Starting phenix.real_space_refine on Fri Mar 6 22:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.map" model { file = "/net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dcc_30635/03_2026/7dcc_30635.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.087 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 156 5.16 5 C 22230 2.51 5 N 5844 2.21 5 O 6789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35019 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "F" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "H" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "I" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "K" Number of atoms: 8310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8304 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 51, 'TRANS': 1009} Chain breaks: 6 bond proxies already assigned to first conformer: 8487 Chain: "M" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1672 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Time building chain proxies: 11.09, per 1000 atoms: 0.32 Number of scatterers: 35019 At special positions: 0 Unit cell: (185.64, 178.5, 201.96, 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 156 16.00 O 6789 8.00 N 5844 7.00 C 22230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 166 " distance=2.03 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 538 " - pdb=" SG CYS I 590 " distance=2.03 Simple disulfide: pdb=" SG CYS I 617 " - pdb=" SG CYS I 649 " distance=2.03 Simple disulfide: pdb=" SG CYS I 662 " - pdb=" SG CYS I 671 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 760 " distance=2.03 Simple disulfide: pdb=" SG CYS I 743 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I1032 " - pdb=" SG CYS I1043 " distance=2.03 Simple disulfide: pdb=" SG CYS I1082 " - pdb=" SG CYS I1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 94 sheets defined 16.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.515A pdb=" N ASP A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.709A pdb=" N THR B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.501A pdb=" N ASP D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 297 through 304 removed outlier: 3.667A pdb=" N CYS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.922A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.677A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 746 through 754 removed outlier: 4.124A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 751 " --> pdb=" O THR E 747 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 780 removed outlier: 3.529A pdb=" N ILE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 removed outlier: 3.585A pdb=" N LEU E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 884 removed outlier: 3.533A pdb=" N ALA E 879 " --> pdb=" O SER E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 removed outlier: 4.001A pdb=" N MET E 902 " --> pdb=" O PHE E 898 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA E 903 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR E 904 " --> pdb=" O MET E 900 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN E 907 " --> pdb=" O ALA E 903 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 908 " --> pdb=" O TYR E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 919 removed outlier: 4.164A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 939 removed outlier: 3.502A pdb=" N ASN E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER E 929 " --> pdb=" O ASN E 925 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 931 " --> pdb=" O PHE E 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY E 932 " --> pdb=" O ASN E 928 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 933 " --> pdb=" O SER E 929 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 954 removed outlier: 4.029A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 965 removed outlier: 3.626A pdb=" N VAL E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 964 " --> pdb=" O ASN E 960 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 965 " --> pdb=" O THR E 961 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 1032 removed outlier: 4.175A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR E1009 " --> pdb=" O GLN E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 3.551A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.539A pdb=" N ASP F 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.956A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 removed outlier: 3.548A pdb=" N TYR F 186 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 182 through 187' Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.980A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 304 removed outlier: 3.923A pdb=" N THR I 299 " --> pdb=" O PRO I 295 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 300 " --> pdb=" O LEU I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 343 Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.515A pdb=" N ASN I 370 " --> pdb=" O SER I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 737 through 743 removed outlier: 3.530A pdb=" N TYR I 741 " --> pdb=" O ASP I 737 " (cutoff:3.500A) Processing helix chain 'I' and resid 753 through 757 removed outlier: 3.587A pdb=" N GLY I 757 " --> pdb=" O LEU I 754 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 782 removed outlier: 3.564A pdb=" N ALA I 771 " --> pdb=" O LEU I 767 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP I 775 " --> pdb=" O ALA I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 816 through 824 removed outlier: 3.656A pdb=" N LEU I 821 " --> pdb=" O PHE I 817 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 882 removed outlier: 3.692A pdb=" N ILE I 882 " --> pdb=" O LEU I 878 " (cutoff:3.500A) Processing helix chain 'I' and resid 897 through 908 removed outlier: 4.028A pdb=" N ALA I 903 " --> pdb=" O ALA I 899 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE I 906 " --> pdb=" O MET I 902 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN I 907 " --> pdb=" O ALA I 903 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY I 908 " --> pdb=" O TYR I 904 " (cutoff:3.500A) Processing helix chain 'I' and resid 913 through 919 removed outlier: 4.312A pdb=" N TYR I 917 " --> pdb=" O GLN I 913 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 941 removed outlier: 3.554A pdb=" N GLN I 926 " --> pdb=" O LEU I 922 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN I 928 " --> pdb=" O ALA I 924 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER I 929 " --> pdb=" O ASN I 925 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 931 " --> pdb=" O PHE I 927 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY I 932 " --> pdb=" O ASN I 928 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 934 " --> pdb=" O ALA I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 965 removed outlier: 4.073A pdb=" N VAL I 951 " --> pdb=" O LYS I 947 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA I 958 " --> pdb=" O GLN I 954 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR I 961 " --> pdb=" O GLN I 957 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 963 " --> pdb=" O LEU I 959 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 964 " --> pdb=" O ASN I 960 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 968 No H-bonds generated for 'chain 'I' and resid 966 through 968' Processing helix chain 'I' and resid 976 through 984 removed outlier: 3.800A pdb=" N ILE I 980 " --> pdb=" O VAL I 976 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU I 981 " --> pdb=" O LEU I 977 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER I 982 " --> pdb=" O ASN I 978 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 1032 removed outlier: 4.076A pdb=" N GLU I 990 " --> pdb=" O PRO I 986 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 991 " --> pdb=" O PRO I 987 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN I 992 " --> pdb=" O GLU I 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR I1027 " --> pdb=" O ASN I1023 " (cutoff:3.500A) Processing helix chain 'I' and resid 1140 through 1147 removed outlier: 3.834A pdb=" N GLU I1144 " --> pdb=" O PRO I1140 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 304 removed outlier: 3.893A pdb=" N THR K 299 " --> pdb=" O PRO K 295 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS K 300 " --> pdb=" O LEU K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 removed outlier: 3.612A pdb=" N TYR K 369 " --> pdb=" O TYR K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 389 removed outlier: 3.665A pdb=" N ASN K 388 " --> pdb=" O PRO K 384 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP K 389 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 410 removed outlier: 3.538A pdb=" N GLN K 409 " --> pdb=" O GLU K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 420 removed outlier: 3.996A pdb=" N ALA K 419 " --> pdb=" O THR K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR K 741 " --> pdb=" O ASP K 737 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE K 742 " --> pdb=" O CYS K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 747 through 752 removed outlier: 3.740A pdb=" N ASN K 751 " --> pdb=" O THR K 747 " (cutoff:3.500A) Processing helix chain 'K' and resid 753 through 757 removed outlier: 3.596A pdb=" N GLY K 757 " --> pdb=" O LEU K 754 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 780 removed outlier: 3.523A pdb=" N ALA K 771 " --> pdb=" O LEU K 767 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR K 778 " --> pdb=" O GLN K 774 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN K 779 " --> pdb=" O ASP K 775 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 824 removed outlier: 3.605A pdb=" N LEU K 821 " --> pdb=" O PHE K 817 " (cutoff:3.500A) Processing helix chain 'K' and resid 866 through 884 removed outlier: 3.697A pdb=" N ALA K 879 " --> pdb=" O SER K 875 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 891 removed outlier: 3.993A pdb=" N ALA K 890 " --> pdb=" O TRP K 886 " (cutoff:3.500A) Processing helix chain 'K' and resid 897 through 908 removed outlier: 3.835A pdb=" N MET K 902 " --> pdb=" O PHE K 898 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA K 903 " --> pdb=" O ALA K 899 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR K 904 " --> pdb=" O