Starting phenix.real_space_refine on Tue May 20 19:42:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097.map" model { file = "/net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vao_43097/05_2025/8vao_43097_trim.cif" } resolution = 2.8 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= 0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 6480 2.51 5 N 1698 2.21 5 O 1977 1.98 5 H 9942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6676 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B Time building chain proxies: 16.45, per 1000 atoms: 0.82 Number of scatterers: 20154 At special positions: 0 Unit cell: (84.6, 87.42, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1977 8.00 N 1698 7.00 C 6480 6.00 H 9942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS B 790 " 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 A 790 " - pdb=" SG CYS C 704 " distance=1.96 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 704 " - pdb=" SG CYS C 790 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 717 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1098 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1098 " Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 53.1% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.931A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.353A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.556A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.800A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.859A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TRP A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 995 " --> pdb=" O TRP A 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.932A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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 783 removed outlier: 3.564A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.352A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.555A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.801A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.538A 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TRP B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.932A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.563A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.353A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.555A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.802A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TRP C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 995 " --> pdb=" O TRP C 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 997 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.951A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.951A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA8, first strand: chain 'B' and resid 1094 through 1098 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB3, first strand: chain 'C' and resid 1094 through 1098 516 hydrogen bonds defined for protein. 1485 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: 7.47 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9942 1.03 - 1.23: 67 1.23 - 1.43: 4238 1.43 - 1.62: 6045 1.62 - 1.82: 78 Bond restraints: 20370 Sorted by residual: bond pdb=" N CYS A 704 " pdb=" CA CYS A 704 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N CYS C 704 " pdb=" CA CYS C 704 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N CYS B 704 " pdb=" CA CYS B 704 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N CYS B 704 " pdb=" H CYS B 704 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N CYS A 704 " pdb=" H CYS A 704 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 20365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 33360 0.94 - 1.89: 3175 1.89 - 2.83: 160 2.83 - 3.77: 55 3.77 - 4.71: 27 Bond angle restraints: 36777 Sorted by residual: angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 126.13 -4.59 1.91e+00 2.74e-01 5.77e+00 angle pdb=" C VAL B1040 " pdb=" N ASP B1041 " pdb=" CA ASP B1041 " ideal model delta sigma weight residual 121.54 125.04 -3.50 1.91e+00 2.74e-01 3.36e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 112.91 -2.21 1.22e+00 6.72e-01 3.29e+00 ... (remaining 36772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8924 17.07 - 34.14: 535 34.14 - 