 TRP cc_start: 0.6715 (t60) cc_final: 0.6365 (t60) REVERT: A 82 MET cc_start: 0.6289 (pmm) cc_final: 0.6038 (pmm) REVERT: A 123 MET cc_start: -0.5884 (mmm) cc_final: -0.7092 (mmm) REVERT: A 189 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 297 MET cc_start: -0.2733 (ptp) cc_final: -0.3168 (ptp) REVERT: A 323 MET cc_start: 0.6152 (ppp) cc_final: 0.5885 (ppp) REVERT: A 366 MET cc_start: 0.7064 (tpt) cc_final: 0.5991 (ppp) REVERT: A 474 MET cc_start: 0.5068 (mmp) cc_final: 0.2674 (tpt) REVERT: A 480 MET cc_start: 0.5749 (ptt) cc_final: 0.5459 (ptt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.4239 time to fit residues: 352.8377 Evaluate side-chains 464 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 24 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 564 GLN D1011 GLN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 928 ASN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** 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 = 0.4810 r_free = 0.4810 target = 0.186224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.148830 restraints weight = 100189.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.152126 restraints weight = 69290.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.154482 restraints weight = 51256.070| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30279 Z= 0.110 Angle : 0.581 11.780 41192 Z= 0.293 Chirality : 0.045 0.272 4592 Planarity : 0.004 0.074 5321 Dihedral : 4.547 33.700 4011 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3691 helix: -0.22 (0.18), residues: 840 sheet: -0.54 (0.22), residues: 495 loop : -1.06 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 461 HIS 0.008 0.001 HIS A 378 PHE 0.029 0.001 PHE C 927 TYR 0.020 0.001 TYR B 501 ARG 0.012 0.001 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 712) hydrogen bonds : angle 5.09405 ( 2055) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.36923 ( 84) covalent geometry : bond 0.00244 (30237) covalent geometry : angle 0.57870 (41108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7382 Ramachandran restraints generated. 3691 Oldfield, 0 Emsley, 3691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 522 time to evaluate : 3.116 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: D 128 ILE cc_start: 0.7475 (mp) cc_final: 0.6496 (mp) REVERT: D 177 MET cc_start: 0.3330 (ptp) cc_final: 0.1123 (ptm) REVERT: D 223 LEU cc_start: 0.8743 (mp) cc_final: 0.8276 (tp) REVERT: D 279 TYR cc_start: 0.8878 (m-80) cc_final: 0.8522 (m-10) REVERT: D 299 THR cc_start: 0.8938 (m) cc_final: 0.8529 (p) REVERT: D 309 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7578 (mp0) REVERT: D 779 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7490 (tm-30) REVERT: D 802 PHE cc_start: 0.7695 (m-10) cc_final: 0.7438 (m-10) REVERT: D 822 LEU cc_start: 0.8635 (mt) cc_final: 0.8420 (mt) REVERT: D 874 THR cc_start: 0.8904 (p) cc_final: 0.8696 (p) REVERT: D 878 LEU cc_start: 0.8877 (mt) cc_final: 0.8650 (mt) REVERT: D 900 MET cc_start: 0.4835 (mpp) cc_final: 0.4601 (mpp) REVERT: D 954 HIS cc_start: 0.8462 (m170) cc_final: 0.8151 (m170) REVERT: D 960 ASN cc_start: 0.8407 (m110) cc_final: 