MET K 900 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG K 905 " --> pdb=" O GLN K 901 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN K 907 " --> pdb=" O ALA K 903 " (cutoff:3.500A) Processing helix chain 'K' and resid 913 through 919 removed outlier: 3.862A pdb=" N TYR K 917 " --> pdb=" O GLN K 913 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 941 removed outlier: 4.019A pdb=" N ALA K 924 " --> pdb=" O GLN K 920 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN K 928 " --> pdb=" O ALA K 924 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER K 929 " --> pdb=" O ASN K 925 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 932 " --> pdb=" O ASN K 928 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 933 " --> pdb=" O SER K 929 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE K 934 " --> pdb=" O ALA K 930 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER K 940 " --> pdb=" O ASP K 936 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR K 941 " --> pdb=" O SER K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 945 through 965 removed outlier: 4.126A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN K 957 " --> pdb=" O ASN K 953 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA K 958 " --> pdb=" O GLN K 954 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN K 960 " --> pdb=" O ALA K 956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR K 961 " --> pdb=" O GLN K 957 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU K 962 " --> pdb=" O ALA K 958 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL K 963 " --> pdb=" O LEU K 959 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 982 removed outlier: 3.626A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU K 981 " --> pdb=" O LEU K 977 " (cutoff:3.500A) Processing helix chain 'K' and resid 988 through 1032 removed outlier: 4.464A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K1003 " --> pdb=" O GLY K 999 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA K1015 " --> pdb=" O GLN K1011 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU K1017 " --> pdb=" O ILE K1013 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE K1018 " --> pdb=" O ARG K1014 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER K1030 " --> pdb=" O ALA K1026 " (cutoff:3.500A) Processing helix chain 'K' and resid 1116 through 1118 No H-bonds generated for 'chain 'K' and resid 1116 through 1118' Processing helix chain 'K' and resid 1140 through 1147 removed outlier: 4.070A pdb=" N GLU K1144 " --> pdb=" O PRO K1140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K1145 " --> pdb=" O LEU K1141 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER K1147 " --> pdb=" O PRO K1143 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.885A pdb=" N LEU M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR M 126 " --> pdb=" O SER M 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 removed outlier: 3.807A pdb=" N GLU M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG M 188 " --> pdb=" O ASP M 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.529A pdb=" N GLN A 3 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.903A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 46 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 98 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 96 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 97 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 108 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 99 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 106 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.903A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 46 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 98 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 96 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.628A pdb=" N THR A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 79 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.585A pdb=" N SER A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 147 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 130 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 146 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 186 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.585A pdb=" N SER A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 147 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 130 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.835A pdb=" N CYS A 201 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 214 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.272A pdb=" N GLN B 5 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 23 " --> pdb=" O GLN B 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 40 removed outlier: 7.192A pdb=" N TRP B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AB2, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.902A pdb=" N TYR B 93 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 113 " --> pdb=" O TYR B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.525A pdb=" N TYR B 99 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 106 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.759A pdb=" N SER B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 181 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 186 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 170 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 160 removed outlier: 4.048A pdb=" N CYS B 201 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 214 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 203 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.557A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.557A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 51 removed outlier: 3.677A pdb=" N LYS D 44 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 96 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 92 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR D 93 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR D 113 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'D' and resid 126 through 130 removed outlier: 3.790A pdb=" N SER D 126 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 130 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 189 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 144 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 185 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 148 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 186 " --> pdb=" O HIS D 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS D 170 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 157 through 160 removed outlier: 3.863A pdb=" N CYS D 201 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 214 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 203 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 30 removed outlier: 3.606A pdb=" N THR E 29 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 43 removed outlier: 5.489A pdb=" N PHE E 43 " --> pdb=" O ARG K 567 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU K 585 " --> pdb=" O VAL K 576 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 550 " --> pdb=" O VAL K 539 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL K 539 " --> pdb=" O GLY K 550 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN K 542 " --> pdb=" O ILE K 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.772A pdb=" N HIS E 49 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 277 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR E 51 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE E 275 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.744A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR E 95 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.744A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR E 95 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 194 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS E 202 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.577A pdb=" N ARG E 237 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY E 107 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 141 through 142 removed outlier: 6.972A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.243A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 325 through 326 removed outlier: 3.752A pdb=" N ASN E 542 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 586 " --> pdb=" O THR E 553 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 565 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.328A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.328A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.831A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.684A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 695 " --> pdb=" O CYS E 671 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.684A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 701 through 704 removed outlier: 5.395A pdb=" N ALA E 701 " --> pdb=" O ILE I 788 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS I 790 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN E 703 " --> pdb=" O LYS I 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 711 through 714 removed outlier: 3.667A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.567A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.917A pdb=" N ALA E1056 " --> pdb=" O GLY E1059 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'E' and resid 787 through 790 removed outlier: 3.809A pdb=" N LYS E 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 1120 through 1122 removed outlier: 3.896A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AE8, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.545A pdb=" N LYS F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 37 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 48 through 49 removed outlier: 3.657A pdb=" N TYR F 49 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AF2, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.975A pdb=" N ASN F 137 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER F 116 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE F 135 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 118 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 