51.21: 207 51.21 - 68.29: 198 68.29 - 85.36: 9 Dihedral angle restraints: 9873 sinusoidal: 5445 harmonic: 4428 Sorted by residual: dihedral pdb=" CD ARG B1107 " pdb=" NE ARG B1107 " pdb=" CZ ARG B1107 " pdb=" NH1 ARG B1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.55 37.55 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CD ARG C1107 " pdb=" NE ARG C1107 " pdb=" CZ ARG C1107 " pdb=" NH1 ARG C1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.43 37.43 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CD ARG A1107 " pdb=" NE ARG A1107 " pdb=" CZ ARG A1107 " pdb=" NH1 ARG A1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.41 37.41 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 9870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 978 0.025 - 0.050: 372 0.050 - 0.075: 181 0.075 - 0.100: 82 0.100 - 0.125: 58 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA VAL B1065 " pdb=" N VAL B1065 " pdb=" C VAL B1065 " pdb=" CB VAL B1065 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A1065 " pdb=" N VAL A1065 " pdb=" C VAL A1065 " pdb=" CB VAL A1065 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL C1065 " pdb=" N VAL C1065 " pdb=" C VAL C1065 " pdb=" CB VAL C1065 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1668 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1107 " 0.504 9.50e-02 1.11e+02 1.70e-01 4.23e+01 pdb=" NE ARG B1107 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B1107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B1107 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG B1107 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG B1107 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B1107 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B1107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1107 " 0.504 9.50e-02 1.11e+02 1.70e-01 4.21e+01 pdb=" NE ARG C1107 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG C1107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG C1107 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C1107 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG C1107 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C1107 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG C1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C1107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1107 " -0.503 9.50e-02 1.11e+02 1.70e-01 4.20e+01 pdb=" NE ARG A1107 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A1107 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A1107 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A1107 " -0.013 2.00e-02 2.50e+03 pdb="HH11 ARG A1107 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1107 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1107 " 0.012 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1007 2.19 - 2.79: 40843 2.79 - 3.39: 54607 3.39 - 4.00: 71110 4.00 - 4.60: 110931 Nonbonded interactions: 278498 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 786 " pdb=" OE1 GLN C 787 " model vdw 1.586 2.450 nonbonded pdb=" HZ1 LYS A 786 " pdb=" OE1 GLN A 787 " model vdw 1.586 2.450 nonbonded pdb=" HZ1 LYS B 786 " pdb=" OE1 GLN B 787 " model vdw 1.586 2.450 nonbonded pdb=" HH TYR A 741 " pdb=" O LEU A 962 " model vdw 1.611 2.450 nonbonded pdb=" HH TYR B 741 " pdb=" O LEU B 962 " model vdw 1.612 2.450 ... (remaining 278493 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.390 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: 0.350 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 50.080 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.003 0.069 10455 Z= 0.138 Angle : 0.517 4.714 14268 Z= 0.257 Chirality : 0.040 0.125 1671 Planarity : 0.011 0.232 1836 Dihedral : 13.268 85.356 3900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -0.67 (0.23), residues: 1305 helix: 0.34 (0.22), residues: 588 sheet: -0.33 (0.36), residues: 150 loop : -1.26 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.004 0.001 HIS A1083 PHE 0.009 0.001 PHE C 759 TYR 0.011 0.001 TYR C1067 ARG 0.050 0.005 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 1.49246 ( 27) hydrogen bonds : bond 0.21424 ( 516) hydrogen bonds : angle 7.86480 ( 1485) SS BOND : bond 0.02233 ( 18) SS BOND : angle 0.90221 ( 36) covalent geometry : bond 0.00301 (10428) covalent