0.8058 (m110) REVERT: D 1000 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8060 (mtt180) REVERT: D 1001 LEU cc_start: 0.9053 (mm) cc_final: 0.8526 (mm) REVERT: D 1005 GLN cc_start: 0.8235 (pt0) cc_final: 0.7728 (pt0) REVERT: D 1007 TYR cc_start: 0.7810 (t80) cc_final: 0.7483 (t80) REVERT: D 1012 LEU cc_start: 0.9119 (mt) cc_final: 0.8771 (mt) REVERT: D 1017 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 1019 ARG cc_start: 0.8352 (tpt90) cc_final: 0.8059 (tpt90) REVERT: D 1023 ASN cc_start: 0.7882 (m-40) cc_final: 0.7549 (m-40) REVERT: D 1030 SER cc_start: 0.7774 (p) cc_final: 0.7495 (p) REVERT: D 1125 ASN cc_start: 0.6706 (p0) cc_final: 0.6338 (p0) REVERT: C 58 PHE cc_start: 0.8460 (m-10) cc_final: 0.8116 (m-10) REVERT: C 287 ASP cc_start: 0.8446 (t0) cc_final: 0.8065 (t0) REVERT: C 294 ASP cc_start: 0.7796 (m-30) cc_final: 0.7569 (m-30) REVERT: C 314 GLN cc_start: 0.8385 (pt0) cc_final: 0.8008 (tm-30) REVERT: C 651 ILE cc_start: 0.5958 (mt) cc_final: 0.5676 (pt) REVERT: C 731 MET cc_start: 0.7923 (pmm) cc_final: 0.7132 (ppp) REVERT: C 733 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8051 (tmtt) REVERT: C 740 MET cc_start: 0.7297 (tpt) cc_final: 0.6152 (tpp) REVERT: C 753 LEU cc_start: 0.8560 (mt) cc_final: 0.8158 (mt) REVERT: C 775 ASP cc_start: 0.8353 (m-30) cc_final: 0.8134 (m-30) REVERT: C 860 VAL cc_start: 0.8581 (t) cc_final: 0.8192 (p) REVERT: C 861 LEU cc_start: 0.9088 (mm) cc_final: 0.8756 (mm) REVERT: C 902 MET cc_start: 0.7302 (mtm) cc_final: 0.6948 (mtm) REVERT: C 914 ASN cc_start: 0.7346 (t0) cc_final: 0.7144 (t0) REVERT: C 928 ASN cc_start: 0.8494 (m-40) cc_final: 0.8261 (m-40) REVERT: C 951 VAL cc_start: 0.8942 (m) cc_final: 0.8509 (p) REVERT: C 954 HIS cc_start: 0.7785 (m90) cc_final: 0.7491 (m90) REVERT: C 955 ASN cc_start: 0.8733 (m-40) cc_final: 0.8454 (m-40) REVERT: C 960 ASN cc_start: 0.8694 (m110) cc_final: 0.8490 (m110) REVERT: C 1002 GLN cc_start: 0.8613 (mt0) cc_final: 0.8183 (mt0) REVERT: C 1010 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7543 (tp40) REVERT: C 1013 ILE cc_start: 0.9052 (pt) cc_final: 0.8807 (pt) REVERT: C 1017 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8316 (mt-10) REVERT: C 1023 ASN cc_start: 0.7986 (m-40) cc_final: 0.7760 (m110) REVERT: C 1075 PHE cc_start: 0.6943 (m-10) cc_final: 0.6663 (m-10) REVERT: C 1109 PHE cc_start: 0.8172 (p90) cc_final: 0.7792 (p90) REVERT: B 49 HIS cc_start: 0.8146 (t-90) cc_final: 0.7929 (t70) REVERT: B 56 LEU cc_start: 0.8044 (tp) cc_final: 0.7611 (tp) REVERT: B 189 LEU cc_start: 0.8683 (pp) cc_final: 0.8449 (mm) REVERT: B 202 LYS cc_start: 0.8025 (tptt) cc_final: 0.7285 (mttm) REVERT: B 273 ARG cc_start: 0.7614 (ptt180) cc_final: 0.7125 (ptt180) REVERT: B 275 PHE cc_start: 0.7313 (m-10) cc_final: 0.6518 (m-10) REVERT: B 278 LYS cc_start: 0.8358 (tmtt) cc_final: 0.8006 (tptt) REVERT: B 280 ASN cc_start: 0.8444 (t0) cc_final: 0.8232 (t0) REVERT: B 303 LEU cc_start: 0.8973 (tt) cc_final: 0.8736 (tt) REVERT: B 313 TYR cc_start: 0.7594 (m-80) cc_final: 0.7322 (m-80) REVERT: B 386 LYS cc_start: 0.9084 (tptp) cc_final: 0.8821 (mtpt) REVERT: B 565 PHE cc_start: 0.7620 (p90) cc_final: 0.7270 (p90) REVERT: B 568 ASP cc_start: 0.8411 (t0) cc_final: 0.8129 (t0) REVERT: B 734 THR cc_start: 0.8746 (t) cc_final: 0.8517 (m) REVERT: B 738 CYS cc_start: 0.5578 (p) cc_final: 0.4707 (p) REVERT: B 763 LEU cc_start: 0.9148 (pp) cc_final: 0.8945 (pp) REVERT: B 764 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8650 (mmtp) REVERT: B 802 PHE cc_start: 0.6050 (m-10) cc_final: 0.5824 (m-10) REVERT: B 861 LEU cc_start: 0.8669 (mm) cc_final: 0.8277 (tp) REVERT: B 919 ASN cc_start: 0.6978 (p0) cc_final: 0.6662 (p0) REVERT: B 935 GLN cc_start: 0.8003 (tp40) cc_final: 0.7727 (tm-30) REVERT: B 949 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7538 (tp-100) REVERT: B 957 GLN cc_start: 0.8599 (tp40) cc_final: 0.8373 (tp40) REVERT: B 964 LYS cc_start: 0.8794 (tttt) cc_final: 0.8533 (tttt) REVERT: B 984 LEU cc_start: 0.6514 (tp) cc_final: 0.6141 (tp) REVERT: B 985 ASP cc_start: 0.8818 (t0) cc_final: 0.8580 (t0) REVERT: B 994 ASP cc_start: 0.8335 (m-30) cc_final: 0.8083 (m-30) REVERT: B 1005 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 1006 THR cc_start: 0.8680 (p) cc_final: 0.8021 (p) REVERT: B 1019 ARG cc_start: 0.8548 (ptm160) cc_final: 0.7829 (ptm160) REVERT: B 1089 PHE cc_start: 0.6852 (m-80) cc_final: 0.6140 (m-80) REVERT: A 48 TRP cc_start: 0.6536 (t60) cc_final: 0.6252 (t60) REVERT: A 82 MET cc_start: 0.6101 (pmm) cc_final: 0.5858 (pmm) REVERT: A 123 MET cc_start: -0.5396 (mmm) cc_final: -0.7055 (mmm) REVERT: A 474 MET cc_start: 0.5282 (mmp) cc_final: 0.3058 (tpt) REVERT: A 480 MET cc_start: 0.5865 (ptt) cc_final: 0.5550 (ptt) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.4107 time to fit residues: 341.0870 Evaluate side-chains 465 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 362 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 135 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 369 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 271 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN B 544 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.183421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.146434 restraints weight = 98445.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.149601 restraints weight = 68233.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.151945 restraints weight = 50887.021| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30279 Z= 0.143 Angle : 0.613 11.840 41192 Z= 0.313 Chirality : 0.045 0.274 4592 Planarity : 0.005 0.076 5321 Dihedral : 4.679 29.910 4011 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3691 helix: -0.29 (0.18), residues: 831 sheet: -0.62 (0.22), residues: 515 loop : -1.05 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 461 HIS 0.009 0.001 HIS A 378 PHE 0.022 0.001 PHE D 220 TYR 0.022 0.002 TYR B 501 ARG 0.019 0.001 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 712) hydrogen bonds : angle 5.30127 ( 2055) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.49735 ( 84) covalent geometry : bond 0.00310 (30237) covalent geometry : angle 0.61024 (41108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13892.03 seconds wall clock time: 240 minutes 54.14 seconds (14454.14 seconds total)