130 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 136 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 146 through 150 removed outlier: 3.813A pdb=" N LYS F 147 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR F 192 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE F 209 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS F 194 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS F 207 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.586A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.518A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 72 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER H 65 " --> pdb=" O THR H 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.722A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.643A pdb=" N THR H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 116 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU H 136 " --> pdb=" O MET H 175 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 176 " --> pdb=" O SER H 162 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.643A pdb=" N THR H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 116 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA H 130 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU H 179 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.716A pdb=" N ARG H 155 " --> pdb=" O TRP H 148 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP H 148 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS H 147 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU H 195 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS H 194 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS H 207 " --> pdb=" O CYS H 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 28 through 30 removed outlier: 3.999A pdb=" N VAL I 267 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 264 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS I 187 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR I 208 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 50 through 55 removed outlier: 4.032A pdb=" N THR I 51 " --> pdb=" O PHE I 275 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE I 275 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP I 53 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 289 " --> pdb=" O LEU I 276 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 84 through 85 removed outlier: 4.167A pdb=" N LEU I 84 " --> pdb=" O PHE I 238 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE I 238 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY I 103 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG I 102 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 121 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 119 " --> pdb=" O TRP I 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS I 131 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 127 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE I 168 " --> pdb=" O VAL I 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 135 through 143 removed outlier: 6.905A pdb=" N ASP I 138 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL I 159 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE I 140 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE I 157 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY I 142 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.756A pdb=" N VAL I 193 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR I 204 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS I 195 " --> pdb=" O LYS I 202 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS I 202 " --> pdb=" O LYS I 195 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE I 201 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP I 228 " --> pdb=" O PHE I 201 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE I 203 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 311 through 318 removed outlier: 6.012A pdb=" N ILE I 312 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR I 599 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN I 314 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL I 597 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY I 594 " --> pdb=" O GLN I 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 356 through 358 removed outlier: 4.004A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 516 " --> pdb=" O ASN I 394 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 356 through 358 removed outlier: 4.004A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 516 " --> pdb=" O ASN I 394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'I' and resid 473 through 474 removed outlier: 3.659A pdb=" N TYR I 473 " --> pdb=" O TYR I 489 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR I 489 " --> pdb=" O TYR I 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'I' and resid 538 through 542 removed outlier: 3.907A pdb=" N GLY I 548 " --> pdb=" O PHE I 541 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 553 " --> pdb=" O ASP I 586 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 565 through 566 removed outlier: 7.211A pdb=" N PHE I 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 654 through 655 removed outlier: 5.786A pdb=" N GLU I 654 " --> pdb=" O ALA I 694 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR I 696 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN I 675 " --> pdb=" O SER I 691 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER I 673 " --> pdb=" O ILE I 693 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE I 670 " --> pdb=" O ILE I 666 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 701 through 703 removed outlier: 5.698A pdb=" N ALA I 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'I' and resid 711 through 714 removed outlier: 3.747A pdb=" N LYS I1073 " --> pdb=" O ILE I 714 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE I1095 " --> pdb=" O ALA I1078 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 718 through 728 removed outlier: 3.799A pdb=" N SER I 721 " --> pdb=" O THR I1066 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU I1063 " --> pdb=" O SER I1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER I1051 " --> pdb=" O LEU I1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL I1065 " --> pdb=" O LEU I1049 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR I1047 " --> pdb=" O TYR I1067 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 718 through 728 removed outlier: 3.799A pdb=" N SER I 721 " --> pdb=" O THR I1066 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA I1056 " --> pdb=" O GLY I1059 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS I 733 " --> pdb=" O LEU I 861 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 1081 through 1082 removed outlier: 3.644A pdb=" N ILE I1081 " --> pdb=" O HIS I1088 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA I1087 " --> pdb=" O SER I1123 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.337A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL K 267 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.337A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL K 267 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA K 264 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR K 95 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR K 266 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL K 90 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE K 194 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 48 through 55 removed outlier: 3.721A pdb=" N HIS K 49 " --> pdb=" O LEU K 277 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE K 275 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP K 53 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 84 through 85 removed outlier: 4.081A pdb=" N LEU K 84 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE K 238 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 107 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS K 131 " --> pdb=" O SER K 116 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE K 168 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 158 through 160 removed outlier: 3.668A pdb=" N ARG K 158 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE K 140 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N LEU K 242 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU K 244 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU K 141 " --> pdb=" O LEU K 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'K' and resid 196 through 197 removed outlier: 3.686A pdb=" N ILE K 197 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 311 through 318 removed outlier: 6.264A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR K 612 " --> pdb=" O CYS K 649 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS K 649 " --> pdb=" O TYR K 612 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 356 through 358 removed outlier: 3.586A pdb=" N LYS K 356 " --> pdb=" O ALA K 397 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL K 395 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 516 " --> pdb=" O ASN K 394 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE K 402 " --> pdb=" O TYR K 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG K 509 " --> pdb=" O TRP K 436 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP K 436 " --> pdb=" O ARG K 509 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AJ2, first strand: chain 'K' and resid 473 through 474 removed outlier: 3.960A pdb=" N TYR K 473 " --> pdb=" O TYR K 489 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR K 489 " --> pdb=" O TYR K 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'K' and resid 654 through 655 removed outlier: 5.766A pdb=" N GLU K 654 " --> pdb=" O ALA K 694 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR K 696 " --> pdb=" O GLU K 654 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN K 675 " --> pdb=" O SER K 691 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 673 " --> pdb=" O ILE K 693 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 712 through 714 Processing sheet with id=AJ5, first strand: chain 'K' and resid 718 through 728 removed outlier: 3.513A pdb=" N VAL K1068 " --> pdb=" O THR K 719 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA K1056 " --> pdb=" O GLY K1059 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET K1050 " --> pdb=" O VAL K1065 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 734 through 736 Processing sheet with id=AJ7, first strand: chain 'K' and resid 1120 through 1122 removed outlier: 3.858A pdb=" N ILE K1081 " --> pdb=" O HIS K1088 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 1094 through 1097 Processing sheet with id=AJ9, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.667A pdb=" N LYS M 24 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AK2, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.708A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'M' and resid 116 through 118 removed outlier: 3.645A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.641A pdb=" N ASN M 145 " --> pdb=" O THR M 197 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS M 194 " --> pdb=" O LYS M 207 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS M 207 " --> pdb=" O CYS M 194 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA M 196 " --> pdb=" O ILE M 205 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE M 205 " --> pdb=" O ALA M 196 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2514 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: 8.78 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11272 1.35 - 1.47: 8892 1.47 - 1.59: 15491 1.59 - 1.70: 0 1.70 - 1.82: 201 Bond restraints: 35856 Sorted by residual: bond pdb=" C GLY E 526 " pdb=" N PRO E 527 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.60e+00 bond pdb=" CA GLN K1142 " pdb=" C GLN K1142 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 2.01e+00 bond pdb=" C GLN I1142 " pdb=" N PRO I1143 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.24e-02 6.50e+03 1.78e+00 bond pdb=" C GLN K1142 " pdb=" N PRO K1143 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.62e+00 bond pdb=" C GLN E1142 " pdb=" N PRO E1143 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.25e-02 6.40e+03 1.61e+00 ... (remaining 35851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 48045 1.59 - 3.18: 690 3.18 - 4.76: 66 4.76 - 6.35: 7 6.35 - 7.94: 8 Bond angle restraints: 48816 Sorted by residual: angle pdb=" C LYS I 150 " pdb=" N SER I 151 " pdb=" CA SER I 151 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N GLY E 526 " pdb=" CA GLY E 526 " pdb=" C GLY E 526 " ideal model delta sigma weight residual 112.34 120.13 -7.79 2.04e+00 2.40e-01 1.46e+01 angle pdb=" C TYR F 94 " pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta sigma weight residual 127.00 134.94 -7.94 2.40e+00 1.74e-01 1.09e+01 angle pdb=" N THR I 333 " pdb=" CA THR I 333 " pdb=" C THR I 333 " ideal model delta sigma weight residual 113.02 116.83 -3.81 1.20e+00 6.94e-01 1.01e+01 angle pdb=" C TRP M 50 " pdb=" N ALA M 51 " pdb=" CA ALA M 51 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 ... (remaining 48811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 20760 17.15 - 34.31: 504 34.31 - 51.46: 85 51.46 - 68.62: 7 68.62 - 85.77: 1 Dihedral angle restraints: 21357 sinusoidal: 8277 harmonic: 13080 Sorted by residual: dihedral pdb=" CB CYS K1032 " pdb=" SG CYS K1032 " pdb=" SG CYS K1043 " pdb=" CB CYS K1043 " ideal model delta sinusoidal sigma weight residual 93.00 136.15 -43.15 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 134.63 -41.63 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 128.20 -35.20 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 21354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3778 0.036 - 0.071: 1103 0.071 - 0.107: 478 0.107 - 0.143: 139 0.143 - 0.179: 4 Chirality restraints: 5502 Sorted by residual: chirality pdb=" CA THR I 333 " pdb=" N THR I 333 " pdb=" C THR I 333 " pdb=" CB THR I 333 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA ILE I 332 " pdb=" N ILE I 332 " pdb=" C ILE I 332 " pdb=" CB ILE I 332 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA GLN I1142 " pdb=" N GLN I1142 " pdb=" C GLN I1142 " pdb=" CB GLN I1142 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 5499 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 986 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO I 987 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 987 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 987 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 526 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO I 527 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO I 527 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 527 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 986 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO K 987 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO K 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 987 " -0.038 5.00e-02 4.00e+02 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9210 2.80 - 3.33: 26076 3.33 - 3.85: 56342 3.85 - 4.38: 61466 4.38 - 4.90: 109522 Nonbonded interactions: 262616 Sorted by model distance: nonbonded pdb=" O THR I 333 " pdb=" CB ASN I 334 " model vdw 2.279 3.440 nonbonded pdb=" O GLN K 957 " pdb=" OG1 THR K 961 " model vdw 2.312 3.040 nonbonded pdb=" O GLY K 880 " pdb=" OG SER K 884 " model vdw 2.320 3.040 nonbonded pdb=" O ASN K 439 " pdb=" OG SER K 443 " model vdw 2.326 3.040 nonbonded pdb=" O ASN I 439 " pdb=" OG SER I 443 " model vdw 2.329 3.040 ... (remaining 262611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 14 through 492 or resid 494 through 1147)) selection = (chain 'I' and (resid 14 through 492 or resid 494 through 1147)) selection = (chain 'K' and (resid 14 through 492 or resid 494 through 1147)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } 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=0.50 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: 7.290 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 36.010 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35905 Z= 0.118 Angle : 0.481 7.940 48914 Z= 0.283 Chirality : 0.042 0.179 5502 Planarity : 0.005 0.073 6303 Dihedral : 7.377 85.773 12810 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 1.39 % Allowed : 3.04 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.10), residues: 4434 helix: -4.75 (0.05), residues: 606 sheet: -1.89 (0.15), residues: 1004 loop : -2.65 (0.09), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 905 TYR 0.011 0.001 TYR B 104 PHE 0.014 0.001 PHE K 329 TRP 0.009 0.001 TRP K 64 HIS 0.002 0.000 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00207 (35856) covalent geometry : angle 0.48059 (48816) SS BOND : bond 0.00119 ( 49) SS BOND : angle 0.44685 ( 98) hydrogen bonds : bond 0.32432 ( 875) hydrogen bonds : angle 11.76255 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 898 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.2841 (tt) cc_final: 0.2588 (tt) REVERT: A 141 MET cc_start: -0.2496 (mtm) cc_final: -0.3212 (ptm) REVERT: A 180 LEU cc_start: -0.2640 (OUTLIER) cc_final: -0.3111 (mm) REVERT: B 172 PHE cc_start: 0.2413 (m-10) cc_final: 0.1954 (m-80) REVERT: D 159 THR cc_start: 0.7206 (p) cc_final: 0.6911 (t) REVERT: D 220 ASP cc_start: 0.6362 (m-30) cc_final: 0.5100 (t0) REVERT: E 277 LEU cc_start: 0.9121 (mt) cc_final: 0.8911 (pp) REVERT: E 462 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7260 (mmtt) REVERT: E 747 THR cc_start: 0.8562 (m) cc_final: 0.8273 (t) REVERT: E 761 THR cc_start: 0.8367 (m) cc_final: 0.8078 (p) REVERT: E 763 LEU cc_start: 0.8660 (mt) cc_final: 0.7794 (mt) REVERT: E 770 ILE cc_start: 0.9129 (mt) cc_final: 0.8479 (mm) REVERT: E 777 ASN cc_start: 0.8607 (m-40) cc_final: 0.7759 (m-40) REVERT: E 869 MET cc_start: 0.8261 (mmt) cc_final: 0.7900 (mmt) REVERT: E 1033 VAL cc_start: 0.8763 (t) cc_final: 0.8420 (t) REVERT: E 1052 PHE cc_start: 0.7822 (m-10) cc_final: 0.7305 (m-10) REVERT: F 134 CYS cc_start: 0.4421 (t) cc_final: 0.3784 (m) REVERT: F 175 MET cc_start: 0.2551 (ppp) cc_final: 0.1607 (ppp) REVERT: H 117 ILE cc_start: 0.0742 (tt) cc_final: 0.0479 (tt) REVERT: H 124 GLN cc_start: 0.1257 (tt0) cc_final: 0.1016 (mt0) REVERT: H 172 THR cc_start: 0.4476 (p) cc_final: 0.3776 (t) REVERT: I 269 TYR cc_start: 0.6594 (m-10) cc_final: 0.5683 (m-80) REVERT: I 335 LEU cc_start: 0.8034 (mt) cc_final: 0.7627 (tp) REVERT: I 614 ASP cc_start: 0.7847 (m-30) cc_final: 0.7637 (t0) REVERT: I 777 ASN cc_start: 0.8275 (m-40) cc_final: 0.5520 (p0) REVERT: I 1007 TYR cc_start: 0.7100 (t80) cc_final: 0.6766 (t80) REVERT: I 1023 ASN cc_start: 0.8827 (m-40) cc_final: 0.8329 (t0) REVERT: I 1104 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6760 (p) REVERT: K 110 LEU cc_start: 0.7763 (mp) cc_final: 0.6845 (mt) REVERT: K 650 LEU cc_start: 0.7461 (tp) cc_final: 0.7101 (pp) REVERT: K 699 LEU cc_start: 0.9096 (mt) cc_final: 0.8695 (tp) REVERT: K 925 ASN cc_start: 0.7565 (m-40) cc_final: 0.7148 (t0) REVERT: K 1033 VAL cc_start: 0.9181 (t) cc_final: 0.8339 (t) REVERT: K 1141 LEU cc_start: 0.8989 (mt) cc_final: 0.8738 (tp) REVERT: M 206 VAL cc_start: 0.6237 (OUTLIER) cc_final: 0.5922 (p) outliers start: 55 outliers final: 7 residues processed: 946 average time/residue: 0.2264 time to fit residues: 343.1748 Evaluate side-chains 412 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 402 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 77 GLN B 43 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS D 161 ASN E 49 HIS E 314 GLN E 901 GLN E 949 GLN E 969 ASN E1005 GLN ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 HIS F 55 HIS F 145 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS I 49 HIS I 779 GLN I 901 GLN I 913 GLN I 992 GLN I1011 GLN K 49 HIS K 354 ASN K 542 ASN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 954 GLN K1002 GLN K1011 GLN K1108 ASN M 157 ASN M 166 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.112993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.093724 restraints weight = 404630.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.096156 restraints weight = 249481.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.096267 restraints weight = 168460.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.097581 restraints weight = 128056.