geometry : angle 0.51176 (14205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.8036 (t0) cc_final: 0.7807 (t0) REVERT: A 748 GLU cc_start: 0.7596 (mp0) cc_final: 0.7309 (mp0) REVERT: A 772 VAL cc_start: 0.8661 (t) cc_final: 0.8386 (m) REVERT: A 814 LYS cc_start: 0.7365 (mmmm) cc_final: 0.7139 (mmpt) REVERT: A 824 ASN cc_start: 0.8361 (m-40) cc_final: 0.8131 (m110) REVERT: A 1009 THR cc_start: 0.8627 (t) cc_final: 0.8351 (m) REVERT: A 1010 GLN cc_start: 0.7966 (tp40) cc_final: 0.7748 (mm-40) REVERT: A 1038 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7832 (mmtm) REVERT: A 1103 PHE cc_start: 0.8059 (m-10) cc_final: 0.7842 (m-80) REVERT: B 737 ASP cc_start: 0.7890 (t0) cc_final: 0.7499 (t0) REVERT: B 748 GLU cc_start: 0.7436 (mp0) cc_final: 0.7235 (mp0) REVERT: B 869 MET cc_start: 0.7596 (mtt) cc_final: 0.7321 (mtm) REVERT: B 950 ASP cc_start: 0.7381 (m-30) cc_final: 0.6908 (m-30) REVERT: B 962 LEU cc_start: 0.8077 (tp) cc_final: 0.7786 (tp) REVERT: B 996 LEU cc_start: 0.7663 (mp) cc_final: 0.7441 (mt) REVERT: B 1009 THR cc_start: 0.8545 (t) cc_final: 0.8240 (m) REVERT: B 1117 THR cc_start: 0.8173 (m) cc_final: 0.7805 (p) REVERT: B 1127 ASP cc_start: 0.7017 (m-30) cc_final: 0.6798 (m-30) REVERT: B 1130 ILE cc_start: 0.8559 (mt) cc_final: 0.8314 (mt) REVERT: C 737 ASP cc_start: 0.8097 (t0) cc_final: 0.7591 (t0) REVERT: C 741 TYR cc_start: 0.8290 (t80) cc_final: 0.8088 (t80) REVERT: C 772 VAL cc_start: 0.8559 (t) cc_final: 0.8352 (m) REVERT: C 836 GLN cc_start: 0.7963 (mt0) cc_final: 0.7703 (mt0) REVERT: C 837 TYR cc_start: 0.8087 (t80) cc_final: 0.7846 (t80) REVERT: C 854 LYS cc_start: 0.7967 (tttp) cc_final: 0.7753 (ttmm) REVERT: C 907 ASN cc_start: 0.7576 (t0) cc_final: 0.7351 (t0) REVERT: C 950 ASP cc_start: 0.7430 (m-30) cc_final: 0.6937 (m-30) REVERT: C 992 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7254 (mm110) REVERT: C 996 LEU cc_start: 0.7822 (mp) cc_final: 0.7568 (mt) REVERT: C 1010 GLN cc_start: 0.7869 (tp40) cc_final: 0.7447 (tm-30) REVERT: C 1038 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7689 (mmtm) outliers start: 0 outliers final: 3 residues processed: 340 average time/residue: 2.3202 time to fit residues: 854.7937 Evaluate side-chains 297 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 805 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 784 GLN A 872 GLN A 992 GLN A1005 GLN B 779 GLN B 784 GLN B 836 GLN B 853 GLN B 895 GLN B 955 ASN B1005 GLN B1101 HIS C 762 GLN C 764 ASN C 784 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104794 restraints weight = 36030.606| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.88 r_work: 0.3221 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10455 Z= 0.253 Angle : 0.611 5.105 14268 Z= 0.321 Chirality : 0.045 0.164 1671 Planarity : 0.005 0.043 1836 Dihedral : 5.840 47.637 1578 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 12.36 % Favored : 85.33 % 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: 0.02 (0.22), residues: 1305 helix: 1.03 (0.21), residues: 606 sheet: -0.15 (0.33), residues: 189 loop : -1.11 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1102 HIS 0.006 0.002 HIS C1064 PHE 0.014 0.002 PHE A 906 TYR 0.017 0.002 TYR C1067 ARG 0.006 0.001 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 9) link_NAG-ASN : angle 2.34940 ( 27) hydrogen bonds : bond 0.06453 ( 516) hydrogen bonds : angle 5.17299 ( 1485) SS BOND : bond 0.00609 ( 18) SS BOND : angle 1.34944 ( 36) covalent geometry : bond 0.00599 (10428) covalent geometry : angle 0.60007 (14205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 326 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 THR cc_start: 0.8160 (t) cc_final: 0.7951 (p) REVERT: A 748 GLU cc_start: 0.7734 (mp0) cc_final: 0.7329 (mp0) REVERT: A 772 VAL cc_start: 0.8808 (t) cc_final: 0.8495 (m) REVERT: A 814 LYS cc_start: 0.7502 (mmmm) cc_final: 0.7091 (mmmt) REVERT: A 824 ASN cc_start: 0.8524 (m-40) cc_final: 0.8289 (m110) REVERT: A 873 TYR cc_start: 0.8275 (m-80) cc_final: 0.7954 (m-80) REVERT: A 900 MET cc_start: 0.8349 (mtp) cc_final: 0.8142 (mtp) REVERT: A 934 ILE cc_start: 0.8030 (tp) cc_final: 0.7793 (pt) REVERT: A 992 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7215 (mm110) REVERT: A 1009 THR cc_start: 0.8483 (t) cc_final: 0.8260 (m) REVERT: A 1038 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7865 (mmtm) REVERT: B 737 ASP cc_start: 0.7983 (t0) cc_final: 0.7503 (t0) REVERT: B 748 GLU cc_start: 0.7659 (mp0) cc_final: 0.7416 (mp0) REVERT: B 864 LEU cc_start: 0.8108 (tp) cc_final: 0.7863 (tt) REVERT: B 873 TYR cc_start: 0.8422 (m-80) cc_final: 0.7809 (m-80) REVERT: B 962 LEU cc_start: 0.8395 (tp) cc_final: 0.8191 (tp) REVERT: B 1117 THR cc_start: 0.8297 (m) cc_final: 0.7906 (p) REVERT: B 1127 ASP cc_start: 0.7281 (m-30) cc_final: 0.7070 (m-30) REVERT: C 725 GLU cc_start: 0.7946 (tt0) cc_final: 0.7742 (tt0) REVERT: C 737 ASP cc_start: 0.8127 (t0) cc_final: 0.7276 (t0) REVERT: C 837 TYR cc_start: 0.8173 (t80) cc_final: 0.7909 (t80) REVERT: C 839 ASP cc_start: 0.7826 (m-30) cc_final: 0.7603 (m-30) REVERT: C 854 LYS cc_start: 0.8156 (tttp) cc_final: 0.7925 (ttmm) REVERT: C 933 LYS cc_start: 0.8192 (mttt) cc_final: 0.7915 (mtpp) REVERT: C 950 ASP cc_start: 0.7578 (m-30) cc_final: 0.7141 (m-30) REVERT: C 992 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7030 (mm110) REVERT: C 1010 GLN cc_start: 0.8067 (tp40) cc_final: 0.7721 (tm-30) REVERT: C 1038 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7993 (mmtm) outliers start: 26 outliers final: 13 residues processed: 340 average time/residue: 2.5331 time to fit residues: 925.6201 Evaluate side-chains 317 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 872 GLN A1005 GLN B 836 GLN B 895 GLN B 955 ASN B 992 GLN B1005 GLN B1106 GLN C 762 GLN C 914 ASN C 969 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102487 restraints weight = 36145.012| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.90 r_work: 0.3182 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10455 Z= 0.245 Angle : 0.581 5.544 14268 Z= 0.303 Chirality : 0.044 0.177 1671 Planarity : 0.005 0.042 1836 Dihedral : 5.735 48.148 1572 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.76 % Allowed : 14.31 % Favored : 82.93 % 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: 0.38 (0.23), residues: 1305 helix: 1.40 (0.21), residues: 612 sheet: 0.03 (0.33), residues: 189 loop : -1.07 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.006 0.002 HIS B1083 PHE 0.013 0.002 PHE A 906 TYR 0.016 0.002 TYR C 904 ARG 0.006 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 9) link_NAG-ASN : angle 2.45497 ( 27) hydrogen bonds : bond 0.05979 ( 516) hydrogen bonds : angle 4.99834 ( 1485) SS BOND : bond 0.00622 ( 18) SS BOND : angle 1.79332 ( 36) covalent geometry : bond 0.00588 (10428) covalent geometry : angle 0.56554 (14205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 313 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8564 (tttm) cc_final: 0.8354 (tttm) REVERT: A 780 GLU cc_start: 0.7748 (tt0) cc_final: 0.7486 (mt-10) REVERT: A 814 LYS cc_start: 0.7500 (mmmm) cc_final: 0.7090 (mmmt) REVERT: A 824 ASN cc_start: 0.8567 (m-40) cc_final: 0.8336 (m110) REVERT: A 934 ILE cc_start: 0.8089 (tp) cc_final: 0.7801 (pt) REVERT: A 992 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7234 (mm110) REVERT: A 1009 THR cc_start: 0.8582 (t) cc_final: 0.8364 (m) REVERT: A 1038 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7985 (mmtm) REVERT: B 748 GLU cc_start: 0.7643 (mp0) cc_final: 0.7388 (mp0) REVERT: B 820 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7832 (t0) REVERT: B 860 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8467 (t) REVERT: B 873 TYR cc_start: 0.8512 (m-80) cc_final: 0.7820 (m-80) REVERT: B 1105 THR cc_start: 0.8614 (p) cc_final: 0.8404 (t) REVERT: B 1117 THR cc_start: 0.8343 (m) cc_final: 0.7874 (p) REVERT: C 737 ASP cc_start: 0.8145 (t0) cc_final: 0.7871 (t0) REVERT: C 835 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7631 (ttmm) REVERT: C 837 TYR cc_start: 0.8175 (t80) cc_final: 0.7886 (t80) REVERT: C 933 LYS cc_start: 0.8175 (mttt) cc_final: 0.7907 (mtpp) REVERT: C 950 ASP cc_start: 0.7610 (m-30) cc_final: 0.7166 (m-30) REVERT: C 983 ARG cc_start: 0.7467 (ttm110) cc_final: 0.7212 (ttm110) REVERT: C 992 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7161 (mm110) REVERT: C 1038 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8049 (mmtm) outliers start: 31 outliers final: 18 residues processed: 325 average time/residue: 2.6448 time to fit residues: 921.2961 Evaluate