Starting phenix.real_space_refine on Fri Jun 27 17:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.map" model { file = "/net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ycz_33743/06_2025/7ycz_33743.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 146 5.16 5 C 20495 2.51 5 N 5324 2.21 5 O 6148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.66s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32113 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8035 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "E" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "G" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain breaks: 1 Chain: "I" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 18.85, per 1000 atoms: 0.59 Number of scatterers: 32113 At special positions: 0 Unit cell: (165.984, 208.544, 213.864, 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 146 16.00 O 6148 8.00 N 5324 7.00 C 20495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.35 Conformation dependent library (CDL) restraints added in 4.1 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7810 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 66 sheets defined 17.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.537A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.119A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.121A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.817A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.427A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.581A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.503A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.575A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.529A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 5.681A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 778 removed outlier: 3.634A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.710A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 879 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.661A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.668A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 958 removed outlier: 3.743A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.713A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.968A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.537A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.566A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.968A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.875A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.933A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.750A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.679A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.113A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.725A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.723A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.940A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.211A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.618A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.425A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1031 removed outlier: 3.556A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.854A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.616A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.644A pdb=" N ASP G 84 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU G 85 " --> pdb=" O ALA G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 85' Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.648A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.527A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE A 199 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 228 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.159A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.556A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.956A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 134 removed outlier: 8.280A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.514A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 4.059A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.754A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.408A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.623A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.659A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.598A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 122 removed outlier: 4.093A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.376A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.672A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.578A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.818A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.894A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.853A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.923A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.819A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.557A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.648A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.657A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.577A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.066A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.809A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 727 removed outlier: 7.232A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.026A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.574A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.752A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 93 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.782A pdb=" N TYR D 152 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF7, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.573A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 89 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.641A pdb=" N SER E 117 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER E 140 " --> pdb=" O SER E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.536A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.742A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 41 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.829A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.522A pdb=" N VAL G 10 " --> pdb=" O THR G 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG6, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.468A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 148 through 149 Processing sheet with id=AG8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.754A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 41 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 93 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AH2, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AH3, first strand: chain 'I' and resid 47 through 51 removed outlier: 5.461A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR I 89 " --> pdb=" O TYR I 38 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.79 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6342 1.33 - 1.45: 8151 1.45 - 1.57: 18200 1.57 - 1.69: 0 1.69 - 1.81: 182 Bond restraints: 32875 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" O PHE B 329 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.05e-02 9.07e+03 7.92e+00 bond pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 1.536 1.503 0.033 1.25e-02 6.40e+03 7.01e+00 bond pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.32e-02 5.74e+03 5.95e+00 bond pdb=" CA PRO B 330 " pdb=" CB PRO B 330 " ideal model delta sigma weight residual 1.533 1.499 0.035 1.42e-02 4.96e+03 5.91e+00 bond pdb=" CA PRO C 330 " pdb=" CB PRO C 330 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.47e-02 4.63e+03 5.27e+00 ... (remaining 32870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 44060 1.77 - 3.55: 681 3.55 - 5.32: 54 5.32 - 7.10: 9 7.10 - 8.87: 4 Bond angle restraints: 44808 Sorted by residual: angle pdb=" N PHE C 329 " pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 109.82 101.09 8.73 1.68e+00 3.54e-01 2.70e+01 angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 120.98 115.99 4.99 1.07e+00 8.73e-01 2.18e+01 angle pdb=" C ILE A 332 " pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 120.44 126.52 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.34 118.27 -6.93 1.55e+00 4.16e-01 2.00e+01 angle pdb=" N PRO B 330 " pdb=" CA PRO B 330 " pdb=" C PRO B 330 " ideal model delta sigma weight residual 112.47 121.34 -8.87 2.06e+00 2.36e-01 1.86e+01 ... (remaining 44803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 18795 17.33 - 34.66: 687 34.66 - 51.99: 130 51.99 - 69.32: 18 69.32 - 86.65: 6 Dihedral angle restraints: 19636 sinusoidal: 7501 harmonic: 12135 Sorted by residual: dihedral pdb=" CA ASP E 52 " pdb=" C ASP E 52 " pdb=" N VAL E 53 " pdb=" CA VAL E 53 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA SER D 120 " pdb=" C SER D 120 " pdb=" N ALA D 121 " pdb=" CA ALA D 121 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 19633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4427 0.057 - 0.113: 689 0.113 - 0.170: 24 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 5143 Sorted by residual: chirality pdb=" CA PRO B 330 " pdb=" N PRO B 330 " pdb=" C PRO B 330 " pdb=" CB PRO B 330 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" C PRO C 330 " pdb=" CB PRO C 330 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 5140 not shown) Planarity restraints: 5765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 328 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C ARG A 328 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG A 328 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 329 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO C 330 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 330 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.027 5.00e-02 4.00e+02 ... (remaining 5762 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3041 2.75 - 3.29: 31491 3.29 - 3.83: 52825 3.83 - 4.36: 62055 4.36 - 4.90: 107184 Nonbonded interactions: 256596 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.214 3.040 nonbonded pdb=" O ILE F 106 " pdb=" OH TYR G 38 " model vdw 2.242 3.040 nonbonded pdb=" O ILE D 106 " pdb=" OH TYR E 38 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.247 3.040 nonbonded pdb=" OG SER E 65 " pdb=" OG1 THR E 76 " model vdw 2.248 3.040 ... (remaining 256591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.050 Extract box with map and model: 1.150 Check model and map are aligned: 0.250 Set scattering table: 0.250 Process input model: 73.280 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.042 32921 Z= 0.130 Angle : 0.541 8.873 44900 Z= 0.329 Chirality : 0.040 0.283 5143 Planarity : 0.004 0.050 5765 Dihedral : 9.011 86.654 11688 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.50 % Favored : 94.45 % Rotamer: Outliers : 4.91 % Allowed : 6.33 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.10), residues: 4110 helix: -3.02 (0.13), residues: 634 sheet: -2.50 (0.15), residues: 942 loop : -3.25 (0.10), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.001 0.000 HIS A1064 PHE 0.010 0.001 PHE B 329 TYR 0.005 0.000 TYR C1067 ARG 0.003 0.000 ARG C 466 Details of bonding type rmsd hydrogen bonds : bond 0.27463 ( 916) hydrogen bonds : angle 9.60497 ( 2493) SS BOND : bond 0.00119 ( 46) SS BOND : angle 0.40329 ( 92) covalent geometry : bond 0.00209 (32875) covalent geometry : angle 0.54136 (44808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1110 time to evaluate : 3.503 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: A 32 PHE cc_start: 0.7896 (m-80) cc_final: 0.7649 (m-80) REVERT: A 49 HIS cc_start: 0.7920 (t-90) cc_final: 0.7704 (t-170) REVERT: A 81 ASN cc_start: 0.7754 (m110) cc_final: 0.7530 (m-40) REVERT: A 90 VAL cc_start: 0.8692 (p) cc_final: 0.8361 (t) REVERT: A 97 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8010 (ttpp) REVERT: A 99 ASN cc_start: 0.7695 (m-40) cc_final: 0.7171 (t0) REVERT: A 129 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7467 (ttpp) REVERT: A 193 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7962 (ptmt) REVERT: A 208 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8276 (pt) REVERT: A 269 TYR cc_start: 0.7961 (m-10) cc_final: 0.7484 (m-80) REVERT: A 331 ASN cc_start: 0.6165 (OUTLIER) cc_final: 0.5325 (m-40) REVERT: A 335 LEU cc_start: 0.8429 (tp) cc_final: 0.8115 (mm) REVERT: A 349 SER cc_start: 0.8234 (m) cc_final: 0.7971 (t) REVERT: A 378 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7532 (mtpt) REVERT: A 403 ARG cc_start: 0.7053 (ttp-170) cc_final: 0.6734 (ttp80) REVERT: A 420 ASP cc_start: 0.6803 (m-30) cc_final: 0.6552 (m-30) REVERT: A 421 TYR cc_start: 0.7113 (m-10) cc_final: 0.6265 (m-80) REVERT: A 439 ASN cc_start: 0.7484 (t0) cc_final: 0.7145 (t0) REVERT: A 440 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7275 (ttpp) REVERT: A 461 LEU cc_start: 0.8434 (tp) cc_final: 0.8022 (tp) REVERT: A 467 ASP cc_start: 0.7118 (t0) cc_final: 0.6750 (p0) REVERT: A 496 SER cc_start: 0.8342 (m) cc_final: 0.8079 (t) REVERT: A 512 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 514 SER cc_start: 0.7628 (m) cc_final: 0.7338 (t) REVERT: A 547 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7790 (mtmm) REVERT: A 551 VAL cc_start: 0.8574 (t) cc_final: 0.8369 (t) REVERT: A 572 THR cc_start: 0.8161 (m) cc_final: 0.7407 (p) REVERT: A 573 THR cc_start: 0.8739 (m) cc_final: 0.8494 (p) REVERT: A 578 ASP cc_start: 0.7501 (t0) cc_final: 0.7108 (t70) REVERT: A 588 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 616 ASN cc_start: 