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.098032 restraints weight = 96136.699| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4401 r_free = 0.4401 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4400 r_free = 0.4400 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35905 Z= 0.131 Angle : 0.578 10.337 48914 Z= 0.303 Chirality : 0.045 0.302 5502 Planarity : 0.005 0.071 6303 Dihedral : 3.314 18.587 4827 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.08 % Allowed : 1.24 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.11), residues: 4434 helix: -2.40 (0.16), residues: 637 sheet: -1.29 (0.15), residues: 1110 loop : -2.12 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I1014 TYR 0.020 0.001 TYR E 145 PHE 0.028 0.001 PHE K 329 TRP 0.017 0.001 TRP E 436 HIS 0.006 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00275 (35856) covalent geometry : angle 0.57641 (48816) SS BOND : bond 0.00292 ( 49) SS BOND : angle 1.23631 ( 98) hydrogen bonds : bond 0.05250 ( 875) hydrogen bonds : angle 7.22157 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 525 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.5066 (tt) cc_final: 0.4622 (tt) REVERT: A 141 MET cc_start: -0.4124 (mtm) cc_final: -0.4340 (ptm) REVERT: E 54 LEU cc_start: 0.8451 (tp) cc_final: 0.8129 (tp) REVERT: E 462 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7583 (mmtt) REVERT: E 869 MET cc_start: 0.8019 (mmt) cc_final: 0.7512 (mmt) REVERT: E 882 ILE cc_start: 0.9067 (mt) cc_final: 0.8821 (mm) REVERT: E 950 ASP cc_start: 0.8855 (p0) cc_final: 0.8634 (p0) REVERT: E 1017 GLU cc_start: 0.7975 (tp30) cc_final: 0.7220 (tp30) REVERT: E 1023 ASN cc_start: 0.8863 (m110) cc_final: 0.8118 (m110) REVERT: E 1041 ASP cc_start: 0.7166 (t0) cc_final: 0.6961 (t0) REVERT: E 1050 MET cc_start: 0.7298 (ptp) cc_final: 0.7092 (ptp) REVERT: E 1052 PHE cc_start: 0.7956 (m-10) cc_final: 0.7697 (m-10) REVERT: F 134 CYS cc_start: 0.6908 (t) cc_final: 0.5262 (m) REVERT: H 172 THR cc_start: 0.3389 (p) cc_final: 0.3130 (t) REVERT: I 269 TYR cc_start: 0.6584 (m-10) cc_final: 0.5996 (m-80) REVERT: I 304 LYS cc_start: 0.8141 (mmpt) cc_final: 0.7648 (tppt) REVERT: I 614 ASP cc_start: 0.7351 (m-30) cc_final: 0.7107 (t0) REVERT: I 734 THR cc_start: 0.8744 (p) cc_final: 0.8503 (p) REVERT: I 988 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8149 (tm-30) REVERT: I 1007 TYR cc_start: 0.7980 (t80) cc_final: 0.7708 (t80) REVERT: I 1030 SER cc_start: 0.9163 (p) cc_final: 0.8941 (p) REVERT: I 1054 GLN cc_start: 0.8032 (mm110) cc_final: 0.7712 (mm-40) REVERT: K 229 LEU cc_start: 0.8028 (mt) cc_final: 0.7758 (mt) REVERT: K 507 PRO cc_start: 0.5342 (Cg_exo) cc_final: 0.4961 (Cg_endo) REVERT: K 546 LEU cc_start: 0.7233 (tp) cc_final: 0.6970 (mm) REVERT: K 650 LEU cc_start: 0.7476 (tp) cc_final: 0.7124 (pp) REVERT: K 739 THR cc_start: 0.8212 (p) cc_final: 0.7990 (t) REVERT: K 752 LEU cc_start: 0.8375 (mt) cc_final: 0.8147 (mt) REVERT: K 917 TYR cc_start: 0.6262 (m-10) cc_final: 0.4692 (m-80) REVERT: K 925 ASN cc_start: 0.7838 (m-40) cc_final: 0.7593 (t0) REVERT: K 951 VAL cc_start: 0.9005 (t) cc_final: 0.8785 (t) REVERT: K 973 ILE cc_start: 0.8637 (mm) cc_final: 0.8340 (pt) REVERT: K 1033 VAL cc_start: 0.9182 (t) cc_final: 0.8850 (t) REVERT: K 1109 PHE cc_start: 0.7218 (t80) cc_final: 0.6535 (t80) REVERT: K 1141 LEU cc_start: 0.8956 (mt) cc_final: 0.8692 (tp) REVERT: M 11 MET cc_start: 0.5786 (ppp) cc_final: 0.3348 (mtm) REVERT: M 212 ASN cc_start: 0.5064 (t0) cc_final: 0.4828 (t0) outliers start: 3 outliers final: 1 residues processed: 527 average time/residue: 0.2058 time to fit residues: 178.5817 Evaluate side-chains 338 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 204 optimal weight: 0.0170 chunk 328 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 391 optimal weight: 0.8980 chunk 420 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 66 HIS E 121 ASN E 125 ASN E 580 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 919 ASN E 935 GLN ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 ASN E1005 GLN E1083 HIS F 8 HIS F 55 HIS F 166 GLN F 189 HIS H 17 HIS H 212 ASN I 23 GLN I 125 ASN I 474 GLN I 655 HIS ** I 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 935 GLN ** I 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN K 125 ASN K 394 ASN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 ASN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 ASN K 949 GLN K 957 GLN M 17 HIS M 55 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.104995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.086471 restraints weight = 473918.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.088982 restraints weight = 289203.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.089640 restraints weight = 191266.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.090798 restraints weight = 132134.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.091206 restraints weight = 97091.554| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4270 r_free = 0.4270 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4270 r_free = 0.4270 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 35905 Z= 0.221 Angle : 0.706 15.667 48914 Z= 0.369 Chirality : 0.047 0.263 5502 Planarity : 0.006 0.122 6303 Dihedral : 4.329 20.829 4827 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.03 % Allowed : 1.98 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4434 helix: -1.24 (0.18), residues: 676 sheet: -1.11 (0.15), residues: 1145 loop : -1.73 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I1019 TYR 0.031 0.002 TYR E1007 PHE 0.032 0.003 PHE K1062 TRP 0.030 0.002 TRP D 160 HIS 0.010 0.002 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00459 (35856) covalent geometry : angle 0.70439 (48816) SS BOND : bond 0.00432 ( 49) SS BOND : angle 1.38547 ( 98) hydrogen bonds : bond 0.04687 ( 875) hydrogen bonds : angle 6.51217 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.3002 (mtm) cc_final: -0.3417 (ppp) REVERT: B 172 PHE cc_start: 0.5790 (m-80) cc_final: 0.5480 (m-80) REVERT: E 32 PHE cc_start: 0.5713 (t80) cc_final: 0.5496 (t80) REVERT: E 303 LEU cc_start: 0.9143 (tp) cc_final: 0.8888 (tp) REVERT: E 450 ASN cc_start: 0.8633 (t0) cc_final: 0.8346 (p0) REVERT: E 773 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 869 MET cc_start: 0.8080 (mmt) cc_final: 0.7769 (mmt) REVERT: E 894 LEU cc_start: 0.8232 (tp) cc_final: 0.8017 (tp) REVERT: E 938 LEU cc_start: 0.7913 (mt) cc_final: 0.7530 (tp) REVERT: E 1002 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8095 (tm-30) REVERT: E 1041 ASP cc_start: 0.7445 (t0) cc_final: 0.7063 (t0) REVERT: F 8 HIS cc_start: 0.8856 (m90) cc_final: 0.8380 (t-90) REVERT: F 11 MET cc_start: 0.4076 (mtt) cc_final: 0.3075 (mtt) REVERT: F 175 MET cc_start: 0.3816 (ppp) cc_final: 0.3208 (ppp) REVERT: H 184 ASP cc_start: 0.8064 (m-30) cc_final: 0.7862 (p0) REVERT: I 304 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7942 (mmmt) REVERT: I 1002 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7408 (tm-30) REVERT: I 1017 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8804 (tm-30) REVERT: I 1018 ILE cc_start: 0.9718 (mm) cc_final: 0.9390 (mm) REVERT: I 1030 SER cc_start: 0.9241 (p) cc_final: 0.8868 (t) REVERT: I 1036 GLN cc_start: 0.6715 (tt0) cc_final: 0.6441 (pm20) REVERT: K 54 LEU cc_start: 0.7705 (tp) cc_final: 0.7343 (tp) REVERT: K 229 LEU cc_start: 0.8166 (mt) cc_final: 0.7870 (mt) REVERT: K 346 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7835 (tmt170) REVERT: K 546 LEU cc_start: 0.7621 (tp) cc_final: 0.7136 (mm) REVERT: K 699 LEU cc_start: 0.9028 (mt) cc_final: 0.8609 (mt) REVERT: K 739 THR cc_start: 0.8307 (p) cc_final: 0.8012 (t) REVERT: K 780 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7397 (tm-30) REVERT: K 925 ASN cc_start: 0.7963 (m-40) cc_final: 0.7432 (t0) REVERT: K 951 VAL cc_start: 0.8657 (t) cc_final: 0.8344 (t) REVERT: K 973 ILE cc_start: 0.8716 (mm) cc_final: 0.8419 (pt) REVERT: K 1050 MET cc_start: 0.8084 (pmm) cc_final: 0.7860 (pmm) REVERT: K 1141 LEU cc_start: 0.8996 (mt) cc_final: 0.8784 (mm) REVERT: M 11 MET cc_start: 0.5758 (ppp) cc_final: 0.3708 (mtm) REVERT: M 77 ASN cc_start: 0.6325 (m110) cc_final: 0.6111 (p0) REVERT: M 175 MET cc_start: -0.3199 (ppp) cc_final: -0.3589 (ppp) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 0.2219 time to fit residues: 165.1240 Evaluate side-chains 293 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 149 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 HIS ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1083 HIS F 55 HIS I 49 HIS I 394 ASN I 913 GLN ** I 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1011 GLN I1023 ASN I1108 ASN K 49 HIS ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 913 GLN K 955 ASN K1083 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.104112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.084497 restraints weight = 429561.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.086287 restraints weight = 252136.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.087428 restraints weight = 164560.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.088100 restraints weight = 117159.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.089163 restraints weight = 88898.926| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4135 r_free = 0.4135 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4135 r_free = 0.4135 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35905 Z= 0.155 Angle : 0.577 9.059 48914 Z= 0.301 Chirality : 0.044 0.234 5502 Planarity : 0.005 0.158 6303 Dihedral : 4.160 22.137 4827 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4434 helix: -0.77 (0.19), residues: 680 sheet: -1.04 (0.15), residues: 1155 loop : -1.58 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 567 TYR 0.018 0.002 TYR E 145 PHE 0.019 0.002 PHE E 275 TRP 0.029 0.001 TRP I 886 HIS 0.006 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00326 (35856) covalent geometry : angle 0.57535 (48816) SS BOND : bond 0.00346 ( 49) SS BOND : angle 1.03498 ( 98) hydrogen bonds : bond 0.03893 ( 875) hydrogen bonds : angle 6.23560 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5166 (m100) cc_final: 0.4927 (m-90) REVERT: A 141 MET cc_start: -0.3747 (mtm) cc_final: -0.3993 (ppp) REVERT: E 32 PHE cc_start: 0.6151 (t80) cc_final: 0.5819 (t80) REVERT: E 177 MET cc_start: 0.4403 (tmm) cc_final: 0.4137 (tmm) REVERT: E 303 LEU cc_start: 0.9360 (tp) cc_final: 0.9077 (tp) REVERT: E 450 ASN cc_start: 0.8624 (t0) cc_final: 0.8297 (p0) REVERT: E 773 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7847 (tm-30) REVERT: E 802 PHE cc_start: 0.6978 (m-80) cc_final: 0.6621 (m-80) REVERT: E 869 MET cc_start: 0.8498 (mmt) cc_final: 0.7733 (mmt) REVERT: E 894 LEU cc_start: 0.8625 (tp) cc_final: 0.8361 (tp) REVERT: E 938 LEU cc_start: 0.8283 (mt) cc_final: 0.7917 (tp) REVERT: E 1002 GLN cc_start: 0.8955 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 1017 GLU cc_start: 0.8521 (tp30) cc_final: 0.8034 (tp30) REVERT: E 1041 ASP cc_start: 0.7676 (t0) cc_final: 0.7338 (t0) REVERT: F 175 MET cc_start: 0.3518 (ppp) cc_final: 0.3072 (ppp) REVERT: H 117 ILE cc_start: -0.1887 (tt) cc_final: -0.2277 (tt) REVERT: I 198 ASP cc_start: 0.7758 (m-30) cc_final: 0.7116 (p0) REVERT: I 389 ASP cc_start: 0.9446 (m-30) cc_final: 0.9132 (p0) REVERT: I 872 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8023 (mm-40) REVERT: I 947 LYS cc_start: 0.9008 (tppt) cc_final: 0.8805 (tppt) REVERT: I 950 ASP cc_start: 0.8769 (p0) cc_final: 0.8298 (p0) REVERT: I 1002 GLN cc_start: 0.8780 (tm-30) cc_final: 0.7704 (tm-30) REVERT: I 1012 LEU cc_start: 0.9553 (pp) cc_final: 0.9322 (tt) REVERT: I 1017 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8979 (tm-30) REVERT: I 1018 ILE cc_start: 0.9663 (mm) cc_final: 0.9381 (mm) REVERT: I 1030 SER cc_start: 0.9234 (p) cc_final: 0.8923 (t) REVERT: K 54 LEU cc_start: 0.8024 (tp) cc_final: 0.7763 (tp) REVERT: K 200 TYR cc_start: 0.8507 (m-80) cc_final: 0.8214 (m-80) REVERT: K 229 LEU cc_start: 0.8409 (mt) cc_final: 0.8198 (mt) REVERT: K 346 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7969 (tmt170) REVERT: K 546 LEU cc_start: 0.7831 (tp) cc_final: 0.7220 (mm) REVERT: K 699 LEU cc_start: 0.8931 (mt) cc_final: 0.7537 (mt) REVERT: K 780 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7961 (tm-30) REVERT: K 925 ASN cc_start: 0.8275 (m-40) cc_final: 0.7556 (t0) REVERT: K 1045 LYS cc_start: 0.9004 (tptp) cc_final: 0.8650 (tppt) REVERT: K 1050 MET cc_start: 0.8349 (pmm) cc_final: 0.8045 (pmm) REVERT: M 11 MET cc_start: 0.5827 (ppp) cc_final: 0.3597 (mtm) REVERT: M 77 ASN cc_start: 0.6291 (m110) cc_final: 0.6067 (p0) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.2236 time to fit residues: 150.0114 Evaluate side-chains 278 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 293 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 408 optimal weight: 0.0370 chunk 354 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 156 optimal weight: 0.0770 chunk 383 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 426 optimal weight: 8.9990 chunk 304 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 100 HIS E 641 ASN ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 17 HIS I 913 GLN ** I 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 ASN I1036 GLN I1054 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 935 GLN K 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.105524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.087422 restraints weight = 416296.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.089667 restraints weight = 258816.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.090205 restraints weight = 170149.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.091176 restraints weight = 122985.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.091717 restraints weight = 90510.268| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4291 r_free = 0.4291 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4291 r_free = 0.4291 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35905 Z= 0.098 Angle : 0.513 8.644 48914 Z= 0.264 Chirality : 0.044 0.251 5502 Planarity : 0.004 0.068 6303 Dihedral : 3.808 20.236 4827 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.12), residues: 4434 helix: -0.53 (0.20), residues: 676 sheet: -0.93 (0.15), residues: 1181 loop : -1.47 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 567 TYR 0.018 0.001 TYR E 145 PHE 0.017 0.001 PHE K 898 TRP 0.022 0.001 TRP K 64 HIS 0.008 0.001 HIS I1048 Details of bonding type rmsd covalent geometry : bond 0.00216 (35856) covalent geometry : angle 0.51235 (48816) SS BOND : bond 0.00201 ( 49) SS BOND : angle 0.82802 ( 98) hydrogen bonds : bond 0.03381 ( 875) hydrogen bonds : angle 5.91624 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.5256 (m100) cc_final: 0.4971 (m-90) REVERT: A 141 MET cc_start: -0.3466 (mtm) cc_final: -0.3908 (ppp) REVERT: E 177 MET cc_start: 0.3973 (tmm) cc_final: 0.2887 (tmm) REVERT: E 303 LEU cc_start: 0.9168 (tp) cc_final: 0.8875 (tp) REVERT: E 450 ASN cc_start: 0.8694 (t0) cc_final: 0.8379 (p0) REVERT: E 773 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7452 (tm-30) REVERT: E 802 PHE cc_start: 0.6319 (m-80) cc_final: 0.6109 (m-80) REVERT: E 900 MET cc_start: 0.8683 (mmt) cc_final: 0.8378 (mmm) REVERT: E 916 LEU cc_start: 0.8007 (tt) cc_final: 0.7632 (tt) REVERT: E 938 LEU cc_start: 0.7969 (mt) cc_final: 0.7766 (tp) REVERT: E 950 ASP cc_start: 0.8868 (p0) cc_final: 0.8660 (p0) REVERT: E 1002 GLN cc_start: 0.8594 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 1019 ARG cc_start: 0.8852 (tpm170) cc_final: 0.8235 (tpp-160) REVERT: E 1023 ASN cc_start: 0.9046 (m110) cc_final: 0.8010 (m-40) REVERT: E 1033 VAL cc_start: 0.9294 (m) cc_final: 0.8914 (p) REVERT: F 175 MET cc_start: 0.3714 (ppp) cc_final: 0.3201 (ppp) REVERT: I 198 ASP cc_start: 0.7357 (m-30) cc_final: 0.6865 (p0) REVERT: I 304 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7996 (mmmt) REVERT: I 389 ASP cc_start: 0.9293 (m-30) cc_final: 0.9015 (p0) REVERT: I 505 TYR cc_start: 0.8448 (m-10) cc_final: 0.8084 (m-80) REVERT: I 734 THR cc_start: 0.8795 (p) cc_final: 0.8589 (p) REVERT: I 898 PHE cc_start: 0.7942 (t80) cc_final: 0.7247 (t80) REVERT: I 1001 LEU cc_start: 0.9429 (pp) cc_final: 0.9206 (pp) REVERT: I 1002 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7776 (tm-30) REVERT: I 1007 TYR cc_start: 0.8022 (t80) cc_final: 0.7716 (t80) REVERT: I 1010 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8558 (tp-100) REVERT: I 1012 LEU cc_start: 0.9433 (pp) cc_final: 0.9110 (tt) REVERT: I 1018 ILE cc_start: 0.9568 (mm) cc_final: 0.9256 (mm) REVERT: K 54 LEU cc_start: 0.7400 (tp) cc_final: 0.7190 (tp) REVERT: K 346 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7850 (tmt170) REVERT: K 546 LEU cc_start: 0.6788 (tp) cc_final: 0.6403 (mm) REVERT: K 780 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7497 (tm-30) REVERT: K 925 ASN cc_start: 0.8028 (m-40) cc_final: 0.7380 (t0) REVERT: M 11 MET cc_start: 0.5308 (ppp) cc_final: 0.3292 (mtm) REVERT: M 77 ASN cc_start: 0.6364 (m110) cc_final: 0.6087 (p0) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2096 time to fit residues: 144.9771 Evaluate side-chains 279 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 442 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 ASN ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS F 55 HIS I 49 HIS I 239 GLN I 804 GLN I 913 GLN I 949 GLN I 978 ASN K 52 GLN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 762 GLN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K 957 GLN K 965 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.098661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.082095 restraints weight = 373227.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.084333 restraints weight = 235542.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.084660 restraints weight = 158679.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.085335 restraints weight = 126012.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.085920 restraints weight = 93835.389| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 35905 Z= 0.252 Angle : 0.769 12.696 48914 Z= 0.401 Chirality : 0.049 0.541 5502 Planarity : 0.006 0.105 6303 Dihedral : 5.100 23.913 4827 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.12), residues: 4434 helix: -0.92 (0.18), residues: 691 sheet: -1.16 (0.15), residues: 1125 loop : -1.59 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG I 765 TYR 0.030 0.003 TYR I 873 PHE 0.040 0.003 PHE I 759 TRP 0.035 0.002 TRP E 436 HIS 0.012 0.002 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00533 (35856) covalent geometry : angle 0.76689 (48816) SS BOND : bond 0.00685 ( 49) SS BOND : angle 1.37077 ( 98) hydrogen bonds : bond 0.04799 ( 875) hydrogen bonds : angle 6.71256 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.2957 (mtm) cc_final: -0.3271 (ppp) REVERT: E 200 TYR cc_start: 0.8754 (m-80) cc_final: 0.8239 (m-80) REVERT: E 303 LEU cc_start: 0.9472 (tp) cc_final: 0.9249 (tp) REVERT: E 450 ASN cc_start: 0.8947 (t0) cc_final: 0.8539 (p0) REVERT: E 773 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 894 LEU cc_start: 0.8906 (tp) cc_final: 0.8455 (tp) REVERT: E 938 LEU cc_start: 0.8596 (mt) cc_final: 0.8256 (tp) REVERT: E 1002 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 1041 ASP cc_start: 0.7576 (t0) cc_final: 0.7216 (t0) REVERT: E 1050 MET cc_start: 0.8917 (ptp) cc_final: 0.8557 (ptt) REVERT: F 175 MET cc_start: 0.3884 (ppp) cc_final: 0.3511 (ppp) REVERT: I 33 THR cc_start: 0.6303 (p) cc_final: 0.4860 (p) REVERT: I 389 ASP cc_start: 0.9557 (m-30) cc_final: 0.9332 (p0) REVERT: I 898 PHE cc_start: 0.8503 (t80) cc_final: 0.7902 (t80) REVERT: I 902 MET cc_start: 0.8505 (mmp) cc_final: 0.8146 (mmp) REVERT: I 950 ASP cc_start: 0.9025 (p0) cc_final: 0.8788 (p0) REVERT: I 1002 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8239 (tm-30) REVERT: I 1010 GLN cc_start: 0.9278 (tp-100) cc_final: 0.8692 (tp-100) REVERT: I 1017 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8758 (tm-30) REVERT: I 1018 ILE cc_start: 0.9762 (mm) cc_final: 0.9337 (mm) REVERT: I 1067 TYR cc_start: 0.7504 (t80) cc_final: 0.7107 (t80) REVERT: K 200 TYR cc_start: 0.8681 (m-80) cc_final: 0.8217 (m-80) REVERT: K 228 ASP cc_start: 0.7826 (m-30) cc_final: 0.7517 (m-30) REVERT: K 346 ARG cc_start: 0.8497 (mtp85) cc_final: 0.7903 (tmt170) REVERT: K 697 MET cc_start: 0.8398 (ptm) cc_final: 0.8142 (ptm) REVERT: K 714 ILE cc_start: 0.7996 (tp) cc_final: 0.7781 (tp) REVERT: K 780 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7959 (tm-30) REVERT: K 864 LEU cc_start: 0.8773 (mt) cc_final: 0.8092 (mt) REVERT: K 957 GLN cc_start: 0.8711 (mm110) cc_final: 0.8406 (mm110) REVERT: K 1050 MET cc_start: 0.8790 (pmm) cc_final: 0.8385 (pmm) REVERT: M 11 MET cc_start: 0.5351 (ppp) cc_final: 0.3092 (mtp) REVERT: M 77 ASN cc_start: 0.6654 (m110) cc_final: 0.6282 (p0) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2109 time to fit residues: 134.5848 Evaluate side-chains 254 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 234 optimal weight: 9.9990 chunk 387 optimal weight: 0.0980 chunk 311 optimal weight: 2.9990 chunk 420 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 436 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 373 optimal weight: 0.7980 chunk 444 optimal weight: 0.1980 chunk 267 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN D 100 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS I 239 GLN I 804 GLN I 913 GLN I1054 GLN K 542 ASN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 913 GLN ** K 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K1083 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.101585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.081915 restraints weight = 457904.