0.5434 (t0) cc_final: 0.5034 (t0) REVERT: A 755 GLN cc_start: 0.7167 (mp-120) cc_final: 0.6712 (mp-120) REVERT: A 776 LYS cc_start: 0.8263 (tmmt) cc_final: 0.7898 (ttmt) REVERT: A 955 ASN cc_start: 0.7158 (m-40) cc_final: 0.6849 (m-40) REVERT: A 990 GLU cc_start: 0.7031 (mp0) cc_final: 0.6358 (mp0) REVERT: A 993 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 998 THR cc_start: 0.8449 (m) cc_final: 0.8135 (p) REVERT: A 1017 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 1028 LYS cc_start: 0.8378 (mttt) cc_final: 0.8023 (mtpt) REVERT: A 1029 MET cc_start: 0.8620 (tpp) cc_final: 0.8413 (tpp) REVERT: A 1081 ILE cc_start: 0.7945 (pt) cc_final: 0.7592 (mt) REVERT: A 1097 SER cc_start: 0.8593 (t) cc_final: 0.8297 (p) REVERT: B 104 TRP cc_start: 0.8449 (m-90) cc_final: 0.7775 (m-90) REVERT: B 105 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7563 (mm) REVERT: B 117 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 221 SER cc_start: 0.8174 (p) cc_final: 0.7970 (p) REVERT: B 277 LEU cc_start: 0.8359 (mt) cc_final: 0.8120 (mp) REVERT: B 331 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6668 (m-40) REVERT: B 356 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8191 (mmmt) REVERT: B 383 SER cc_start: 0.8030 (m) cc_final: 0.7541 (p) REVERT: B 394 ASN cc_start: 0.7552 (p0) cc_final: 0.6645 (p0) REVERT: B 434 ILE cc_start: 0.8486 (mt) cc_final: 0.8261 (mm) REVERT: B 437 ASN cc_start: 0.7960 (t0) cc_final: 0.7456 (t0) REVERT: B 440 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8197 (tppt) REVERT: B 456 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6809 (p90) REVERT: B 532 ASN cc_start: 0.7936 (m-40) cc_final: 0.7728 (m-40) REVERT: B 541 PHE cc_start: 0.7803 (p90) cc_final: 0.7567 (p90) REVERT: B 586 ASP cc_start: 0.7590 (t0) cc_final: 0.7187 (t0) REVERT: B 616 ASN cc_start: 0.7154 (t0) cc_final: 0.6271 (t0) REVERT: B 707 TYR cc_start: 0.8092 (t80) cc_final: 0.7706 (t80) REVERT: B 711 SER cc_start: 0.8153 (t) cc_final: 0.7908 (p) REVERT: B 762 GLN cc_start: 0.7658 (pt0) cc_final: 0.7351 (pt0) REVERT: B 787 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7474 (mm-40) REVERT: B 854 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8103 (ttmm) REVERT: B 868 GLU cc_start: 0.7337 (tp30) cc_final: 0.6927 (tp30) REVERT: B 888 PHE cc_start: 0.8653 (p90) cc_final: 0.8369 (p90) REVERT: B 921 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7755 (mmmt) REVERT: B 922 LEU cc_start: 0.8812 (tp) cc_final: 0.8601 (tp) REVERT: B 933 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8175 (mtmm) REVERT: B 964 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7932 (ttmm) REVERT: B 968 SER cc_start: 0.8367 (m) cc_final: 0.8026 (p) REVERT: B 1017 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6554 (tm-30) REVERT: B 1019 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6755 (ttp80) REVERT: B 1111 GLU cc_start: 0.7791 (tt0) cc_final: 0.7564 (tt0) REVERT: B 1118 ASP cc_start: 0.7394 (t70) cc_final: 0.7183 (t0) REVERT: B 1136 THR cc_start: 0.8461 (t) cc_final: 0.8197 (t) REVERT: B 1141 LEU cc_start: 0.8423 (tp) cc_final: 0.7969 (tp) REVERT: C 47 VAL cc_start: 0.8808 (m) cc_final: 0.8566 (p) REVERT: C 81 ASN cc_start: 0.7904 (p0) cc_final: 0.7369 (p0) REVERT: C 85 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.6539 (Cg_exo) REVERT: C 121 ASN cc_start: 0.6742 (t0) cc_final: 0.6374 (t0) REVERT: C 132 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6635 (tp30) REVERT: C 224 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6477 (mm-30) REVERT: C 281 GLU cc_start: 0.6623 (pp20) cc_final: 0.6024 (pp20) REVERT: C 287 ASP cc_start: 0.7428 (p0) cc_final: 0.7056 (p0) REVERT: C 290 ASP cc_start: 0.7446 (t0) cc_final: 0.7220 (t0) REVERT: C 362 VAL cc_start: 0.8278 (t) cc_final: 0.7961 (p) REVERT: C 366 SER cc_start: 0.8662 (m) cc_final: 0.8195 (p) REVERT: C 429 PHE cc_start: 0.7871 (t80) cc_final: 0.7667 (t80) REVERT: C 433 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 454 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.6839 (ttm-80) REVERT: C 456 PHE cc_start: 0.6957 (m-80) cc_final: 0.6484 (m-80) REVERT: C 461 LEU cc_start: 0.7237 (tp) cc_final: 0.6941 (tp) REVERT: C 462 LYS cc_start: 0.7724 (ptpp) cc_final: 0.7451 (ptpp) REVERT: C 465 GLU cc_start: 0.6760 (tt0) cc_final: 0.6251 (tt0) REVERT: C 470 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.6890 (p) REVERT: C 511 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (t) REVERT: C 514 SER cc_start: 0.8363 (m) cc_final: 0.8010 (p) REVERT: C 616 ASN cc_start: 0.4976 (t0) cc_final: 0.4399 (t0) REVERT: C 654 GLU cc_start: 0.7243 (pm20) cc_final: 0.6869 (pm20) REVERT: C 742 ILE cc_start: 0.8727 (mm) cc_final: 0.8448 (mt) REVERT: C 762 GLN cc_start: 0.7655 (tt0) cc_final: 0.7376 (tt0) REVERT: C 776 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7923 (ttpt) REVERT: C 823 PHE cc_start: 0.7325 (m-80) cc_final: 0.7091 (m-80) REVERT: C 868 GLU cc_start: 0.7315 (tp30) cc_final: 0.6766 (tp30) REVERT: C 922 LEU cc_start: 0.8757 (tp) cc_final: 0.8501 (tt) REVERT: C 927 PHE cc_start: 0.8314 (t80) cc_final: 0.8038 (t80) REVERT: C 964 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7810 (ttpp) REVERT: C 990 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7313 (mm-30) REVERT: C 993 ILE cc_start: 0.9037 (tp) cc_final: 0.8763 (tt) REVERT: C 1002 GLN cc_start: 0.7031 (tp-100) cc_final: 0.6731 (tp-100) REVERT: C 1017 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 1038 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7944 (mtmm) REVERT: C 1072 GLU cc_start: 0.7722 (pm20) cc_final: 0.7462 (pm20) REVERT: C 1084 ASP cc_start: 0.7826 (m-30) cc_final: 0.7623 (m-30) REVERT: C 1118 ASP cc_start: 0.6793 (t0) cc_final: 0.6551 (t0) REVERT: C 1123 SER cc_start: 0.8698 (t) cc_final: 0.8192 (p) REVERT: C 1134 ASN cc_start: 0.5488 (m-40) cc_final: 0.5225 (m-40) REVERT: D 3 THR cc_start: 0.7272 (p) cc_final: 0.7021 (p) REVERT: D 15 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6568 (mmtm) REVERT: D 59 LYS cc_start: 0.7689 (mttp) cc_final: 0.7325 (mttp) REVERT: D 78 ASN cc_start: 0.6614 (m110) cc_final: 0.6375 (m110) REVERT: D 182 LEU cc_start: 0.7751 (mt) cc_final: 0.7402 (pp) REVERT: E 104 THR cc_start: 0.7862 (m) cc_final: 0.7510 (p) REVERT: E 120 LEU cc_start: 0.1108 (OUTLIER) cc_final: 0.0836 (pp) REVERT: F 2 VAL cc_start: 0.8244 (t) cc_final: 0.7938 (p) REVERT: F 23 THR cc_start: 0.7825 (m) cc_final: 0.7585 (p) REVERT: H 29 LEU cc_start: 0.9150 (tp) cc_final: 0.8842 (tp) outliers start: 176 outliers final: 74 residues processed: 1229 average time/residue: 0.4539 time to fit residues: 883.0101 Evaluate side-chains 977 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 888 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 6.9990 chunk 313 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 0.0670 chunk 324 optimal weight: 0.0050 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 ASN A 121 ASN A 125 ASN A 137 ASN A 186 ASN A 331 ASN A 343 ASN A 417 ASN A 540 ASN A 644 GLN A 709 ASN A 784 GLN A 913 GLN A 914 ASN A 965 GLN A1011 GLN A1048 HIS A1074 ASN B 81 ASN B 164 ASN B 165 ASN B 173 GLN B 194 ASN B 205 HIS B 218 GLN B 271 GLN B 331 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 703 ASN B 762 GLN B 784 GLN B 853 GLN B 901 GLN B 992 GLN B1002 GLN B1005 GLN B1011 GLN B1048 HIS B1054 GLN B1119 ASN C 81 ASN C 87 ASN C 173 GLN C 186 ASN C 194 ASN C 370 ASN C 409 GLN C 505 HIS C 540 ASN C 563 GLN C 710 ASN C 762 GLN C 853 GLN C 901 GLN C 913 GLN C 914 ASN C1011 GLN C1048 HIS C1125 ASN D 41 GLN D 199 GLN E 6 GLN E 39 GLN E 41 HIS E 111 GLN E 197 GLN F 41 GLN F 199 GLN G 39 GLN G 71 ASN G 81 GLN G 111 GLN G 197 GLN H 41 GLN I 39 GLN I 40 GLN I 41 HIS I 81 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.164766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129344 restraints weight = 53660.722| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.36 r_work: 0.3503 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 32921 Z= 0.133 Angle : 0.615 15.837 44900 Z= 0.312 Chirality : 0.045 0.368 5143 Planarity : 0.005 0.046 5765 Dihedral : 6.512 77.014 4638 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.52 % Allowed : 12.79 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.12), residues: 4110 helix: -0.63 (0.19), residues: 667 sheet: -1.97 (0.15), residues: 985 loop : -2.79 (0.11), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 55 HIS 0.007 0.001 HIS C 505 PHE 0.028 0.002 PHE C 55 TYR 0.024 0.001 TYR A1067 ARG 0.009 0.001 ARG D 217 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 916) hydrogen bonds : angle 6.23046 ( 2493) SS BOND : bond 0.00474 ( 46) SS BOND : angle 2.27923 ( 92) covalent geometry : bond 0.00292 (32875) covalent geometry : angle 0.60645 (44808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 879 time to evaluate : 3.574 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 32 PHE cc_start: 0.8305 (m-80) cc_final: 0.8017 (m-10) REVERT: A 58 PHE cc_start: 0.8744 (m-10) cc_final: 0.8291 (m-80) REVERT: A 97 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8178 (ttpp) REVERT: A 121 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.6737 (p0) REVERT: A 193 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8338 (ptmm) REVERT: A 228 ASP cc_start: 0.7819 (t0) cc_final: 0.7508 (t0) REVERT: A 235 ILE cc_start: 0.8500 (mm) cc_final: 0.8268 (tp) REVERT: A 269 TYR cc_start: 0.8403 (m-10) cc_final: 0.7802 (m-10) REVERT: A 287 ASP cc_start: 0.8142 (p0) cc_final: 0.7882 (p0) REVERT: A 335 LEU cc_start: 0.8516 (tp) cc_final: 0.8256 (mm) REVERT: A 353 TRP cc_start: 0.8787 (p-90) cc_final: 0.8464 (p-90) REVERT: A 378 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7754 (mtpt) REVERT: A 392 PHE cc_start: 0.8421 (m-80) cc_final: 0.8211 (m-10) REVERT: A 398 ASP cc_start: 0.7941 (m-30) cc_final: 0.7433 (m-30) REVERT: A 403 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7643 (mtp180) REVERT: A 420 ASP cc_start: 0.7218 (m-30) cc_final: 0.6867 (m-30) REVERT: A 421 TYR cc_start: 0.7472 (m-10) cc_final: 0.6493 (m-80) REVERT: A 440 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7773 (ttpp) REVERT: A 448 ASN cc_start: 0.8201 (t0) cc_final: 0.7276 (t0) REVERT: A 451 TYR cc_start: 0.7191 (m-80) cc_final: 0.6923 (m-80) REVERT: A 465 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 467 ASP cc_start: 0.7931 (t0) cc_final: 0.6954 (p0) REVERT: A 496 SER cc_start: 0.8705 (m) cc_final: 0.8434 (t) REVERT: A 514 SER cc_start: 0.8006 (m) cc_final: 0.7587 (p) REVERT: A 547 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8297 (mtpp) REVERT: A 568 ASP cc_start: 0.7672 (p0) cc_final: 0.7185 (p0) REVERT: A 572 THR cc_start: 0.8353 (m) cc_final: 0.7686 (p) REVERT: A 573 THR cc_start: 0.8856 (m) cc_final: 0.8605 (p) REVERT: A 578 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t70) REVERT: A 588 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 616 ASN cc_start: 0.6201 (t0) cc_final: 0.5714 (t0) REVERT: A 643 PHE cc_start: 0.8209 (t80) cc_final: 0.7944 (t80) REVERT: A 697 MET cc_start: 0.8437 (ttp) cc_final: 0.8167 (ttm) REVERT: A 752 LEU cc_start: 0.8338 (mm) cc_final: 0.7986 (mm) REVERT: A 755 GLN cc_start: 0.7620 (mp-120) cc_final: 0.7112 (mp-120) REVERT: A 776 LYS cc_start: 0.8626 (tmmt) cc_final: 0.8318 (ttpp) REVERT: A 790 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8322 (mtmm) REVERT: A 921 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8094 (mtpp) REVERT: A 945 LEU cc_start: 0.8491 (mm) cc_final: 0.8195 (mp) REVERT: A 949 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7896 (mm-40) REVERT: A 957 GLN cc_start: 0.8330 (pt0) cc_final: 0.8069 (pt0) REVERT: A 990 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 1017 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 1034 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8990 (mt) REVERT: A 1073 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8152 (ttpt) REVERT: A 1081 ILE cc_start: 0.8300 (pt) cc_final: 0.7901 (mt) REVERT: A 1097 SER cc_start: 0.8531 (t) cc_final: 0.8191 (p) REVERT: B 104 TRP cc_start: 0.8777 (m-90) cc_final: 0.8500 (m-90) REVERT: B 105 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 117 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 158 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5393 (tmm160) REVERT: B 221 SER cc_start: 0.8323 (p) cc_final: 0.8073 (p) REVERT: B 223 LEU cc_start: 0.8056 (mp) cc_final: 0.7794 (mt) REVERT: B 239 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 356 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8365 (tttm) REVERT: B 394 ASN cc_start: 0.8044 (p0) cc_final: 0.7450 (p0) REVERT: B 414 GLN cc_start: 0.7751 (mp10) cc_final: 0.7031 (mp10) REVERT: B 440 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8381 (tppt) REVERT: B 456 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6977 (p90) REVERT: B 557 LYS cc_start: 0.8682 (mttp) cc_final: 0.8463 (mtmm) REVERT: B 586 ASP cc_start: 0.8181 (t0) cc_final: 0.7926 (t0) REVERT: B 587 ILE cc_start: 0.8654 (mt) cc_final: 0.8412 (mm) REVERT: B 615 VAL cc_start: 0.8562 (t) cc_final: 0.8215 (m) REVERT: B 616 ASN cc_start: 0.7768 (t0) cc_final: 0.7442 (t0) REVERT: B 651 ILE cc_start: 0.8865 (pt) cc_final: 0.8635 (pt) REVERT: B 695 TYR cc_start: 0.8597 (p90) cc_final: 0.7867 (p90) REVERT: B 711 SER cc_start: 0.8636 (t) cc_final: 0.8409 (p) REVERT: B 731 MET cc_start: 0.8859 (ptp) cc_final: 0.8656 (ptm) REVERT: B 750 SER cc_start: 0.8929 (m) cc_final: 0.8707 (p) REVERT: B 787 GLN cc_start: 0.8242 (mm-40) cc_final: 0.8015 (mm-40) REVERT: B 803 SER cc_start: 0.8672 (m) cc_final: 0.8397 (p) REVERT: B 820 ASP cc_start: 0.7963 (t0) cc_final: 0.7713 (m-30) REVERT: B 851 CYS cc_start: 