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.083901 restraints weight = 268197.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.085402 restraints weight = 174906.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.085987 restraints weight = 122598.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.086635 restraints weight = 92015.431| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35905 Z= 0.115 Angle : 0.564 9.397 48914 Z= 0.291 Chirality : 0.045 0.228 5502 Planarity : 0.004 0.062 6303 Dihedral : 4.388 21.440 4827 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4434 helix: -0.51 (0.19), residues: 688 sheet: -1.06 (0.15), residues: 1155 loop : -1.48 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 765 TYR 0.020 0.001 TYR E 145 PHE 0.022 0.001 PHE F 10 TRP 0.021 0.001 TRP I 886 HIS 0.006 0.001 HIS I1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (35856) covalent geometry : angle 0.56186 (48816) SS BOND : bond 0.00459 ( 49) SS BOND : angle 1.25776 ( 98) hydrogen bonds : bond 0.03510 ( 875) hydrogen bonds : angle 6.13151 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.3374 (mtm) cc_final: -0.3601 (ppp) REVERT: E 32 PHE cc_start: 0.6246 (t80) cc_final: 0.5942 (t80) REVERT: E 177 MET cc_start: 0.4549 (tmm) cc_final: 0.4259 (tmm) REVERT: E 200 TYR cc_start: 0.8800 (m-80) cc_final: 0.8223 (m-80) REVERT: E 450 ASN cc_start: 0.8868 (t0) cc_final: 0.8478 (p0) REVERT: E 773 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 938 LEU cc_start: 0.8436 (mt) cc_final: 0.8219 (tt) REVERT: E 1017 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8638 (tp30) REVERT: E 1019 ARG cc_start: 0.8964 (tpm170) cc_final: 0.8362 (tpp-160) REVERT: E 1023 ASN cc_start: 0.9175 (m110) cc_final: 0.8293 (m-40) REVERT: E 1050 MET cc_start: 0.8662 (ptp) cc_final: 0.8436 (ptt) REVERT: F 175 MET cc_start: 0.3708 (ppp) cc_final: 0.3341 (ppp) REVERT: I 33 THR cc_start: 0.5974 (p) cc_final: 0.4497 (p) REVERT: I 389 ASP cc_start: 0.9558 (m-30) cc_final: 0.9332 (p0) REVERT: I 505 TYR cc_start: 0.8364 (m-10) cc_final: 0.8046 (m-10) REVERT: I 543 PHE cc_start: 0.8041 (t80) cc_final: 0.7060 (t80) REVERT: I 546 LEU cc_start: 0.8152 (tt) cc_final: 0.7864 (tt) REVERT: I 775 ASP cc_start: 0.8883 (m-30) cc_final: 0.8583 (m-30) REVERT: I 776 LYS cc_start: 0.9680 (tmtt) cc_final: 0.9398 (tptp) REVERT: I 898 PHE cc_start: 0.8483 (t80) cc_final: 0.7871 (t80) REVERT: I 902 MET cc_start: 0.8527 (mmp) cc_final: 0.8181 (mmp) REVERT: I 950 ASP cc_start: 0.8877 (p0) cc_final: 0.8632 (p0) REVERT: I 1002 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8632 (tm-30) REVERT: I 1010 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8623 (tp-100) REVERT: I 1012 LEU cc_start: 0.9485 (pp) cc_final: 0.9239 (tt) REVERT: I 1017 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8623 (tm-30) REVERT: I 1018 ILE cc_start: 0.9762 (mm) cc_final: 0.9341 (mm) REVERT: I 1067 TYR cc_start: 0.7208 (t80) cc_final: 0.7001 (t80) REVERT: K 56 LEU cc_start: 0.9170 (tp) cc_final: 0.8772 (tt) REVERT: K 200 TYR cc_start: 0.8648 (m-80) cc_final: 0.8356 (m-80) REVERT: K 346 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8063 (tmt170) REVERT: K 780 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8051 (tm-30) REVERT: K 864 LEU cc_start: 0.8734 (mt) cc_final: 0.8228 (mt) REVERT: K 867 ASP cc_start: 0.8120 (m-30) cc_final: 0.7479 (t70) REVERT: K 1018 ILE cc_start: 0.9583 (tp) cc_final: 0.9227 (tt) REVERT: K 1045 LYS cc_start: 0.9064 (tptp) cc_final: 0.8845 (tppt) REVERT: K 1050 MET cc_start: 0.8721 (pmm) cc_final: 0.8418 (pmm) REVERT: K 1118 ASP cc_start: 0.8916 (p0) cc_final: 0.8678 (m-30) REVERT: M 11 MET cc_start: 0.5291 (ppp) cc_final: 0.2937 (mtm) REVERT: M 77 ASN cc_start: 0.6523 (m110) cc_final: 0.6165 (p0) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.2018 time to fit residues: 130.3145 Evaluate side-chains 276 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 197 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 438 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 435 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN E 121 ASN E 580 GLN E 907 ASN ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN I 137 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 804 GLN I 913 GLN ** I 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1054 GLN ** I1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 218 GLN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 762 GLN K 925 ASN ** K 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 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 = 0.4160 r_free = 0.4160 target = 0.093335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.076608 restraints weight = 401704.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.078363 restraints weight = 240905.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.079438 restraints weight = 158909.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.080253 restraints weight = 114258.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.080636 restraints weight = 87802.748| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.8783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 35905 Z= 0.386 Angle : 0.988 18.091 48914 Z= 0.522 Chirality : 0.055 0.336 5502 Planarity : 0.007 0.078 6303 Dihedral : 6.457 37.714 4827 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.48 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4434 helix: -1.27 (0.18), residues: 689 sheet: -1.44 (0.15), residues: 1108 loop : -2.00 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG K 567 TYR 0.046 0.004 TYR B 181 PHE 0.044 0.004 PHE E 275 TRP 0.046 0.004 TRP F 50 HIS 0.018 0.003 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00797 (35856) covalent geometry : angle 0.98490 (48816) SS BOND : bond 0.00761 ( 49) SS BOND : angle 2.10487 ( 98) hydrogen bonds : bond 0.05832 ( 875) hydrogen bonds : angle 7.59918 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: -0.2413 (mtm) cc_final: -0.2626 (ppp) REVERT: E 54 LEU cc_start: 0.8847 (tp) cc_final: 0.8642 (tp) REVERT: E 200 TYR cc_start: 0.8981 (m-80) cc_final: 0.8382 (m-80) REVERT: E 450 ASN cc_start: 0.9158 (t0) cc_final: 0.8597 (p0) REVERT: E 725 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7324 (tm-30) REVERT: E 727 LEU cc_start: 0.8854 (mt) cc_final: 0.8512 (mt) REVERT: E 869 MET cc_start: 0.8727 (mtm) cc_final: 0.8418 (mtp) REVERT: E 894 LEU cc_start: 0.8966 (tp) cc_final: 0.8506 (tp) REVERT: E 907 ASN cc_start: 0.8521 (m110) cc_final: 0.8275 (m110) REVERT: E 938 LEU cc_start: 0.8729 (mt) cc_final: 0.8475 (tp) REVERT: F 80 SER cc_start: 0.5037 (m) cc_final: 0.4777 (p) REVERT: H 107 LYS cc_start: 0.4671 (mtpt) cc_final: 0.4395 (tptt) REVERT: I 33 THR cc_start: 0.6688 (p) cc_final: 0.5164 (p) REVERT: I 304 LYS cc_start: 0.8571 (mmmt) cc_final: 0.7917 (tppt) REVERT: I 610 VAL cc_start: 0.8702 (t) cc_final: 0.8392 (p) REVERT: I 751 ASN cc_start: 0.8653 (m-40) cc_final: 0.8434 (m-40) REVERT: I 898 PHE cc_start: 0.8631 (t80) cc_final: 0.7932 (t80) REVERT: I 902 MET cc_start: 0.8302 (mmp) cc_final: 0.7943 (mmp) REVERT: I 950 ASP cc_start: 0.8900 (p0) cc_final: 0.8577 (p0) REVERT: I 1001 LEU cc_start: 0.9637 (pp) cc_final: 0.9392 (pp) REVERT: I 1002 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8791 (tm-30) REVERT: I 1017 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8817 (tm-30) REVERT: I 1018 ILE cc_start: 0.9762 (mm) cc_final: 0.9282 (mm) REVERT: I 1067 TYR cc_start: 0.7545 (t80) cc_final: 0.7248 (t80) REVERT: K 346 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8150 (tmt170) REVERT: K 697 MET cc_start: 0.8768 (ptm) cc_final: 0.8188 (ptm) REVERT: K 780 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8272 (tm-30) REVERT: K 950 ASP cc_start: 0.8451 (p0) cc_final: 0.8212 (p0) REVERT: K 957 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8570 (mm110) REVERT: K 1050 MET cc_start: 0.9054 (pmm) cc_final: 0.8520 (pmm) REVERT: M 11 MET cc_start: 0.5643 (ppp) cc_final: 0.3740 (mtp) REVERT: M 77 ASN cc_start: 0.7031 (m110) cc_final: 0.6675 (p0) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2153 time to fit residues: 117.3048 Evaluate side-chains 223 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 406 optimal weight: 2.9990 chunk 427 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 GLN I 239 GLN I 506 GLN I 804 GLN I 913 GLN ** I1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** K 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 957 GLN K1083 HIS K1108 ASN M 212 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.097032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.079268 restraints weight = 387777.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.081015 restraints weight = 229825.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.082189 restraints weight = 152929.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.082761 restraints weight = 108697.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.083433 restraints weight = 84685.196| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35905 Z= 0.155 Angle : 0.653 10.407 48914 Z= 0.341 Chirality : 0.047 0.239 5502 Planarity : 0.005 0.064 6303 Dihedral : 5.422 32.064 4827 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.12), residues: 4434 helix: -0.75 (0.19), residues: 695 sheet: -1.40 (0.15), residues: 1120 loop : -1.80 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 214 TYR 0.023 0.002 TYR K 707 PHE 0.025 0.002 PHE K1109 TRP 0.029 0.002 TRP K 64 HIS 0.008 0.001 HIS I1048 Details of bonding type rmsd covalent geometry : bond 0.00340 (35856) covalent geometry : angle 0.65055 (48816) SS BOND : bond 0.00429 ( 49) SS BOND : angle 1.43272 ( 98) hydrogen bonds : bond 0.03890 ( 875) hydrogen bonds : angle 6.75080 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.4026 (m-30) cc_final: 0.3692 (m-30) REVERT: A 141 MET cc_start: -0.3047 (mtm) cc_final: -0.3261 (ppp) REVERT: E 54 LEU cc_start: 0.8550 (tp) cc_final: 0.8313 (tp) REVERT: E 200 TYR cc_start: 0.8945 (m-80) cc_final: 0.8362 (m-80) REVERT: E 450 ASN cc_start: 0.9058 (t0) cc_final: 0.8556 (p0) REVERT: E 725 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7609 (tm-30) REVERT: E 869 MET cc_start: 0.8717 (mtm) cc_final: 0.8407 (mtp) REVERT: E 894 LEU cc_start: 0.8895 (tp) cc_final: 0.8600 (tp) REVERT: E 907 ASN cc_start: 0.8611 (m110) cc_final: 0.8375 (m-40) REVERT: E 1050 MET cc_start: 0.8889 (ptp) cc_final: 0.8453 (ptt) REVERT: F 175 MET cc_start: 0.4222 (ppp) cc_final: 0.3876 (ppp) REVERT: H 4 MET cc_start: 0.1178 (mtt) cc_final: 0.0678 (mtt) REVERT: H 61 ARG cc_start: 0.5294 (ptt-90) cc_final: 0.4970 (ptt180) REVERT: H 140 TYR cc_start: 0.5060 (t80) cc_final: 0.4830 (t80) REVERT: I 360 ASN cc_start: 0.8956 (m-40) cc_final: 0.8748 (m-40) REVERT: I 505 TYR cc_start: 0.8367 (m-10) cc_final: 0.8120 (m-10) REVERT: I 543 PHE cc_start: 0.8204 (t80) cc_final: 0.7519 (t80) REVERT: I 546 LEU cc_start: 0.8408 (tt) cc_final: 0.8022 (tt) REVERT: I 775 ASP cc_start: 0.9052 (m-30) cc_final: 0.8821 (m-30) REVERT: I 776 LYS cc_start: 0.9693 (tmtt) cc_final: 0.9256 (tptp) REVERT: I 779 GLN cc_start: 0.9163 (mp10) cc_final: 0.8857 (mp10) REVERT: I 898 PHE cc_start: 0.8553 (t80) cc_final: 0.7908 (t80) REVERT: I 950 ASP cc_start: 0.8950 (p0) cc_final: 0.8611 (p0) REVERT: I 983 ARG cc_start: 0.9409 (ttm-80) cc_final: 0.9114 (mtm180) REVERT: I 1002 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8840 (tm-30) REVERT: I 1010 GLN cc_start: 0.9238 (tp-100) cc_final: 0.8694 (tp-100) REVERT: I 1012 LEU cc_start: 0.9510 (pp) cc_final: 0.9287 (tt) REVERT: I 1017 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8681 (tm-30) REVERT: I 1018 ILE cc_start: 0.9764 (mm) cc_final: 0.9343 (mm) REVERT: I 1023 ASN cc_start: 0.9411 (t0) cc_final: 0.9071 (t0) REVERT: I 1147 SER cc_start: 0.6607 (t) cc_final: 0.6359 (p) REVERT: K 200 TYR cc_start: 0.8778 (m-80) cc_final: 0.8393 (m-80) REVERT: K 346 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8108 (tmt170) REVERT: K 697 MET cc_start: 0.8620 (ptm) cc_final: 0.8242 (ptm) REVERT: K 764 ASN cc_start: 0.8497 (m-40) cc_final: 0.8269 (m110) REVERT: K 780 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8152 (tm-30) REVERT: K 864 LEU cc_start: 0.9018 (mt) cc_final: 0.8581 (mt) REVERT: K 882 ILE cc_start: 0.9038 (mt) cc_final: 0.8647 (mt) REVERT: K 957 GLN cc_start: 0.8638 (mm110) cc_final: 0.8269 (pm20) REVERT: K 1010 GLN cc_start: 0.8959 (pm20) cc_final: 0.8705 (pm20) REVERT: K 1118 ASP cc_start: 0.8983 (p0) cc_final: 0.8669 (m-30) REVERT: M 11 MET cc_start: 0.5192 (ppp) cc_final: 0.3233 (mtm) REVERT: M 77 ASN cc_start: 0.6750 (m110) cc_final: 0.6409 (p0) outliers start: 2 outliers final: 1 residues processed: 361 average time/residue: 0.2103 time to fit residues: 127.6067 Evaluate side-chains 258 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 375 optimal weight: 0.6980 chunk 427 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 428 optimal weight: 5.9990 chunk 356 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 0.0870 chunk 91 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN E 907 ASN ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS H 6 GLN I 121 ASN I 137 ASN I 239 GLN I 542 ASN I 872 GLN I 913 GLN K 52 GLN K 146 HIS K 751 ASN ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 913 GLN K1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.098891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.082417 restraints weight = 351810.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.084584 restraints weight = 217282.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.085079 restraints weight = 149190.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.086074 restraints weight = 109038.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.086442 restraints weight = 79817.534| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35905 Z= 0.115 Angle : 0.590 9.298 48914 Z= 0.303 Chirality : 0.046 0.224 5502 Planarity : 0.005 0.066 6303 Dihedral : 4.751 25.792 4827 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.12), residues: 4434 helix: -0.43 (0.19), residues: 687 sheet: -1.24 (0.15), residues: 1163 loop : -1.65 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 765 TYR 0.024 0.001 TYR E 145 PHE 0.018 0.002 PHE K 192 TRP 0.026 0.002 TRP K 64 HIS 0.007 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00256 (35856) covalent geometry : angle 0.58901 (48816) SS BOND : bond 0.00426 ( 49) SS BOND : angle 1.06444 ( 98) hydrogen bonds : bond 0.03445 ( 875) hydrogen bonds : angle 6.28067 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 1.301 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: A 98 ASP cc_start: 0.2941 (m-30) cc_final: 0.2442 (m-30) REVERT: A 141 MET cc_start: -0.2400 (mtm) cc_final: -0.2842 (ppp) REVERT: D 141 MET cc_start: 0.3597 (tpt) cc_final: 0.3380 (tpt) REVERT: E 200 TYR cc_start: 0.8995 (m-80) cc_final: 0.8434 (m-80) REVERT: E 450 ASN cc_start: 0.9029 (t0) cc_final: 0.8552 (p0) REVERT: E 725 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7616 (tm-30) REVERT: E 802 PHE cc_start: 0.7338 (m-80) cc_final: 0.7070 (m-80) REVERT: E 869 MET cc_start: 0.8620 (mtm) cc_final: 0.8408 (mtp) REVERT: E 894 LEU cc_start: 0.8890 (tp) cc_final: 0.8608 (tp) REVERT: E 950 ASP cc_start: 0.9111 (p0) cc_final: 0.8895 (p0) REVERT: E 1050 MET cc_start: 0.8856 (ptp) cc_final: 0.8402 (ptt) REVERT: F 134 CYS cc_start: 0.8054 (t) cc_final: 0.7354 (m) REVERT: F 175 MET cc_start: 0.4405 (ppp) cc_final: 0.3575 (ppp) REVERT: H 4 MET cc_start: 0.0672 (mtt) cc_final: 0.0194 (mtt) REVERT: I 33 THR cc_start: 0.6058 (p) cc_final: 0.5616 (t) REVERT: I 360 ASN cc_start: 0.8988 (m-40) cc_final: 0.8755 (m-40) REVERT: I 505 TYR cc_start: 0.8491 (m-10) cc_final: 0.8234 (m-10) REVERT: I 517 LEU cc_start: 0.8081 (mt) cc_final: 0.7725 (pp) REVERT: I 543 PHE cc_start: 0.8062 (t80) cc_final: 0.7365 (t80) REVERT: I 546 LEU cc_start: 0.8280 (tt) cc_final: 0.7985 (tt) REVERT: I 774 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8556 (mm-40) REVERT: I 775 ASP cc_start: 0.9062 (m-30) cc_final: 0.8859 (m-30) REVERT: I 776 LYS cc_start: 0.9618 (tmtt) cc_final: 0.9246 (tptp) REVERT: I 779 GLN cc_start: 0.9165 (mp10) cc_final: 0.8890 (mp10) REVERT: I 869 MET cc_start: 0.8793 (mpp) cc_final: 0.8556 (mpp) REVERT: I 1002 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8770 (tm-30) REVERT: I 1010 GLN cc_start: 0.9243 (tp-100) cc_final: 0.8683 (tp-100) REVERT: I 1017 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8704 (tm-30) REVERT: I 1018 ILE cc_start: 0.9744 (mm) cc_final: 0.9356 (mm) REVERT: I 1023 ASN cc_start: 0.9410 (t0) cc_final: 0.9103 (t0) REVERT: K 56 LEU cc_start: 0.9333 (tp) cc_final: 0.8987 (tt) REVERT: K 153 MET cc_start: 0.8268 (mmp) cc_final: 0.8017 (mmm) REVERT: K 200 TYR cc_start: 0.8748 (m-80) cc_final: 0.8486 (m-80) REVERT: K 346 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8162 (tmt170) REVERT: K 697 MET cc_start: 0.8403 (ptm) cc_final: 0.8085 (ptm) REVERT: K 707 TYR cc_start: 0.7024 (t80) cc_final: 0.6695 (t80) REVERT: K 764 ASN cc_start: 0.8475 (m-40) cc_final: 0.8228 (m110) REVERT: K 864 LEU cc_start: 0.8948 (mt) cc_final: 0.8585 (mt) REVERT: K 957 GLN cc_start: 0.8745 (mm110) cc_final: 0.8323 (pm20) REVERT: K 1010 GLN cc_start: 0.8992 (pm20) cc_final: 0.8692 (pm20) REVERT: K 1047 TYR cc_start: 0.8425 (m-10) cc_final: 0.8137 (m-80) REVERT: K 1109 PHE cc_start: 0.7965 (t80) cc_final: 0.7730 (t80) REVERT: K 1118 ASP cc_start: 0.9015 (p0) cc_final: 0.8729 (m-30) REVERT: M 11 MET cc_start: 0.5181 (ppp) cc_final: 0.3551 (ttp) REVERT: M 77 ASN cc_start: 0.6775 (m110) cc_final: 0.6384 (p0) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.2011 time to fit residues: 123.7308 Evaluate side-chains 263 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 252 optimal weight: 10.0000 chunk 356 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 328 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 100 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 66 HIS ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 55 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 913 GLN K 317 ASN ** K 901 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 = 0.4268 r_free = 0.4268 target = 0.098390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.080041 restraints weight = 424551.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.082041 restraints weight = 249199.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.083186 restraints weight = 162356.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.084173 restraints weight = 115523.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.084586 restraints weight = 86298.965| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.8379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35905 Z= 0.128 Angle : 0.584 8.572 48914 Z= 0.303 Chirality : 0.045 0.193 5502 Planarity : 0.005 0.066 6303 Dihedral : 4.677 24.534 4827 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4434 helix: -0.48 (0.19), residues: 684 sheet: -1.15 (0.15), residues: 1151 loop : -1.59 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 214 TYR 0.023 0.001 TYR E 145 PHE 0.059 0.002 PHE K 898 TRP 0.024 0.002 TRP K 64 HIS 0.007 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00283 (35856) covalent geometry : angle 0.58299 (48816) SS BOND : bond 0.00283 ( 49) SS BOND : angle 1.09595 ( 98) hydrogen bonds : bond 0.03508 ( 875) hydrogen bonds : angle 6.16239 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9757.19 seconds wall clock time: 167 minutes 54.73 seconds (10074.73 seconds total)