0.8629 (m) cc_final: 0.8062 (p) REVERT: B 854 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8238 (ttmm) REVERT: B 964 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8631 (ttmm) REVERT: B 968 SER cc_start: 0.8779 (m) cc_final: 0.8519 (p) REVERT: B 985 ASP cc_start: 0.8024 (p0) cc_final: 0.7757 (p0) REVERT: B 990 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 993 ILE cc_start: 0.8617 (tp) cc_final: 0.8348 (tt) REVERT: B 994 ASP cc_start: 0.8394 (m-30) cc_final: 0.7960 (t70) REVERT: B 1014 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8339 (mtm-85) REVERT: B 1017 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 1118 ASP cc_start: 0.8356 (t70) cc_final: 0.8115 (t0) REVERT: B 1136 THR cc_start: 0.8773 (t) cc_final: 0.8557 (t) REVERT: B 1141 LEU cc_start: 0.8789 (tp) cc_final: 0.8350 (tp) REVERT: C 41 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: C 47 VAL cc_start: 0.8958 (m) cc_final: 0.8753 (p) REVERT: C 81 ASN cc_start: 0.8540 (p0) cc_final: 0.8084 (p0) REVERT: C 121 ASN cc_start: 0.7413 (t0) cc_final: 0.7132 (t0) REVERT: C 132 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6706 (tp30) REVERT: C 206 THR cc_start: 0.8690 (t) cc_final: 0.8393 (p) REVERT: C 223 LEU cc_start: 0.8436 (mp) cc_final: 0.8086 (mp) REVERT: C 224 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7443 (mp0) REVERT: C 310 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8561 (ttpp) REVERT: C 395 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8473 (t) REVERT: C 417 ASN cc_start: 0.7845 (t0) cc_final: 0.7442 (t0) REVERT: C 418 ILE cc_start: 0.8548 (pt) cc_final: 0.8225 (pt) REVERT: C 454 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7200 (ttm170) REVERT: C 467 ASP cc_start: 0.7799 (p0) cc_final: 0.7268 (p0) REVERT: C 503 VAL cc_start: 0.8468 (t) cc_final: 0.8171 (m) REVERT: C 511 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8468 (t) REVERT: C 559 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8005 (t80) REVERT: C 599 THR cc_start: 0.8463 (m) cc_final: 0.8258 (t) REVERT: C 615 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (t) REVERT: C 616 ASN cc_start: 0.5585 (t0) cc_final: 0.5164 (t0) REVERT: C 654 GLU cc_start: 0.8022 (pm20) cc_final: 0.7700 (pm20) REVERT: C 660 TYR cc_start: 0.8659 (m-80) cc_final: 0.8262 (m-80) REVERT: C 695 TYR cc_start: 0.8514 (p90) cc_final: 0.8178 (p90) REVERT: C 742 ILE cc_start: 0.8770 (mm) cc_final: 0.8514 (mt) REVERT: C 752 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8641 (mm) REVERT: C 765 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7926 (ttp80) REVERT: C 776 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8382 (ttpt) REVERT: C 859 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8093 (p) REVERT: C 868 GLU cc_start: 0.7863 (tp30) cc_final: 0.7314 (tp30) REVERT: C 902 MET cc_start: 0.8544 (tpp) cc_final: 0.8074 (mmm) REVERT: C 947 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8240 (mtpp) REVERT: C 964 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8332 (ttpp) REVERT: C 993 ILE cc_start: 0.9085 (tp) cc_final: 0.8860 (tp) REVERT: C 1002 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7321 (tp-100) REVERT: C 1005 GLN cc_start: 0.8667 (tp40) cc_final: 0.8306 (tp40) REVERT: C 1017 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 1018 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8143 (mp) REVERT: C 1073 LYS cc_start: 0.8222 (tttm) cc_final: 0.7991 (ttmm) REVERT: C 1102 TRP cc_start: 0.8730 (m100) cc_final: 0.8226 (m100) REVERT: C 1118 ASP cc_start: 0.8067 (t0) cc_final: 0.7767 (t0) REVERT: C 1123 SER cc_start: 0.9095 (t) cc_final: 0.8581 (p) REVERT: C 1134 ASN cc_start: 0.6028 (m-40) cc_final: 0.5717 (m110) REVERT: D 2 VAL cc_start: 0.8943 (t) cc_final: 0.8702 (p) REVERT: D 4 LEU cc_start: 0.8208 (mt) cc_final: 0.7974 (mt) REVERT: D 15 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6390 (mmtm) REVERT: D 29 LEU cc_start: 0.9183 (tp) cc_final: 0.8891 (tt) REVERT: D 59 LYS cc_start: 0.8197 (mttp) cc_final: 0.7884 (mttp) REVERT: D 84 MET cc_start: 0.7644 (ptp) cc_final: 0.7419 (ptp) REVERT: E 104 THR cc_start: 0.8066 (m) cc_final: 0.7863 (p) REVERT: F 2 VAL cc_start: 0.8502 (t) cc_final: 0.8170 (p) REVERT: F 20 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5822 (tt) REVERT: H 84 MET cc_start: 0.3800 (pmm) cc_final: 0.1832 (tpp) outliers start: 198 outliers final: 107 residues processed: 1002 average time/residue: 0.4562 time to fit residues: 723.1145 Evaluate side-chains 926 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 799 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 268 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 370 optimal weight: 40.0000 chunk 294 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 336 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 81 ASN A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 913 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 580 GLN B 965 GLN C 165 ASN C 505 HIS C 542 ASN C 954 HIS C1002 GLN C1048 HIS E 33 ASN I 33 ASN I 41 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.160839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124921 restraints weight = 54118.748| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.36 r_work: 0.3445 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32921 Z= 0.185 Angle : 0.619 17.089 44900 Z= 0.313 Chirality : 0.045 0.318 5143 Planarity : 0.005 0.069 5765 Dihedral : 6.319 76.133 4602 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.30 % Allowed : 15.33 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 4110 helix: 0.20 (0.20), residues: 658 sheet: -1.61 (0.15), residues: 991 loop : -2.57 (0.11), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.008 0.001 HIS B 205 PHE 0.028 0.002 PHE C 429 TYR 0.045 0.002 TYR A 170 ARG 0.012 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 916) hydrogen bonds : angle 5.68955 ( 2493) SS BOND : bond 0.00823 ( 46) SS BOND : angle 1.85068 ( 92) covalent geometry : bond 0.00413 (32875) covalent geometry : angle 0.61438 (44808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 841 time to evaluate : 3.375 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 164 ASN cc_start: 0.7238 (m-40) cc_final: 0.7000 (m-40) REVERT: A 205 HIS cc_start: 0.7778 (t-90) cc_final: 0.7456 (t-90) REVERT: A 209 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 228 ASP cc_start: 0.8019 (t0) cc_final: 0.7626 (t0) REVERT: A 269 TYR cc_start: 0.8449 (m-10) cc_final: 0.7972 (m-10) REVERT: A 287 ASP cc_start: 0.8141 (p0) cc_final: 0.7911 (p0) REVERT: A 290 ASP cc_start: 0.7425 (t70) cc_final: 0.6997 (t0) REVERT: A 335 LEU cc_start: 0.8690 (tp) cc_final: 0.8466 (mm) REVERT: A 353 TRP cc_start: 0.8847 (p-90) cc_final: 0.8255 (p-90) REVERT: A 378 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7969 (mtpt) REVERT: A 392 PHE cc_start: 0.8580 (m-80) cc_final: 0.8212 (m-80) REVERT: A 398 ASP cc_start: 0.7897 (m-30) cc_final: 0.7434 (m-30) REVERT: A 403 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7458 (mtp-110) REVERT: A 421 TYR cc_start: 0.7640 (m-10) cc_final: 0.6664 (m-80) REVERT: A 440 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7933 (ttpp) REVERT: A 448 ASN cc_start: 0.8176 (t0) cc_final: 0.7446 (t0) REVERT: A 451 TYR cc_start: 0.7399 (m-80) cc_final: 0.6983 (m-80) REVERT: A 461 LEU cc_start: 0.8726 (tp) cc_final: 0.8512 (tp) REVERT: A 496 SER cc_start: 0.8818 (m) cc_final: 0.8483 (t) REVERT: A 514 SER cc_start: 0.8143 (m) cc_final: 0.7659 (p) REVERT: A 547 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8297 (mtpp) REVERT: A 573 THR cc_start: 0.8890 (m) cc_final: 0.8556 (p) REVERT: A 588 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 697 MET cc_start: 0.8537 (ttp) cc_final: 0.8215 (ttm) REVERT: A 719 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (p) REVERT: A 776 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8358 (ttpp) REVERT: A 902 MET cc_start: 0.8665 (mmm) cc_final: 0.8452 (mmt) REVERT: A 921 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: A 945 LEU cc_start: 0.8528 (mm) cc_final: 0.8290 (mp) REVERT: A 949 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7891 (mm-40) REVERT: A 990 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: A 1017 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 1019 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7778 (ttp80) REVERT: A 1073 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8203 (ttpt) REVERT: A 1081 ILE cc_start: 0.8392 (pt) cc_final: 0.8073 (mt) REVERT: A 1097 SER cc_start: 0.8541 (t) cc_final: 0.8263 (p) REVERT: B 96 GLU cc_start: 0.7229 (pt0) cc_final: 0.6908 (pt0) REVERT: B 105 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 117 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8262 (tt) REVERT: B 158 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5409 (tmm160) REVERT: B 221 SER cc_start: 0.8476 (p) cc_final: 0.8269 (p) REVERT: B 237 ARG cc_start: 0.8457 (mtm180) cc_final: 0.8220 (mtp85) REVERT: B 239 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 273 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7864 (tpp80) REVERT: B 386 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7872 (mmmt) REVERT: B 394 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7256 (p0) REVERT: B 414 GLN cc_start: 0.7849 (mp10) cc_final: 0.7051 (mp10) REVERT: B 440 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8378 (tppt) REVERT: B 456 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6476 (p90) REVERT: B 568 ASP cc_start: 0.7945 (p0) cc_final: 0.7640 (p0) REVERT: B 649 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 651 ILE cc_start: 0.8947 (pt) cc_final: 0.8732 (pt) REVERT: B 655 TYR cc_start: 0.8636 (t80) cc_final: 0.8321 (t80) REVERT: B 695 TYR cc_start: 0.8594 (p90) cc_final: 0.7823 (p90) REVERT: B 711 SER cc_start: 0.8721 (t) cc_final: 0.8455 (p) REVERT: B 723 THR cc_start: 0.8719 (t) cc_final: 0.8505 (p) REVERT: B 759 PHE cc_start: 0.7313 (t80) cc_final: 0.6465 (t80) REVERT: B 779 GLN cc_start: 0.8437 (tp40) cc_final: 0.8229 (tp40) REVERT: B 787 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8071 (mm-40) REVERT: B 803 SER cc_start: 0.8706 (m) cc_final: 0.8450 (p) REVERT: B 851 CYS cc_start: 0.8604 (m) cc_final: 0.7920 (p) REVERT: B 854 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8318 (ttmm) REVERT: B 868 GLU cc_start: 0.8044 (tp30) cc_final: 0.7666 (tp30) REVERT: B 964 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8620 (ttmm) REVERT: B 965 GLN cc_start: 0.8991 (mm110) cc_final: 0.8764 (mm-40) REVERT: B 968 SER cc_start: 0.8971 (m) cc_final: 0.8615 (p) REVERT: B 985 ASP cc_start: 0.7970 (p0) cc_final: 0.7646 (p0) REVERT: B 990 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7823 (mm-30) REVERT: B 993 ILE cc_start: 0.8650 (tp) cc_final: 0.8418 (tp) REVERT: B 1002 GLN cc_start: 0.8519 (tt0) cc_final: 0.8251 (tt0) REVERT: B 1107 ARG cc_start: 0.7697 (mtt90) cc_final: 0.7394 (mtt90) REVERT: B 1141 LEU cc_start: 0.8837 (tp) cc_final: 0.8369 (tp) REVERT: C 30 ASN cc_start: 0.8651 (t0) cc_final: 0.8389 (p0) REVERT: C 53 ASP cc_start: 0.7505 (m-30) cc_final: 0.7295 (m-30) REVERT: C 121 ASN cc_start: 0.7537 (t0) cc_final: 0.7244 (t0) REVERT: C 132 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6558 (tp30) REVERT: C 206 THR cc_start: 0.8792 (t) cc_final: 0.8556 (p) REVERT: C 223 LEU cc_start: 0.8506 (mp) cc_final: 0.8259 (mp) REVERT: C 224 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7543 (mp0) REVERT: C 239 GLN cc_start: 0.7775 (tp40) cc_final: 0.7528 (tt0) REVERT: C 310 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (ttpt) REVERT: C 324 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 386 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8140 (ptpp) REVERT: C 417 ASN cc_start: 0.8114 (t0) cc_final: 0.7355 (t0) REVERT: C 468 ILE cc_start: 0.8453 (tp) cc_final: 0.8244 (tp) REVERT: C 503 VAL cc_start: 0.8614 (t) cc_final: 0.8390 (m) REVERT: C 511 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8462 (t) REVERT: C 532 ASN cc_start: 0.8843 (t0) cc_final: 0.8594 (m-40) REVERT: C 556 ASN cc_start: 0.8604 (m110) cc_final: 0.8396 (p0) REVERT: C 578 ASP cc_start: 0.7890 (t0) cc_final: 0.7582 (t70) REVERT: C 599 THR cc_start: 0.8622 (m) cc_final: 0.8396 (t) REVERT: C 654 GLU cc_start: 0.8058 (pm20) cc_final: 0.7792 (pm20) REVERT: C 737 ASP cc_start: 0.7451 (t70) cc_final: 0.7218 (t0) REVERT: C 776 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8443 (ttpt) REVERT: C 859 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8112 (p) REVERT: C 868 GLU cc_start: 0.7906 (tp30) cc_final: 0.7337 (tp30) REVERT: C 902 MET cc_start: 0.8506 (tpp) cc_final: 0.8122 (mmm) REVERT: C 960 ASN cc_start: 0.8805 (t0) cc_final: 0.8555 (t0) REVERT: C 964 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8369 (ttpp) REVERT: C 969 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: C 993 ILE cc_start: 0.9137 (tp) cc_final: 0.8861 (tp) REVERT: C 1002 GLN cc_start: 0.7930 (tp40) cc_final: 0.7099 (tp40) REVERT: C 1005 GLN cc_start: 0.8689 (tp40) cc_final: 0.8265 (tp40) REVERT: C 1017 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7817 (tm-30) REVERT: C 1018 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 1072 GLU cc_start: 0.8499 (pm20) cc_final: 0.8220 (pm20) REVERT: C 1073 LYS cc_start: 0.8221 (tttm) cc_final: 0.7972 (ttmm) REVERT: C 1123 SER cc_start: 0.9082 (t) cc_final: 0.8680 (m) REVERT: C 1127 ASP cc_start: 0.7388 (p0) cc_final: 0.7081 (p0) REVERT: C 1134 ASN cc_start: 0.6383 (m-40) cc_final: 0.6114 (m110) REVERT: D 2 VAL cc_start: 0.8966 (t) cc_final: 0.8717 (p) REVERT: D 15 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6489 (mmtm) REVERT: D 59 LYS cc_start: 0.8301 (mttp) cc_final: 0.7937 (mttp) REVERT: D 84 MET cc_start: 0.7760 (ptp) cc_final: 0.7500 (ptp) REVERT: D 182 LEU cc_start: 0.7990 (mt) cc_final: 0.7789 (mt) REVERT: E 44 GLN cc_start: 0.7811 (mp10) cc_final: 0.7375 (mp10) REVERT: E 104 THR cc_start: 0.8110 (m) cc_final: 0.7834 (p) REVERT: F 2 VAL cc_start: 0.8513 (t) cc_final: 0.8179 (p) REVERT: H 84 MET cc_start: 0.4291 (pmm) cc_final: 0.1450 (tpt) outliers start: 190 outliers final: 122 residues processed: 949 average time/residue: 0.4804 time to fit residues: 721.9509 Evaluate side-chains 932 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 792 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 245 optimal weight: 0.1980 chunk 7 optimal weight: 0.0770 chunk 91 optimal weight: 0.0270 chunk 138 optimal weight: 6.9990 chunk 396 optimal weight: 0.7980 chunk 266 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 310 optimal weight: 0.9980 chunk 359 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 165 ASN A 218 GLN A1088 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 675 GLN B1083 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 616 ASN C 913 GLN C 955 ASN E 39 GLN G 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126084 restraints weight = 54184.778| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.74 r_work: 0.3448 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 32921 Z= 0.107 Angle : 0.581 12.950 44900 Z= 0.290 Chirality : 0.044 0.253 5143 Planarity : 0.004 0.057 5765 Dihedral : 6.166 76.142 4593 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.91 % Allowed : 16.67 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 4110 helix: 0.65 (0.21), residues: 661 sheet: -1.34 (0.16), residues: 995 loop : -2.39 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 55 HIS 0.007 0.001 HIS B 205 PHE 0.028 0.001 PHE C 429 TYR 0.039 0.001 TYR A 170 ARG 0.009 0.000 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 916) hydrogen bonds : angle 5.37253 ( 2493) SS BOND : bond 0.00390 ( 46) SS BOND : angle 1.42843 ( 92) covalent geometry : bond 0.00242 (32875) covalent geometry : angle 0.57794 (44808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 808 time to evaluate : 3.462 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: A 87 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.6698 (p0) REVERT: A 99 ASN cc_start: 0.7760 (m-40) cc_final: 0.7461 (t0) REVERT: A 108 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7450 (t) REVERT: A 205 HIS cc_start: 0.7581 (t-90) cc_final: 0.7285 (t-90) REVERT: A 209 ILE cc_start: 0.8518 (tt) cc_final: 0.8248 (mp) REVERT: A 228 ASP cc_start: 0.7677 (t0) cc_final: 0.7229 (t0) REVERT: A 269 TYR cc_start: 0.8267 (m-10) cc_final: 0.7739 (m-10) REVERT: A 287 ASP cc_start: 0.7965 (p0) cc_final: 0.7689 (p0) REVERT: A 290 ASP cc_start: 0.7133 (t70) cc_final: 0.6871 (t0) REVERT: A 332 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7201 (mp) REVERT: A 335 LEU cc_start: 0.8582 (tp) cc_final: 0.8336 (mm) REVERT: A 353 TRP cc_start: 0.8705 (p-90) cc_final: 0.7981 (p-90) REVERT: A 378 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7577 (mtpt) REVERT: A 392 PHE cc_start: 0.8459 (m-80) cc_final: 0.8247 (m-80) REVERT: A 403 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7493 (mtp85) REVERT: A 421 TYR cc_start: 0.7428 (m-10) cc_final: 0.6485 (m-80) REVERT: A 440 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7641 (ttpp) REVERT: A 448 ASN cc_start: 0.8050 (t0) cc_final: 0.7514 (t0) REVERT: A 451 TYR cc_start: 0.7172 (m-80) cc_final: 0.6841 (m-80) REVERT: A 514 SER cc_start: 0.7955 (m) cc_final: 0.7561 (p) REVERT: A 547 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8142 (mtpp) REVERT: A 572 THR cc_start: 0.8769 (t) cc_final: 0.8315 (p) REVERT: A 573 THR cc_start: 0.8806 (m) cc_final: 0.8507 (p) REVERT: A 588 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 599 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8364 (p) REVERT: A 752 LEU cc_start: 0.8259 (mm) cc_final: 0.8035 (mm) REVERT: A 755 GLN cc_start: 0.7614 (mp-120) cc_final: 0.7044 (mp-120) REVERT: A 776 LYS cc_start: 0.8528 (tmmt) cc_final: 0.8178 (ttpp) REVERT: A 900 MET cc_start: 0.8309 (mtp) cc_final: 0.8095 (mtt) REVERT: A 921 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7913 (mtpp) REVERT: A 945 LEU cc_start: 0.8361 (mm) cc_final: 0.8161 (mp) REVERT: A 949 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7782 (mm-40) REVERT: A 990 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 1017 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 1073 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8000 (ttpp) REVERT: A 1081 ILE cc_start: 0.8169 (pt) cc_final: 0.7862 (mt) REVERT: A 1097 SER cc_start: 0.8398 (t) cc_final: 0.8089 (p) REVERT: A 1107 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7049 (mtt-85) REVERT: B 96 GLU cc_start: 0.6919 (pt0) cc_final: 0.6610 (pt0) REVERT: B 105 ILE cc_start: 0.8243 (mm) cc_final: 0.7845 (mp) REVERT: B 158 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5330 (tmm160) REVERT: B 189 GLU cc_start: 0.7509 (pt0) cc_final: 0.7122 (pt0) REVERT: B 237 ARG cc_start: 0.8292 (mtm180) cc_final: 0.8005 (mtp85) REVERT: B 239 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 269 TYR cc_start: 0.8047 (m-80) cc_final: 0.7812 (m-80) REVERT: B 358 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 386 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7817 (mmmt) REVERT: B 393 THR cc_start: 0.8741 (p) cc_final: 0.8383 (t) REVERT: B 414 GLN cc_start: 0.7909 (mp10) cc_final: 0.7236 (mp10) REVERT: B 440 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8224 (tppt) REVERT: B 456 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7035 (p90) REVERT: B 568 ASP cc_start: 0.7702 (p0) cc_final: 0.7377 (p0) REVERT: B 587 ILE cc_start: 0.8677 (mt) cc_final: 0.8441 (mm) REVERT: B 655 TYR cc_start: 0.8456 (t80) cc_final: 0.8109 (t80) REVERT: B 695 TYR cc_start: 0.8465 (p90) cc_final: 0.7685 (p90) REVERT: B 711 SER cc_start: 0.8627 (t) cc_final: 0.8313 (p) REVERT: B 723 THR cc_start: 0.8619 (t) cc_final: 0.8384 (p) REVERT: B 751 ASN cc_start: 0.8559 (m-40) cc_final: 0.8328 (m110) REVERT: B 759 PHE cc_start: 0.6783 (t80) cc_final: 0.6354 (t80) REVERT: B 779 GLN cc_start: 0.8269 (tp40) cc_final: 0.8031 (tp40) REVERT: B 803 SER cc_start: 0.8593 (m) cc_final: 0.8363 (p) REVERT: B 851 CYS cc_start: 0.8378 (m) cc_final: 0.7685 (p) REVERT: B 854 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8162 (ttmm) REVERT: B 868 GLU cc_start: 0.7782 (tp30) cc_final: 0.7345 (tp30) REVERT: B 957 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: B 964 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8382 (ttmm) REVERT: B 968 SER cc_start: 0.8851 (m) cc_final: 0.8545 (p) REVERT: B 985 ASP cc_start: 0.7726 (p0) cc_final: 0.7442 (p0) REVERT: B 993 ILE cc_start: 0.8506 (tp) cc_final: 0.8253 (tp) REVERT: B 994 ASP cc_start: 0.8005 (m-30) cc_final: 0.7746 (t0) REVERT: B 1005 GLN cc_start: 0.8052 (tp40) cc_final: 0.7693 (tp40) REVERT: B 1014 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8131 (mtm-85) REVERT: C 121 ASN cc_start: 0.7320 (t0) cc_final: 0.7074 (t0) REVERT: C 132 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6471 (tp30) REVERT: C 206 THR cc_start: 0.8738 (t) cc_final: 0.8535 (p) REVERT: C 223 LEU cc_start: 0.8413 (mp) cc_final: 0.8156 (mp) REVERT: C 224 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7297 (mp0) REVERT: C 310 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8465 (ttpt) REVERT: C 324 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: C 331 ASN cc_start: 0.7534 (t0) cc_final: 0.7238 (p0) REVERT: C 467 ASP cc_start: 0.7762 (p0) cc_final: 0.7561 (p0) REVERT: C 503 VAL cc_start: 0.8504 (t) cc_final: 0.8256 (m) REVERT: C 511 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8312 (t) REVERT: C 532 ASN cc_start: 0.8681 (t0) cc_final: 0.8422 (m-40) REVERT: C 559 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7923 (t80) REVERT: C 574 ASP cc_start: 0.7961 (t70) cc_final: 0.7721 (t70) REVERT: C 599 THR cc_start: 0.8548 (m) cc_final: 0.8310 (t) REVERT: C 654 GLU cc_start: 0.7814 (pm20) cc_final: 0.7594 (pm20) REVERT: C 695 TYR cc_start: 0.8441 (p90) cc_final: 0.8079 (p90) REVERT: C 737 ASP cc_start: 0.7099 (t70) cc_final: 0.6883 (t0) REVERT: C 752 LEU cc_start: 0.8868 (mp) cc_final: 0.8651 (mm) REVERT: C 776 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8283 (ttpt) REVERT: C 859 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (p) REVERT: C 868 GLU cc_start: 0.7651 (tp30) cc_final: 0.7091 (tp30) REVERT: C 933 LYS cc_start: 0.8235 (mttm) cc_final: 0.7958 (mtpt) REVERT: C 960 ASN cc_start: 0.8585 (t0) cc_final: 0.8293 (t0) REVERT: C 964 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8263 (ttpp) REVERT: C 969 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7592 (ptpp) REVERT: C 993 ILE cc_start: 0.9089 (tp) cc_final: 0.8754 (tp) REVERT: C 1002 GLN cc_start: 0.7625 (tp40) cc_final: 0.6847 (tp40) REVERT: C 1005 GLN cc_start: 0.8401 (tp40) cc_final: 0.8158 (tp40) REVERT: C 1017 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 1018 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8007 (mp) REVERT: C 1072 GLU cc_start: 0.8249 (pm20) cc_final: 0.7978 (pm20) REVERT: C 1073 LYS cc_start: 0.8047 (tttm) cc_final: 0.7807 (ttmm) REVERT: C 1118 ASP cc_start: 0.7810 (t0) cc_final: 0.7469 (t0) REVERT: C 1123 SER cc_start: 0.8988 (t) cc_final: 0.8539 (m) REVERT: C 1127 ASP cc_start: 0.7194 (p0) cc_final: 0.6863 (p0) REVERT: C 1141 LEU cc_start: 0.8595 (mm) cc_final: 0.8353 (mm) REVERT: D 2 VAL cc_start: 0.8928 (t) cc_final: 0.8683 (p) REVERT: D 15 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6406 (mmtm) REVERT: D 59 LYS cc_start: 0.8137 (mttp) cc_final: 0.7765 (mttp) REVERT: D 84 MET cc_start: 0.7510 (ptp) cc_final: 0.7277 (ptp) REVERT: D 182 LEU cc_start: 0.8013 (mt) cc_final: 0.7812 (mt) REVERT: E 44 GLN cc_start: 0.7650 (mp10) cc_final: 0.7254 (mp10) REVERT: E 104 THR cc_start: 0.7983 (m) cc_final: 0.7761 (p) REVERT: F 2 VAL cc_start: 0.8513 (t) cc_final: 0.8179 (p) REVERT: G 194 TYR cc_start: 0.0814 (OUTLIER) cc_final: -0.0991 (m-80) REVERT: H 84 MET cc_start: 0.3698 (pmm) cc_final: 0.1154 (tpp) outliers start: 176 outliers final: 122 residues processed: 911 average time/residue: 0.4488 time to fit residues: 644.3442 Evaluate side-chains 916 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 775 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 167 optimal weight: 4.9990 chunk 374 optimal weight: 30.0000 chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 306 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 580 GLN B 690 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 616 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN D 79 GLN ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123139 restraints weight = 53839.360| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.34 r_work: 0.3406 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32921 Z= 0.214 Angle : 0.628 11.882 44900 Z= 0.318 Chirality : 0.046 0.388 5143 Planarity : 0.004 0.057 5765 Dihedral : 6.235 75.343 4581 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.13 % Allowed : 17.06 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 4110 helix: 0.67 (0.21), residues: 669 sheet: -1.25 (0.15), residues: 1026 loop : -2.27 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 55 HIS 0.007 0.001 HIS B 205 PHE 0.031 0.002 PHE C 429 TYR 0.018 0.002 TYR C 453 ARG 0.011 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 916) hydrogen bonds : angle 5.34212 ( 2493) SS BOND : bond 0.00590 ( 46) SS BOND : angle 1.79399 ( 92) covalent geometry : bond 0.00481 (32875) covalent geometry : angle 0.62308 (44808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 809 time to evaluate : 3.308 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: A 87 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7189 (p0) REVERT: A 99 ASN cc_start: 0.8150 (m-40) cc_final: 0.7598 (t160) REVERT: A 205 HIS cc_start: 0.7882 (t-90) cc_final: 0.7624 (t-90) REVERT: A 209 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (pt) REVERT: A 269 TYR cc_start: 0.8477 (m-10) cc_final: 0.8014 (m-10) REVERT: A 287 ASP cc_start: 0.8165 (p0) cc_final: 0.7922 (p0) REVERT: A 290 ASP cc_start: 0.7495 (t70) cc_final: 0.7218 (t0) REVERT: A 332 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7555 (mp) REVERT: A 335 LEU cc_start: 0.8813 (tp) cc_final: 0.8571 (mm) REVERT: A 353 TRP cc_start: 0.8888 (p-90) cc_final: 0.8464 (p-90) REVERT: A 378 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7920 (mtpt) REVERT: A 388 ASN cc_start: 0.8333 (m-40) cc_final: 0.8115 (m-40) REVERT: A 392 PHE cc_start: 0.8659 (m-80) cc_final: 0.8187 (m-80) REVERT: A 396 TYR cc_start: 0.8342 (m-10) cc_final: 0.8131 (m-10) REVERT: A 403 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7667 (mtp85) REVERT: A 421 TYR cc_start: 0.7758 (m-10) cc_final: 0.6734 (m-80) REVERT: A 440 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7942 (ttpp) REVERT: A 448 ASN cc_start: 0.8205 (t0) cc_final: 0.7765 (t0) REVERT: A 451 TYR cc_start: 0.7528 (m-80) cc_final: 0.7065 (m-80) REVERT: A 465 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 514 SER cc_start: 0.8196 (m) cc_final: 0.7807 (p) REVERT: A 547 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8283 (mtpp) REVERT: A 588 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 697 MET cc_start: 0.8440 (ttm) cc_final: 0.8152 (mtp) REVERT: A 725 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 776 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8310 (ttpp) REVERT: A 790 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8194 (mtmm) REVERT: A 900 MET cc_start: 0.8606 (mtp) cc_final: 0.8351 (mtt) REVERT: A 921 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8148 (mtpp) REVERT: A 935 GLN cc_start: 0.8508 (tt0) cc_final: 0.8185 (mt0) REVERT: A 947 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8198 (mtpp) REVERT: A 949 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 990 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 1017 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 1073 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8164 (ttpt) REVERT: A 1081 ILE cc_start: 0.8486 (pt) cc_final: 0.8134 (mt) REVERT: A 1097 SER cc_start: 0.8519 (t) cc_final: 0.8271 (p) REVERT: A 1107 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7736 (mtm-85) REVERT: B 96 GLU cc_start: 0.7138 (pt0) cc_final: 0.6836 (pt0) REVERT: B 105 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 239 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 273 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8068 (tpp80) REVERT: B 360 ASN cc_start: 0.8319 (m110) cc_final: 0.8099 (m110) REVERT: B 386 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7997 (mmmt) REVERT: B 393 THR cc_start: 0.8714 (p) cc_final: 0.8452 (t) REVERT: B 406 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 414 GLN cc_start: 0.8056 (mp10) cc_final: 0.7495 (mp10) REVERT: B 440 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8373 (tppt) REVERT: B 695 TYR cc_start: 0.8575 (p90) cc_final: 0.7863 (p90) REVERT: B 711 SER cc_start: 0.8824 (t) cc_final: 0.8483 (p) REVERT: B 723 THR cc_start: 0.8746 (t) cc_final: 0.8509 (p) REVERT: B 751 ASN cc_start: 0.8758 (m-40) cc_final: 0.8547 (m-40) REVERT: B 779 GLN cc_start: 0.8541 (tp40) cc_final: 0.8330 (tp40) REVERT: B 811 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8224 (mmtt) REVERT: B 854 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8363 (ttmm) REVERT: B 868 GLU cc_start: 0.8067 (tp30) cc_final: 0.7654 (tp30) REVERT: B 964 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8668 (ttmm) REVERT: B 968 SER cc_start: 0.9052 (m) cc_final: 0.8686 (p) REVERT: B 976 VAL cc_start: 0.8785 (t) cc_final: 0.8521 (m) REVERT: B 979 ASP cc_start: 0.7884 (m-30) cc_final: 0.7610 (m-30) REVERT: B 985 ASP cc_start: 0.7982 (p0) cc_final: 0.7678 (p0) REVERT: B 990 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 993 ILE cc_start: 0.8677 (tp) cc_final: 0.8427 (tp) REVERT: B 994 ASP cc_start: 0.8321 (m-30) cc_final: 0.7955 (t70) REVERT: B 1005 GLN cc_start: 0.8372 (tp40) cc_final: 0.7798 (tp40) REVERT: B 1031 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 1107 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7357 (mtt90) REVERT: C 102 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6731 (mtp85) REVERT: C 121 ASN cc_start: 0.7745 (t0) cc_final: 0.7168 (t0) REVERT: C 132 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6440 (tp30) REVERT: C 224 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7571 (mp0) REVERT: C 298 GLU cc_start: 0.8420 (tp30) cc_final: 0.8195 (tp30) REVERT: C 310 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8656 (ttpt) REVERT: C 324 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: C 385 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 457 ARG cc_start: 0.6537 (ttt180) cc_final: 0.6278 (ttt90) REVERT: C 467 ASP cc_start: 0.8041 (p0) cc_final: 0.7517 (p0) REVERT: C 511 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8465 (t) REVERT: C 532 ASN cc_start: 0.8953 (t0) cc_final: 0.8739 (m-40) REVERT: C 574 ASP cc_start: 0.8216 (t70) cc_final: 0.7993 (t70) REVERT: C 599 THR cc_start: 0.8761 (m) cc_final: 0.8516 (t) REVERT: C 615 VAL cc_start: 0.8441 (t) cc_final: 0.8203 (m) REVERT: C 698 SER cc_start: 0.9107 (t) cc_final: 0.8679 (p) REVERT: C 752 LEU cc_start: 0.8977 (mp) cc_final: 0.8734 (mm) REVERT: C 859 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8162 (p) REVERT: C 868 GLU cc_start: 0.7993 (tp30) cc_final: 0.7428 (tp30) REVERT: C 904 TYR cc_start: 0.7987 (m-10) cc_final: 0.7774 (m-10) REVERT: C 933 LYS cc_start: 0.8358 (mttm) cc_final: 0.8062 (mtpt) REVERT: C 960 ASN cc_start: 0.8829 (t0) cc_final: 0.8572 (t0) REVERT: C 964 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8456 (ttpp) REVERT: C 969 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7888 (ptpp) REVERT: C 993 ILE cc_start: 0.9136 (tp) cc_final: 0.8754 (tp) REVERT: C 1005 GLN cc_start: 0.8668 (tp40) cc_final: 0.8383 (tp40) REVERT: C 1017 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 1018 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8216 (mp) REVERT: C 1072 GLU cc_start: 0.8489 (pm20) cc_final: 0.8273 (pm20) REVERT: C 1073 LYS cc_start: 0.8239 (tttm) cc_final: 0.7984 (ttmm) REVERT: C 1123 SER cc_start: 0.9000 (t) cc_final: 0.8656 (m) REVERT: D 2 VAL cc_start: 0.8989 (t) cc_final: 0.8728 (p) REVERT: D 15 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6644 (mmtm) REVERT: D 59 LYS cc_start: 0.8468 (mttp) cc_final: 0.8129 (mttp) REVERT: D 84 MET cc_start: 0.7897 (ptp) cc_final: 0.7616 (ptp) REVERT: D 182 LEU cc_start: 0.8174 (mt) cc_final: 0.7756 (mt) REVERT: E 44 GLN cc_start: 0.7889 (mp10) cc_final: 0.7463 (mp10) REVERT: E 104 THR cc_start: 0.8180 (m) cc_final: 0.7806 (p) REVERT: F 2 VAL cc_start: 0.8555 (t) cc_final: 0.8233 (p) REVERT: G 194 TYR cc_start: 0.0892 (OUTLIER) cc_final: -0.0790 (m-80) REVERT: H 84 MET cc_start: 0.4251 (pmm) cc_final: 0.1270 (tpp) outliers start: 184 outliers final: 138 residues processed: 916 average time/residue: 0.4575 time to fit residues: 658.9552 Evaluate side-chains 931 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 778 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 20 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 394 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 241 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 317 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 580 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN G 41 HIS ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124693 restraints weight = 53635.034| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.34 r_work: 0.3437 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32921 Z= 0.125 Angle : 0.596 15.364 44900 Z= 0.298 Chirality : 0.045 0.401 5143 Planarity : 0.004 0.052 5765 Dihedral : 6.133 75.438 4578 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.46 % Allowed : 17.67 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 4110 helix: 0.88 (0.21), residues: 676 sheet: -1.11 (0.16), residues: 1019 loop : -2.16 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 55 HIS 0.023 0.001 HIS C 505 PHE 0.030 0.001 PHE C 429 TYR 0.025 0.001 TYR A 655 ARG 0.009 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 916) hydrogen bonds : angle 5.17006 ( 2493) SS BOND : bond 0.00447 ( 46) SS BOND : angle 1.58155 ( 92) covalent geometry : bond 0.00286 (32875) covalent geometry : angle 0.59198 (44808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 795 time to evaluate : 3.175 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: A 87 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7112 (p0) REVERT: A 99 ASN cc_start: 0.8091 (m-40) cc_final: 0.7554 (t0) REVERT: A 169 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 205 HIS cc_start: 0.7883 (t-90) cc_final: 0.7619 (t-90) REVERT: A 209 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8275 (pt) REVERT: A 237 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8166 (mtm110) REVERT: A 269 TYR cc_start: 0.8442 (m-10) cc_final: 0.8014 (m-10) REVERT: A 287 ASP cc_start: 0.8182 (p0) cc_final: 0.7919 (p0) REVERT: A 290 ASP cc_start: 0.7463 (t70) cc_final: 0.7199 (t0) REVERT: A 301 CYS cc_start: 0.8649 (m) cc_final: 0.8420 (m) REVERT: A 332 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7449 (mp) REVERT: A 335 LEU cc_start: 0.8771 (tp) cc_final: 0.8517 (mm) REVERT: A 353 TRP cc_start: 0.8812 (p-90) cc_final: 0.8369 (p-90) REVERT: A 378 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8041 (mtpt) REVERT: A 392 PHE cc_start: 0.8636 (m-80) cc_final: 0.8374 (m-80) REVERT: A 403 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7657 (mtp85) REVERT: A 408 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: A 421 TYR cc_start: 0.7733 (m-10) cc_final: 0.6815 (m-80) REVERT: A 440 LYS cc_start: 0.8101 (ttpp) cc_final: 0.7793 (ttpp) REVERT: A 448 ASN cc_start: 0.8237 (t0) cc_final: 0.7801 (t0) REVERT: A 451 TYR cc_start: 0.7500 (m-80) cc_final: 0.7056 (m-80) REVERT: A 465 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7121 (tm-30) REVERT: A 473 TYR cc_start: 0.7084 (t80) cc_final: 0.6598 (t80) REVERT: A 514 SER cc_start: 0.8127 (m) cc_final: 0.7717 (p) REVERT: A 547 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8257 (mtpp) REVERT: A 573 THR cc_start: 0.8888 (m) cc_final: 0.8532 (p) REVERT: A 588 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 599 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 643 PHE cc_start: 0.7978 (t80) cc_final: 0.7765 (t80) REVERT: A 725 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 776 LYS cc_start: 0.8622 (tmmt) cc_final: 0.8294 (ttpp) REVERT: A 900 MET cc_start: 0.8528 (mtp) cc_final: 0.8301 (mtt) REVERT: A 921 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8126 (mtpp) REVERT: A 945 LEU cc_start: 0.8467 (mm) cc_final: 0.8230 (mp) REVERT: A 947 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8204 (mtpp) REVERT: A 949 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8018 (mm-40) REVERT: A 990 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 1002 GLN cc_start: 0.7613 (mt0) cc_final: 0.7306 (mt0) REVERT: A 1017 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 1073 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8163 (ttpt) REVERT: A 1081 ILE cc_start: 0.8366 (pt) cc_final: 0.8050 (mt) REVERT: A 1097 SER cc_start: 0.8511 (t) cc_final: 0.8244 (p) REVERT: A 1107 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7657 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: B 96 GLU cc_start: 0.7122 (pt0) cc_final: 0.6834 (pt0) REVERT: B 105 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 239 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 360 ASN cc_start: 0.8318 (m110) cc_final: 0.8096 (m110) REVERT: B 386 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8011 (mmmt) REVERT: B 394 ASN cc_start: 0.7975 (p0) cc_final: 0.7396 (p0) REVERT: B 400 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6618 (p90) REVERT: B 406 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 414 GLN cc_start: 0.8077 (mp10) cc_final: 0.7561 (mp10) REVERT: B 433 VAL cc_start: 0.8898 (t) cc_final: 0.8533 (p) REVERT: B 440 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8348 (tppt) REVERT: B 581 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 587 ILE cc_start: 0.8746 (mt) cc_final: 0.8531 (mm) REVERT: B 695 TYR cc_start: 0.8579 (p90) cc_final: 0.7859 (p90) REVERT: B 711 SER cc_start: 0.8790 (t) cc_final: 0.8446 (p) REVERT: B 723 THR cc_start: 0.8739 (t) cc_final: 0.8497 (p) REVERT: B 740 MET cc_start: 0.8246 (tpp) cc_final: 0.7969 (tpp) REVERT: B 779 GLN cc_start: 0.8535 (tp40) cc_final: 0.8281 (tp40) REVERT: B 854 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8308 (ttmm) REVERT: B 868 GLU cc_start: 0.8056 (tp30) cc_final: 0.7667 (tp30) REVERT: B 964 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8612 (ttmm) REVERT: B 968 SER cc_start: 0.9007 (m) cc_final: 0.8694 (p) REVERT: B 976 VAL cc_start: 0.8709 (t) cc_final: 0.8456 (m) REVERT: B 979 ASP cc_start: 0.7825 (m-30) cc_final: 0.7561 (m-30) REVERT: B 985 ASP cc_start: 0.7894 (p0) cc_final: 0.7603 (p0) REVERT: B 990 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 993 ILE cc_start: 0.8645 (tp) cc_final: 0.8410 (tp) REVERT: B 994 ASP cc_start: 0.8308 (m-30) cc_final: 0.7754 (t0) REVERT: B 1005 GLN cc_start: 0.8371 (tp40) cc_final: 0.7894 (tp40) REVERT: B 1141 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 29 THR cc_start: 0.8845 (t) cc_final: 0.7594 (p) REVERT: C 102 ARG cc_start: 0.7183 (mtp85) cc_final: 0.6680 (mtp85) REVERT: C 121 ASN cc_start: 0.7616 (t0) cc_final: 0.6990 (t0) REVERT: C 189 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7313 (mt-10) REVERT: C 224 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7364 (mm-30) REVERT: C 281 GLU cc_start: 0.7798 (pp20) cc_final: 0.7426 (pp20) REVERT: C 298 GLU cc_start: 0.8375 (tp30) cc_final: 0.8123 (tp30) REVERT: C 310 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8626 (ttpt) REVERT: C 324 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: C 331 ASN cc_start: 0.7579 (t0) cc_final: 0.7326 (p0) REVERT: C 340 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 385 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 467 ASP cc_start: 0.7985 (p0) cc_final: 0.7570 (p0) REVERT: C 511 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 532 ASN cc_start: 0.8945 (t0) cc_final: 0.8741 (m-40) REVERT: C 543 PHE cc_start: 0.8599 (m-10) cc_final: 0.8194 (m-10) REVERT: C 599 THR cc_start: 0.8739 (m) cc_final: 0.8495 (t) REVERT: C 615 VAL cc_start: 0.8412 (t) cc_final: 0.8168 (m) REVERT: C 698 SER cc_start: 0.9103 (t) cc_final: 0.8666 (p) REVERT: C 752 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8648 (mm) REVERT: C 780 GLU cc_start: 0.7757 (pt0) cc_final: 0.7482 (pt0) REVERT: C 859 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8155 (p) REVERT: C 868 GLU cc_start: 0.7951 (tp30) cc_final: 0.7372 (tp30) REVERT: C 902 MET cc_start: 0.8404 (tpp) cc_final: 0.7949 (mmm) REVERT: C 904 TYR cc_start: 0.7921 (m-10) cc_final: 0.7696 (m-10) REVERT: C 933 LYS cc_start: 0.8337 (mttm) cc_final: 0.8051 (mtpt) REVERT: C 960 ASN cc_start: 0.8776 (t0) cc_final: 0.8493 (t0) REVERT: C 964 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8438 (ttpp) REVERT: C 969 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7869 (ptpp) REVERT: C 993 ILE cc_start: 0.9113 (tp) cc_final: 0.8755 (tp) REVERT: C 1005 GLN cc_start: 0.8639 (tp40) cc_final: 0.8147 (tp40) REVERT: C 1017 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 1018 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8164 (mp) REVERT: C 1073 LYS cc_start: 0.8218 (tttm) cc_final: 0.8018 (ttmm) REVERT: C 1102 TRP cc_start: 0.8852 (m100) cc_final: 0.8235 (m100) REVERT: C 1123 SER cc_start: 0.8930 (t) cc_final: 0.8665 (m) REVERT: D 15 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6735 (mmtm) REVERT: D 45 LYS cc_start: 0.8231 (mppt) cc_final: 0.7830 (mppt) REVERT: D 59 LYS cc_start: 0.8444 (mttp) cc_final: 0.8080 (mttp) REVERT: D 84 MET cc_start: 0.7822 (ptp) cc_final: 0.7603 (ptp) REVERT: D 87 MET cc_start: 0.5917 (ttp) cc_final: 0.5648 (ttp) REVERT: D 182 LEU cc_start: 0.8175 (mt) cc_final: 0.7826 (mt) REVERT: E 44 GLN cc_start: 0.7850 (mp10) cc_final: 0.7418 (mp10) REVERT: E 104 THR cc_start: 0.8206 (m) cc_final: 0.7845 (p) REVERT: E 128 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4930 (mm) REVERT: F 2 VAL cc_start: 0.8541 (t) cc_final: 0.8224 (p) REVERT: G 194 TYR cc_start: 0.0663 (OUTLIER) cc_final: -0.1015 (m-80) REVERT: I 18 ILE cc_start: 0.6948 (mm) cc_final: 0.6559 (mt) outliers start: 196 outliers final: 142 residues processed: 909 average time/residue: 0.5430 time to fit residues: 779.4444 Evaluate side-chains 938 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 772 time to evaluate : 6.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 287 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 335 optimal weight: 0.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123447 restraints weight = 53797.872| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.36 r_work: 0.3418 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32921 Z= 0.157 Angle : 0.605 13.645 44900 Z= 0.303 Chirality : 0.045 0.357 5143 Planarity : 0.004 0.052 5765 Dihedral : 6.068 75.143 4575 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.13 % Allowed : 18.90 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 4110 helix: 0.91 (0.21), residues: 676 sheet: -1.04 (0.15), residues: 1033 loop : -2.08 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 55 HIS 0.005 0.001 HIS C 505 PHE 0.032 0.002 PHE C 429 TYR 0.019 0.001 TYR A 655 ARG 0.010 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 916) hydrogen bonds : angle 5.09880 ( 2493) SS BOND : bond 0.00470 ( 46) SS BOND : angle 1.63409 ( 92) covalent geometry : bond 0.00358 (32875) covalent geometry : angle 0.60104 (44808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 791 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7151 (p0) REVERT: A 99 ASN cc_start: 0.8194 (m-40) cc_final: 0.7641 (t160) REVERT: A 205 HIS cc_start: 0.7881 (t-90) cc_final: 0.7625 (t-90) REVERT: A 209 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8286 (pt) REVERT: A 235 ILE cc_start: 0.8462 (mm) cc_final: 0.8221 (tp) REVERT: A 269 TYR cc_start: 0.8449 (m-10) cc_final: 0.8019 (m-10) REVERT: A 287 ASP cc_start: 0.8170 (p0) cc_final: 0.7911 (p0) REVERT: A 290 ASP cc_start: 0.7492 (t70) cc_final: 0.7221 (t0) REVERT: A 301 CYS cc_start: 0.8668 (m) cc_final: 0.8427 (m) REVERT: A 332 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7415 (mp) REVERT: A 335 LEU cc_start: 0.8803 (tp) cc_final: 0.8547 (mm) REVERT: A 353 TRP cc_start: 0.8826 (p-90) cc_final: 0.8371 (p-90) REVERT: A 378 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7986 (mtpt) REVERT: A 403 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7654 (mtp85) REVERT: A 421 TYR cc_start: 0.7778 (m-10) cc_final: 0.6860 (m-80) REVERT: A 440 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7805 (ttpp) REVERT: A 448 ASN cc_start: 0.8216 (t0) cc_final: 0.7949 (t0) REVERT: A 451 TYR cc_start: 0.7550 (m-80) cc_final: 0.7106 (m-80) REVERT: A 465 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 473 TYR cc_start: 0.7115 (t80) cc_final: 0.6610 (t80) REVERT: A 514 SER cc_start: 0.8157 (m) cc_final: 0.7772 (p) REVERT: A 547 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8248 (mtpp) REVERT: A 573 THR cc_start: 0.8892 (m) cc_final: 0.8531 (p) REVERT: A 588 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 599 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 697 MET cc_start: 0.8372 (ttm) cc_final: 0.8023 (mtp) REVERT: A 725 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 776 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8260 (ttpp) REVERT: A 779 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8268 (tp40) REVERT: A 900 MET cc_start: 0.8566 (mtp) cc_final: 0.8321 (mtt) REVERT: A 921 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8138 (mtpp) REVERT: A 945 LEU cc_start: 0.8456 (mm) cc_final: 0.8195 (mp) REVERT: A 947 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8213 (mtpp) REVERT: A 949 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8022 (mm-40) REVERT: A 990 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 1002 GLN cc_start: 0.7699 (mt0) cc_final: 0.7382 (mt0) REVERT: A 1017 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 1073 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8227 (ttpt) REVERT: A 1081 ILE cc_start: 0.8407 (pt) cc_final: 0.8087 (mt) REVERT: A 1097 SER cc_start: 0.8589 (t) cc_final: 0.8271 (p) REVERT: A 1107 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: B 83 VAL cc_start: 0.7763 (t) cc_final: 0.7398 (t) REVERT: B 96 GLU cc_start: 0.7125 (pt0) cc_final: 0.6831 (pt0) REVERT: B 105 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 226 LEU cc_start: 0.8563 (tp) cc_final: 0.8230 (mt) REVERT: B 239 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 270 LEU cc_start: 0.8798 (mp) cc_final: 0.8575 (mt) REVERT: B 273 ARG cc_start: 0.8338 (tpp80) cc_final: 0.7982 (tpp80) REVERT: B 386 LYS cc_start: 0.8315 (mmmt) cc_final: 0.8080 (mmmt) REVERT: B 394 ASN cc_start: 0.8075 (p0) cc_final: 0.7468 (p0) REVERT: B 400 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6685 (p90) REVERT: B 406 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 414 GLN cc_start: 0.8065 (mp10) cc_final: 0.7568 (mp10) REVERT: B 433 VAL cc_start: 0.8924 (t) cc_final: 0.8577 (p) REVERT: B 440 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8356 (tppt) REVERT: B 587 ILE cc_start: 0.8792 (mt) cc_final: 0.8552 (mm) REVERT: B 695 TYR cc_start: 0.8572 (p90) cc_final: 0.7859 (p90) REVERT: B 711 SER cc_start: 0.8825 (t) cc_final: 0.8467 (p) REVERT: B 723 THR cc_start: 0.8741 (t) cc_final: 0.8504 (p) REVERT: B 740 MET cc_start: 0.8319 (tpp) cc_final: 0.8065 (tpp) REVERT: B 854 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8352 (ttmm) REVERT: B 868 GLU cc_start: 0.8064 (tp30) cc_final: 0.7675 (tp30) REVERT: B 964 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8636 (ttmm) REVERT: B 968 SER cc_start: 0.9002 (m) cc_final: 0.8674 (p) REVERT: B 976 VAL cc_start: 0.8734 (t) cc_final: 0.8468 (m) REVERT: B 979 ASP cc_start: 0.7849 (m-30) cc_final: 0.7598 (m-30) REVERT: B 985 ASP cc_start: 0.7878 (p0) cc_final: 0.7570 (p0) REVERT: B 990 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 993 ILE cc_start: 0.8657 (tp) cc_final: 0.8443 (tp) REVERT: B 994 ASP cc_start: 0.8259 (m-30) cc_final: 0.7763 (t0) REVERT: B 1001 LEU cc_start: 0.9083 (mt) cc_final: 0.8809 (mt) REVERT: B 1005 GLN cc_start: 0.8389 (tp40) cc_final: 0.7877 (tp40) REVERT: B 1031 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 1141 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 29 THR cc_start: 0.8832 (t) cc_final: 0.7582 (p) REVERT: C 102 ARG cc_start: 0.7208 (mtp85) cc_final: 0.6704 (mtp85) REVERT: C 121 ASN cc_start: 0.7648 (t0) cc_final: 0.7085 (t0) REVERT: C 189 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 281 GLU cc_start: 0.7741 (pp20) cc_final: 0.7367 (pp20) REVERT: C 298 GLU cc_start: 0.8399 (tp30) cc_final: 0.8181 (tp30) REVERT: C 310 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8644 (ttpt) REVERT: C 324 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: C 331 ASN cc_start: 0.7596 (t0) cc_final: 0.7365 (p0) REVERT: C 340 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 385 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8760 (p) REVERT: C 467 ASP cc_start: 0.8045 (p0) cc_final: 0.7552 (p0) REVERT: C 511 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8435 (t) REVERT: C 532 ASN cc_start: 0.8973 (t0) cc_final: 0.8764 (m-40) REVERT: C 615 VAL cc_start: 0.8405 (t) cc_final: 0.8179 (m) REVERT: C 698 SER cc_start: 0.9109 (t) cc_final: 0.8691 (p) REVERT: C 780 GLU cc_start: 0.7808 (pt0) cc_final: 0.7565 (pt0) REVERT: C 859 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8161 (p) REVERT: C 868 GLU cc_start: 0.7960 (tp30) cc_final: 0.7384 (tp30) REVERT: C 904 TYR cc_start: 0.7930 (m-10) cc_final: 0.7689 (m-10) REVERT: C 933 LYS cc_start: 0.8374 (mttm) cc_final: 0.8072 (mtpt) REVERT: C 947 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8251 (mtpp) REVERT: C 960 ASN cc_start: 0.8778 (t0) cc_final: 0.8495 (t0) REVERT: C 964 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8442 (ttpp) REVERT: C 969 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7854 (ptpp) REVERT: C 993 ILE cc_start: 0.9073 (tp) cc_final: 0.8712 (tp) REVERT: C 1005 GLN cc_start: 0.8643 (tp40) cc_final: 0.8123 (tp40) REVERT: C 1017 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 1018 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8238 (mp) REVERT: C 1091 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7816 (mtt-85) REVERT: C 1114 ILE cc_start: 0.8725 (mm) cc_final: 0.8502 (tp) REVERT: C 1123 SER cc_start: 0.8855 (t) cc_final: 0.8620 (m) REVERT: D 15 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6678 (mppt) REVERT: D 45 LYS cc_start: 0.8284 (mppt) cc_final: 0.7940 (mppt) REVERT: D 59 LYS cc_start: 0.8495 (mttp) cc_final: 0.8125 (mttp) REVERT: D 84 MET cc_start: 0.7871 (ptp) cc_final: 0.7591 (ptp) REVERT: D 182 LEU cc_start: 0.8216 (mt) cc_final: 0.7882 (mt) REVERT: E 19 THR cc_start: 0.8439 (p) cc_final: 0.8155 (p) REVERT: E 44 GLN cc_start: 0.7840 (mp10) cc_final: 0.7425 (mp10) REVERT: E 104 THR cc_start: 0.8185 (m) cc_final: 0.7844 (p) REVERT: E 128 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4787 (mm) REVERT: F 2 VAL cc_start: 0.8545 (t) cc_final: 0.8232 (p) REVERT: I 18 ILE cc_start: 0.6838 (mm) cc_final: 0.6442 (mt) outliers start: 184 outliers final: 143 residues processed: 896 average time/residue: 0.4548 time to fit residues: 639.6932 Evaluate side-chains 942 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 779 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 129 optimal weight: 0.8980 chunk 296 optimal weight: 0.0570 chunk 359 optimal weight: 3.9990 chunk 276 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 357 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 751 ASN B 935 GLN B 965 GLN B1002 GLN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN D 16 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124698 restraints weight = 54017.050| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.38 r_work: 0.3444 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32921 Z= 0.117 Angle : 0.599 13.549 44900 Z= 0.298 Chirality : 0.044 0.323 5143 Planarity : 0.004 0.051 5765 Dihedral : 5.993 75.245 4575 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.16 % Allowed : 19.26 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4110 helix: 1.01 (0.21), residues: 680 sheet: -0.96 (0.16), residues: 1029 loop : -2.00 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 55 HIS 0.005 0.001 HIS A 49 PHE 0.033 0.001 PHE A 168 TYR 0.018 0.001 TYR A 655 ARG 0.010 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 916) hydrogen bonds : angle 5.01653 ( 2493) SS BOND : bond 0.00426 ( 46) SS BOND : angle 1.28994 ( 92) covalent geometry : bond 0.00270 (32875) covalent geometry : angle 0.59658 (44808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 795 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7095 (p0) REVERT: A 97 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8053 (ttpp) REVERT: A 99 ASN cc_start: 0.8172 (m-40) cc_final: 0.7664 (t160) REVERT: A 186 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 205 HIS cc_start: 0.7867 (t-90) cc_final: 0.7510 (t-90) REVERT: A 209 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8279 (pt) REVERT: A 231 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8060 (pt) REVERT: A 235 ILE cc_start: 0.8435 (mm) cc_final: 0.8210 (tp) REVERT: A 269 TYR cc_start: 0.8416 (m-10) cc_final: 0.7957 (m-10) REVERT: A 281 GLU cc_start: 0.7682 (pp20) cc_final: 0.7193 (pp20) REVERT: A 287 ASP cc_start: 0.8188 (p0) cc_final: 0.7921 (p0) REVERT: A 290 ASP cc_start: 0.7459 (t70) cc_final: 0.7185 (t0) REVERT: A 301 CYS cc_start: 0.8587 (m) cc_final: 0.8354 (m) REVERT: A 332 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 335 LEU cc_start: 0.8782 (tp) cc_final: 0.8534 (mm) REVERT: A 353 TRP cc_start: 0.8732 (p-90) cc_final: 0.8352 (p-90) REVERT: A 360 ASN cc_start: 0.8393 (m-40) cc_final: 0.8173 (m110) REVERT: A 392 PHE cc_start: 0.8439 (m-80) cc_final: 0.8235 (m-10) REVERT: A 403 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7643 (mtp85) REVERT: A 421 TYR cc_start: 0.7719 (m-10) cc_final: 0.6885 (m-80) REVERT: A 440 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7767 (ttpp) REVERT: A 448 ASN cc_start: 0.8215 (t0) cc_final: 0.7999 (t0) REVERT: A 451 TYR cc_start: 0.7529 (m-80) cc_final: 0.7159 (m-80) REVERT: A 465 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 473 TYR cc_start: 0.7046 (t80) cc_final: 0.6558 (t80) REVERT: A 514 SER cc_start: 0.8104 (m) cc_final: 0.7724 (p) REVERT: A 547 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8220 (mtpp) REVERT: A 573 THR cc_start: 0.8862 (m) cc_final: 0.8502 (p) REVERT: A 588 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8473 (p) REVERT: A 599 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 697 MET cc_start: 0.8371 (ttm) cc_final: 0.8151 (mtp) REVERT: A 725 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 776 LYS cc_start: 0.8609 (tmmt) cc_final: 0.8252 (ttpp) REVERT: A 779 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8249 (tp40) REVERT: A 900 MET cc_start: 0.8541 (mtp) cc_final: 0.8300 (mtt) REVERT: A 921 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8122 (mtpp) REVERT: A 945 LEU cc_start: 0.8436 (mm) cc_final: 0.8195 (mp) REVERT: A 947 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8311 (mtpp) REVERT: A 949 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8089 (mm-40) REVERT: A 990 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 1017 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 1073 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8228 (ttpt) REVERT: A 1081 ILE cc_start: 0.8332 (pt) cc_final: 0.8033 (mt) REVERT: A 1097 SER cc_start: 0.8556 (t) cc_final: 0.8230 (p) REVERT: A 1107 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 105 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (mp) REVERT: B 239 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 273 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7971 (tpp80) REVERT: B 386 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8051 (mmmt) REVERT: B 394 ASN cc_start: 0.8009 (p0) cc_final: 0.7450 (p0) REVERT: B 400 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6681 (p90) REVERT: B 414 GLN cc_start: 0.8086 (mp10) cc_final: 0.7618 (mp10) REVERT: B 433 VAL cc_start: 0.8907 (t) cc_final: 0.8548 (p) REVERT: B 440 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8298 (tppt) REVERT: B 568 ASP cc_start: 0.7927 (p0) cc_final: 0.7653 (p0) REVERT: B 587 ILE cc_start: 0.8766 (mt) cc_final: 0.8533 (mm) REVERT: B 695 TYR cc_start: 0.8558 (p90) cc_final: 0.7875 (p90) REVERT: B 698 SER cc_start: 0.8940 (t) cc_final: 0.8546 (p) REVERT: B 711 SER cc_start: 0.8809 (t) cc_final: 0.8449 (p) REVERT: B 723 THR cc_start: 0.8731 (t) cc_final: 0.8494 (p) REVERT: B 740 MET cc_start: 0.8199 (tpp) cc_final: 0.7964 (tpp) REVERT: B 825 LYS cc_start: 0.8856 (mttm) cc_final: 0.8514 (mttt) REVERT: B 854 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8337 (ttmm) REVERT: B 868 GLU cc_start: 0.8071 (tp30) cc_final: 0.7688 (tp30) REVERT: B 964 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8606 (ttmm) REVERT: B 968 SER cc_start: 0.8975 (m) cc_final: 0.8693 (p) REVERT: B 976 VAL cc_start: 0.8710 (t) cc_final: 0.8161 (m) REVERT: B 979 ASP cc_start: 0.7844 (m-30) cc_final: 0.7476 (m-30) REVERT: B 985 ASP cc_start: 0.7965 (p0) cc_final: 0.7656 (p0) REVERT: B 990 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 993 ILE cc_start: 0.8629 (tp) cc_final: 0.8420 (tp) REVERT: B 994 ASP cc_start: 0.8174 (m-30) cc_final: 0.7686 (t0) REVERT: B 1001 LEU cc_start: 0.9075 (mt) cc_final: 0.8804 (mt) REVERT: B 1005 GLN cc_start: 0.8375 (tp40) cc_final: 0.7956 (tp40) REVERT: B 1031 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 1141 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8500 (mp) REVERT: C 29 THR cc_start: 0.8769 (t) cc_final: 0.7504 (p) REVERT: C 34 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7292 (mtp-110) REVERT: C 102 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6685 (mtp85) REVERT: C 116 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8201 (p) REVERT: C 121 ASN cc_start: 0.7648 (t0) cc_final: 0.7021 (t0) REVERT: C 132 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6183 (tp30) REVERT: C 189 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7144 (mt-10) REVERT: C 281 GLU cc_start: 0.7807 (pp20) cc_final: 0.7459 (pp20) REVERT: C 310 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (ttpt) REVERT: C 324 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: C 385 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8728 (p) REVERT: C 467 ASP cc_start: 0.7998 (p0) cc_final: 0.7598 (p0) REVERT: C 511 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8424 (t) REVERT: C 532 ASN cc_start: 0.8957 (t0) cc_final: 0.8743 (m-40) REVERT: C 543 PHE cc_start: 0.8753 (m-10) cc_final: 0.8093 (m-10) REVERT: C 615 VAL cc_start: 0.8408 (t) cc_final: 0.8172 (m) REVERT: C 655 TYR cc_start: 0.8638 (t80) cc_final: 0.8321 (t80) REVERT: C 698 SER cc_start: 0.9139 (t) cc_final: 0.8692 (p) REVERT: C 859 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8160 (p) REVERT: C 868 GLU cc_start: 0.7915 (tp30) cc_final: 0.7334 (tp30) REVERT: C 902 MET cc_start: 0.8381 (tpp) cc_final: 0.7928 (mmm) REVERT: C 904 TYR cc_start: 0.7890 (m-10) cc_final: 0.7682 (m-10) REVERT: C 933 LYS cc_start: 0.8398 (mttm) cc_final: 0.8102 (mtpt) REVERT: C 960 ASN cc_start: 0.8745 (t0) cc_final: 0.8430 (t0) REVERT: C 964 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8416 (ttpp) REVERT: C 969 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7853 (ptpp) REVERT: C 993 ILE cc_start: 0.9059 (tp) cc_final: 0.8710 (tp) REVERT: C 1005 GLN cc_start: 0.8620 (tp40) cc_final: 0.8110 (tp40) REVERT: C 1017 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7878 (tm-30) REVERT: C 1018 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8210 (mp) REVERT: C 1091 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7712 (mtt-85) REVERT: C 1114 ILE cc_start: 0.8723 (mm) cc_final: 0.8519 (tp) REVERT: C 1123 SER cc_start: 0.8794 (t) cc_final: 0.8556 (m) REVERT: C 1144 GLU cc_start: 0.7666 (pp20) cc_final: 0.7378 (pp20) REVERT: D 15 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7030 (mppt) REVERT: D 29 LEU cc_start: 0.9111 (tp) cc_final: 0.8816 (tt) REVERT: D 45 LYS cc_start: 0.8243 (mppt) cc_final: 0.7920 (mppt) REVERT: D 59 LYS cc_start: 0.8482 (mttp) cc_final: 0.8107 (mttp) REVERT: D 84 MET cc_start: 0.7833 (ptp) cc_final: 0.7575 (ptp) REVERT: E 44 GLN cc_start: 0.7840 (mp10) cc_final: 0.7409 (mp10) REVERT: E 104 THR cc_start: 0.8143 (m) cc_final: 0.7803 (p) REVERT: E 128 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4542 (mm) REVERT: F 2 VAL cc_start: 0.8523 (t) cc_final: 0.8204 (p) REVERT: I 18 ILE cc_start: 0.6880 (mm) cc_final: 0.6512 (mt) outliers start: 185 outliers final: 141 residues processed: 909 average time/residue: 0.5836 time to fit residues: 839.8739 Evaluate side-chains 945 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 780 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 280 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 chunk 407 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN B 949 GLN B 965 GLN C 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.158959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123196 restraints weight = 54068.319| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.35 r_work: 0.3423 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32921 Z= 0.163 Angle : 0.638 20.235 44900 Z= 0.320 Chirality : 0.046 0.364 5143 Planarity : 0.004 0.053 5765 Dihedral : 6.045 74.947 4574 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.10 % Allowed : 19.59 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 4110 helix: 0.98 (0.21), residues: 672 sheet: -0.89 (0.15), residues: 1052 loop : -1.94 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 49 HIS 0.022 0.001 HIS C 505 PHE 0.037 0.002 PHE C 429 TYR 0.019 0.001 TYR A 160 ARG 0.010 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 916) hydrogen bonds : angle 5.04216 ( 2493) SS BOND : bond 0.00524 ( 46) SS BOND : angle 1.98410 ( 92) covalent geometry : bond 0.00372 (32875) covalent geometry : angle 0.63241 (44808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 803 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7209 (p0) REVERT: A 97 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8240 (ttpp) REVERT: A 99 ASN cc_start: 0.8220 (m-40) cc_final: 0.7704 (t160) REVERT: A 186 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.6974 (p0) REVERT: A 205 HIS cc_start: 0.7927 (t-90) cc_final: 0.7597 (t-90) REVERT: A 209 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8280 (pt) REVERT: A 231 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8040 (pt) REVERT: A 269 TYR cc_start: 0.8450 (m-10) cc_final: 0.8038 (m-10) REVERT: A 281 GLU cc_start: 0.7734 (pp20) cc_final: 0.7206 (pp20) REVERT: A 287 ASP cc_start: 0.8165 (p0) cc_final: 0.7907 (p0) REVERT: A 290 ASP cc_start: 0.7494 (t70) cc_final: 0.7223 (t0) REVERT: A 301 CYS cc_start: 0.8618 (m) cc_final: 0.8390 (m) REVERT: A 332 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 335 LEU cc_start: 0.8820 (tp) cc_final: 0.8578 (mm) REVERT: A 353 TRP cc_start: 0.8795 (p-90) cc_final: 0.8341 (p-90) REVERT: A 360 ASN cc_start: 0.8406 (m-40) cc_final: 0.8185 (m110) REVERT: A 378 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7589 (mtpt) REVERT: A 403 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7654 (mtp85) REVERT: A 421 TYR cc_start: 0.7712 (m-10) cc_final: 0.6855 (m-80) REVERT: A 440 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7797 (ttpp) REVERT: A 448 ASN cc_start: 0.8237 (t0) cc_final: 0.7986 (t0) REVERT: A 451 TYR cc_start: 0.7575 (m-80) cc_final: 0.7142 (m-80) REVERT: A 465 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 473 TYR cc_start: 0.7108 (t80) cc_final: 0.6646 (t80) REVERT: A 514 SER cc_start: 0.8137 (m) cc_final: 0.7766 (p) REVERT: A 547 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8241 (mtpp) REVERT: A 573 THR cc_start: 0.8871 (m) cc_final: 0.8516 (p) REVERT: A 588 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 599 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 725 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 776 LYS cc_start: 0.8609 (tmmt) cc_final: 0.8255 (ttpp) REVERT: A 779 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8273 (tp40) REVERT: A 900 MET cc_start: 0.8578 (mtp) cc_final: 0.8335 (mtt) REVERT: A 921 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: A 945 LEU cc_start: 0.8442 (mm) cc_final: 0.8185 (mp) REVERT: A 947 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8304 (mtpp) REVERT: A 949 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8082 (mm-40) REVERT: A 990 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 1017 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 1073 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8255 (ttpt) REVERT: A 1081 ILE cc_start: 0.8403 (pt) cc_final: 0.8090 (mt) REVERT: A 1097 SER cc_start: 0.8579 (t) cc_final: 0.8262 (p) REVERT: A 1144 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 83 VAL cc_start: 0.7696 (t) cc_final: 0.7487 (t) REVERT: B 105 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7978 (mp) REVERT: B 226 LEU cc_start: 0.8553 (tp) cc_final: 0.8240 (mt) REVERT: B 239 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 241 LEU cc_start: 0.7945 (mt) cc_final: 0.6951 (mt) REVERT: B 270 LEU cc_start: 0.8826 (mp) cc_final: 0.8590 (mt) REVERT: B 273 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7907 (tpp80) REVERT: B 360 ASN cc_start: 0.8320 (m110) cc_final: 0.8099 (m110) REVERT: B 386 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8056 (mmmt) REVERT: B 394 ASN cc_start: 0.7913 (p0) cc_final: 0.7409 (p0) REVERT: B 400 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6755 (p90) REVERT: B 406 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 414 GLN cc_start: 0.8091 (mp10) cc_final: 0.7624 (mp10) REVERT: B 433 VAL cc_start: 0.8929 (t) cc_final: 0.8587 (p) REVERT: B 440 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8047 (mmmm) REVERT: B 587 ILE cc_start: 0.8788 (mt) cc_final: 0.8556 (mm) REVERT: B 695 TYR cc_start: 0.8565 (p90) cc_final: 0.7888 (p90) REVERT: B 711 SER cc_start: 0.8836 (t) cc_final: 0.8470 (p) REVERT: B 723 THR cc_start: 0.8720 (t) cc_final: 0.8480 (p) REVERT: B 740 MET cc_start: 0.8186 (tpp) cc_final: 0.7952 (tpp) REVERT: B 854 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8379 (ttmm) REVERT: B 868 GLU cc_start: 0.8076 (tp30) cc_final: 0.7684 (tp30) REVERT: B 900 MET cc_start: 0.8654 (mtp) cc_final: 0.8419 (mtm) REVERT: B 964 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8617 (ttmm) REVERT: B 968 SER cc_start: 0.9005 (m) cc_final: 0.8700 (p) REVERT: B 976 VAL cc_start: 0.8750 (t) cc_final: 0.8187 (m) REVERT: B 979 ASP cc_start: 0.7862 (m-30) cc_final: 0.7494 (m-30) REVERT: B 985 ASP cc_start: 0.7976 (p0) cc_final: 0.7667 (p0) REVERT: B 990 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 993 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 994 ASP cc_start: 0.8193 (m-30) cc_final: 0.7703 (t0) REVERT: B 1001 LEU cc_start: 0.9066 (mt) cc_final: 0.8809 (mt) REVERT: B 1005 GLN cc_start: 0.8383 (tp40) cc_final: 0.7894 (tp40) REVERT: B 1031 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 1141 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 29 THR cc_start: 0.8775 (t) cc_final: 0.7499 (p) REVERT: C 34 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7326 (mtp-110) REVERT: C 102 ARG cc_start: 0.7207 (mtp85) cc_final: 0.6725 (mtp85) REVERT: C 116 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8265 (p) REVERT: C 121 ASN cc_start: 0.7621 (t0) cc_final: 0.7039 (t0) REVERT: C 132 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6425 (mm-30) REVERT: C 189 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7063 (mt-10) REVERT: C 281 GLU cc_start: 0.7809 (pp20) cc_final: 0.7464 (pp20) REVERT: C 310 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8632 (ttpt) REVERT: C 324 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: C 385 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8769 (p) REVERT: C 467 ASP cc_start: 0.8038 (p0) cc_final: 0.7737 (p0) REVERT: C 511 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8432 (t) REVERT: C 532 ASN cc_start: 0.8980 (t0) cc_final: 0.8761 (m-40) REVERT: C 543 PHE cc_start: 0.8754 (m-10) cc_final: 0.8420 (m-80) REVERT: C 615 VAL cc_start: 0.8394 (t) cc_final: 0.8153 (m) REVERT: C 698 SER cc_start: 0.9175 (t) cc_final: 0.8713 (p) REVERT: C 859 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8149 (p) REVERT: C 868 GLU cc_start: 0.7916 (tp30) cc_final: 0.7339 (tp30) REVERT: C 902 MET cc_start: 0.8424 (tpp) cc_final: 0.8049 (mmm) REVERT: C 933 LYS cc_start: 0.8359 (mttm) cc_final: 0.8062 (mtpt) REVERT: C 947 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8158 (mtpp) REVERT: C 960 ASN cc_start: 0.8751 (t0) cc_final: 0.8444 (t0) REVERT: C 964 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8421 (ttpp) REVERT: C 969 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7939 (ptpp) REVERT: C 984 LEU cc_start: 0.8943 (mt) cc_final: 0.8742 (tp) REVERT: C 993 ILE cc_start: 0.9064 (tp) cc_final: 0.8706 (tp) REVERT: C 1005 GLN cc_start: 0.8633 (tp40) cc_final: 0.8095 (tp40) REVERT: C 1017 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7878 (tm-30) REVERT: C 1018 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 1091 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7816 (mtt-85) REVERT: C 1123 SER cc_start: 0.8782 (t) cc_final: 0.8562 (m) REVERT: D 15 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7069 (mppt) REVERT: D 59 LYS cc_start: 0.8562 (mttp) cc_final: 0.8172 (mttp) REVERT: D 84 MET cc_start: 0.7907 (ptp) cc_final: 0.7621 (ptp) REVERT: D 182 LEU cc_start: 0.7856 (mt) cc_final: 0.7417 (mt) REVERT: E 44 GLN cc_start: 0.7868 (mp10) cc_final: 0.7452 (mp10) REVERT: E 104 THR cc_start: 0.8131 (m) cc_final: 0.7809 (p) REVERT: E 128 LEU cc_start: 0.5183 (OUTLIER) cc_final: 0.4949 (mm) REVERT: F 2 VAL cc_start: 0.8521 (t) cc_final: 0.8198 (p) REVERT: I 18 ILE cc_start: 0.6912 (mm) cc_final: 0.6545 (mt) outliers start: 183 outliers final: 139 residues processed: 908 average time/residue: 0.4584 time to fit residues: 655.8926 Evaluate side-chains 955 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 791 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 305 optimal weight: 0.7980 chunk 336 optimal weight: 0.0170 chunk 199 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 402 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN B 949 GLN B 965 GLN C 331 ASN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.160277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124331 restraints weight = 53781.194| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.38 r_work: 0.3439 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32921 Z= 0.129 Angle : 0.638 19.553 44900 Z= 0.318 Chirality : 0.045 0.284 5143 Planarity : 0.004 0.052 5765 Dihedral : 6.036 74.819 4572 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.79 % Allowed : 20.15 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 4110 helix: 1.14 (0.21), residues: 663 sheet: -0.79 (0.16), residues: 1037 loop : -1.91 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 49 HIS 0.004 0.001 HIS A 49 PHE 0.037 0.001 PHE A 168 TYR 0.017 0.001 TYR C 170 ARG 0.010 0.001 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 916) hydrogen bonds : angle 4.99500 ( 2493) SS BOND : bond 0.00477 ( 46) SS BOND : angle 1.97562 ( 92) covalent geometry : bond 0.00298 (32875) covalent geometry : angle 0.63202 (44808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 793 time to evaluate : 3.334 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: A 87 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7191 (p0) REVERT: A 97 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8254 (ttpp) REVERT: A 99 ASN cc_start: 0.8235 (m-40) cc_final: 0.7702 (t160) REVERT: A 186 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.6979 (p0) REVERT: A 205 HIS cc_start: 0.7960 (t-90) cc_final: 0.7643 (t-90) REVERT: A 209 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8285 (pt) REVERT: A 231 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7991 (pt) REVERT: A 269 TYR cc_start: 0.8437 (m-10) cc_final: 0.8002 (m-10) REVERT: A 281 GLU cc_start: 0.7724 (pp20) cc_final: 0.7203 (pp20) REVERT: A 287 ASP cc_start: 0.8182 (p0) cc_final: 0.7916 (p0) REVERT: A 290 ASP cc_start: 0.7470 (t70) cc_final: 0.7204 (t0) REVERT: A 301 CYS cc_start: 0.8601 (m) cc_final: 0.8380 (m) REVERT: A 332 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 335 LEU cc_start: 0.8816 (tp) cc_final: 0.8581 (mm) REVERT: A 353 TRP cc_start: 0.8717 (p-90) cc_final: 0.8345 (p-90) REVERT: A 360 ASN cc_start: 0.8406 (m-40) cc_final: 0.8184 (m110) REVERT: A 378 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7476 (mtpt) REVERT: A 403 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7686 (mtp85) REVERT: A 421 TYR cc_start: 0.7667 (m-10) cc_final: 0.6818 (m-80) REVERT: A 440 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7764 (ttpp) REVERT: A 448 ASN cc_start: 0.8243 (t0) cc_final: 0.8013 (t0) REVERT: A 451 TYR cc_start: 0.7528 (m-80) cc_final: 0.7171 (m-80) REVERT: A 473 TYR cc_start: 0.7035 (t80) cc_final: 0.6585 (t80) REVERT: A 547 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8203 (mtpp) REVERT: A 573 THR cc_start: 0.8855 (m) cc_final: 0.8507 (p) REVERT: A 588 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (p) REVERT: A 599 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 697 MET cc_start: 0.8154 (mtm) cc_final: 0.7953 (mtp) REVERT: A 725 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 776 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8259 (ttpp) REVERT: A 779 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8252 (tp40) REVERT: A 900 MET cc_start: 0.8531 (mtp) cc_final: 0.8281 (mtt) REVERT: A 921 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: A 945 LEU cc_start: 0.8399 (mm) cc_final: 0.8153 (mp) REVERT: A 947 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8257 (mtpp) REVERT: A 949 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8081 (mm-40) REVERT: A 990 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 1017 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 1073 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8239 (ttpt) REVERT: A 1081 ILE cc_start: 0.8338 (pt) cc_final: 0.8034 (mt) REVERT: A 1097 SER cc_start: 0.8556 (t) cc_final: 0.8244 (p) REVERT: A 1107 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: A 1144 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: B 83 VAL cc_start: 0.7657 (t) cc_final: 0.7456 (t) REVERT: B 105 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 239 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 241 LEU cc_start: 0.7932 (mt) cc_final: 0.6968 (mt) REVERT: B 270 LEU cc_start: 0.8793 (mp) cc_final: 0.8562 (mt) REVERT: B 273 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7865 (tpp80) REVERT: B 360 ASN cc_start: 0.8300 (m110) cc_final: 0.8088 (m110) REVERT: B 386 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8049 (mmmt) REVERT: B 394 ASN cc_start: 0.7933 (p0) cc_final: 0.7432 (p0) REVERT: B 400 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6745 (p90) REVERT: B 406 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 414 GLN cc_start: 0.8066 (mp10) cc_final: 0.7593 (mp10) REVERT: B 433 VAL cc_start: 0.8885 (t) cc_final: 0.8538 (p) REVERT: B 440 LYS cc_start: 0.8627 (ttpp) cc_final: 0.7930 (mmmm) REVERT: B 587 ILE cc_start: 0.8762 (mt) cc_final: 0.8530 (mm) REVERT: B 695 TYR cc_start: 0.8557 (p90) cc_final: 0.7855 (p90) REVERT: B 698 SER cc_start: 0.8942 (t) cc_final: 0.8558 (p) REVERT: B 711 SER cc_start: 0.8824 (t) cc_final: 0.8446 (p) REVERT: B 723 THR cc_start: 0.8721 (t) cc_final: 0.8480 (p) REVERT: B 740 MET cc_start: 0.8147 (tpp) cc_final: 0.7912 (tpp) REVERT: B 825 LYS cc_start: 0.8846 (mttm) cc_final: 0.8499 (mttt) REVERT: B 854 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8345 (ttmm) REVERT: B 868 GLU cc_start: 0.8095 (tp30) cc_final: 0.7709 (tp30) REVERT: B 900 MET cc_start: 0.8624 (mtp) cc_final: 0.8384 (mtm) REVERT: B 964 LYS cc_start: 0.8958 (ttpp) cc_final: 0.8593 (ttmm) REVERT: B 968 SER cc_start: 0.8980 (m) cc_final: 0.8706 (p) REVERT: B 976 VAL cc_start: 0.8717 (t) cc_final: 0.8166 (m) REVERT: B 979 ASP cc_start: 0.7859 (m-30) cc_final: 0.7498 (m-30) REVERT: B 985 ASP cc_start: 0.7941 (p0) cc_final: 0.7629 (p0) REVERT: B 990 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 993 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 994 ASP cc_start: 0.8208 (m-30) cc_final: 0.7694 (t0) REVERT: B 1001 LEU cc_start: 0.9058 (mt) cc_final: 0.8786 (mt) REVERT: B 1005 GLN cc_start: 0.8385 (tp40) cc_final: 0.7980 (tp40) REVERT: B 1031 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: B 1141 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 29 THR cc_start: 0.8704 (t) cc_final: 0.7364 (p) REVERT: C 34 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7279 (mtp-110) REVERT: C 102 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6843 (mtp85) REVERT: C 116 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8266 (p) REVERT: C 121 ASN cc_start: 0.7656 (t0) cc_final: 0.7066 (t0) REVERT: C 132 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6388 (mm-30) REVERT: C 189 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7092 (mt-10) REVERT: C 237 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.7714 (mtp-110) REVERT: C 241 LEU cc_start: 0.8091 (pp) cc_final: 0.7831 (pp) REVERT: C 281 GLU cc_start: 0.7848 (pp20) cc_final: 0.7514 (pp20) REVERT: C 310 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8628 (ttpt) REVERT: C 324 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: C 385 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8777 (p) REVERT: C 467 ASP cc_start: 0.7943 (p0) cc_final: 0.7676 (p0) REVERT: C 511 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8441 (t) REVERT: C 543 PHE cc_start: 0.8752 (m-10) cc_final: 0.8423 (m-80) REVERT: C 615 VAL cc_start: 0.8385 (t) cc_final: 0.8128 (m) REVERT: C 655 TYR cc_start: 0.8645 (t80) cc_final: 0.8376 (t80) REVERT: C 698 SER cc_start: 0.9172 (t) cc_final: 0.8707 (p) REVERT: C 780 GLU cc_start: 0.7753 (pt0) cc_final: 0.7532 (pt0) REVERT: C 859 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8159 (p) REVERT: C 868 GLU cc_start: 0.7935 (tp30) cc_final: 0.7358 (tp30) REVERT: C 902 MET cc_start: 0.8390 (tpp) cc_final: 0.8001 (mmm) REVERT: C 904 TYR cc_start: 0.7945 (m-10) cc_final: 0.7593 (m-10) REVERT: C 933 LYS cc_start: 0.8355 (mttm) cc_final: 0.8078 (mtmm) REVERT: C 947 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8098 (mtpp) REVERT: C 960 ASN cc_start: 0.8724 (t0) cc_final: 0.8421 (t0) REVERT: C 964 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8441 (ttpp) REVERT: C 969 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7852 (ptpp) REVERT: C 993 ILE cc_start: 0.9046 (tp) cc_final: 0.8776 (tp) REVERT: C 1005 GLN cc_start: 0.8612 (tp40) cc_final: 0.8088 (tp40) REVERT: C 1017 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 1018 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8228 (mp) REVERT: C 1091 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7819 (mtt-85) REVERT: C 1123 SER cc_start: 0.8740 (t) cc_final: 0.8509 (m) REVERT: D 29 LEU cc_start: 0.9010 (tp) cc_final: 0.8765 (tt) REVERT: D 59 LYS cc_start: 0.8573 (mttp) cc_final: 0.8347 (mttp) REVERT: D 84 MET cc_start: 0.7944 (ptp) cc_final: 0.7660 (ptp) REVERT: E 19 THR cc_start: 0.8456 (p) cc_final: 0.8147 (p) REVERT: E 34 TYR cc_start: 0.8521 (m-80) cc_final: 0.8053 (m-80) REVERT: E 44 GLN cc_start: 0.7864 (mp10) cc_final: 0.7453 (mp10) REVERT: E 104 THR cc_start: 0.8144 (m) cc_final: 0.7818 (p) REVERT: E 128 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5300 (mm) REVERT: F 2 VAL cc_start: 0.8525 (t) cc_final: 0.8215 (p) REVERT: I 18 ILE cc_start: 0.6935 (mm) cc_final: 0.6533 (mt) outliers start: 172 outliers final: 133 residues processed: 898 average time/residue: 0.4600 time to fit residues: 651.0344 Evaluate side-chains 947 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 790 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 131 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 321 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 388 ASN A 901 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 564 GLN B 935 GLN B 949 GLN C 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119441 restraints weight = 53843.735| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.72 r_work: 0.3345 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 32921 Z= 0.330 Angle : 0.739 20.385 44900 Z= 0.377 Chirality : 0.050 0.314 5143 Planarity : 0.005 0.055 5765 Dihedral : 6.290 74.274 4562 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.88 % Allowed : 20.46 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.13), residues: 4110 helix: 0.69 (0.21), residues: 678 sheet: -0.97 (0.15), residues: 1064 loop : -1.93 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 64 HIS 0.011 0.001 HIS B1064 PHE 0.041 0.003 PHE C 429 TYR 0.039 0.002 TYR A 170 ARG 0.011 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 916) hydrogen bonds : angle 5.28087 ( 2493) SS BOND : bond 0.00676 ( 46) SS BOND : angle 2.40501 ( 92) covalent geometry : bond 0.00742 (32875) covalent geometry : angle 0.73214 (44808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26464.05 seconds wall clock time: 458 minutes 11.63 seconds (27491.63 seconds total)