side-chains 323 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 779 GLN B 836 GLN B 895 GLN B 969 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1074 ASN C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102055 restraints weight = 36364.044| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.91 r_work: 0.3176 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10455 Z= 0.199 Angle : 0.550 4.770 14268 Z= 0.284 Chirality : 0.042 0.175 1671 Planarity : 0.005 0.048 1836 Dihedral : 5.697 50.465 1572 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.67 % Allowed : 15.47 % Favored : 81.87 % 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: 0.71 (0.23), residues: 1305 helix: 1.73 (0.21), residues: 612 sheet: -0.02 (0.34), residues: 189 loop : -0.88 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS A1101 PHE 0.010 0.001 PHE A 906 TYR 0.014 0.002 TYR C1067 ARG 0.008 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 9) link_NAG-ASN : angle 2.30370 ( 27) hydrogen bonds : bond 0.05404 ( 516) hydrogen bonds : angle 4.84434 ( 1485) SS BOND : bond 0.00460 ( 18) SS BOND : angle 1.51312 ( 36) covalent geometry : bond 0.00472 (10428) covalent geometry : angle 0.53643 (14205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8740 (t) cc_final: 0.8429 (m) REVERT: A 780 GLU cc_start: 0.7708 (tt0) cc_final: 0.7473 (mt-10) REVERT: A 824 ASN cc_start: 0.8532 (m-40) cc_final: 0.8303 (m110) REVERT: A 992 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7127 (mm-40) REVERT: A 1002 GLN cc_start: 0.8296 (mm110) cc_final: 0.8046 (mm110) REVERT: A 1038 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8069 (mmtm) REVERT: B 737 ASP cc_start: 0.7928 (t70) cc_final: 0.7432 (t0) REVERT: B 748 GLU cc_start: 0.7641 (mp0) cc_final: 0.7382 (mp0) REVERT: B 820 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7823 (t0) REVERT: B 860 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 873 TYR cc_start: 0.8562 (m-80) cc_final: 0.7838 (m-80) REVERT: B 1002 GLN cc_start: 0.8066 (mm110) cc_final: 0.7823 (mm110) REVERT: B 1117 THR cc_start: 0.8228 (m) cc_final: 0.7764 (p) REVERT: C 835 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7669 (ttmm) REVERT: C 837 TYR cc_start: 0.8185 (t80) cc_final: 0.7836 (t80) REVERT: C 933 LYS cc_start: 0.8226 (mttt) cc_final: 0.7940 (mtpp) REVERT: C 983 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7233 (ttm110) REVERT: C 992 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7269 (mm110) REVERT: C 1038 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8029 (mmtm) outliers start: 30 outliers final: 17 residues processed: 329 average time/residue: 2.6577 time to fit residues: 936.8685 Evaluate side-chains 327 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 779 GLN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 935 GLN B 955 ASN B 969 ASN B1002 GLN B1005 GLN B1074 ASN C 901 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101130 restraints weight = 36441.671| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.91 r_work: 0.3162 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10455 Z= 0.230 Angle : 0.562 5.085 14268 Z= 0.291 Chirality : 0.043 0.175 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.866 53.152 1572 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.11 % Allowed : 15.02 % Favored : 81.87 % 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: 0.80 (0.23), residues: 1305 helix: 1.82 (0.21), residues: 609 sheet: 0.00 (0.34), residues: 189 loop : -0.84 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.005 0.001 HIS A1101 PHE 0.013 0.002 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.004 0.001 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 9) link_NAG-ASN : angle 2.44094 ( 27) hydrogen bonds : bond 0.05560 ( 516) hydrogen bonds : angle 4.87339 ( 1485) SS BOND : bond 0.00582 ( 18) SS BOND : angle 1.60855 ( 36) covalent geometry : bond 0.00550 (10428) covalent geometry : angle 0.54732 (14205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7739 (tt0) cc_final: 0.7519 (mt-10) REVERT: A 824 ASN cc_start: 0.8553 (m-40) cc_final: 0.8325 (m110) REVERT: A 979 ASP cc_start: 0.7554 (m-30) cc_final: 0.7192 (m-30) REVERT: A 1038 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8099 (mmtm) REVERT: B 737 ASP cc_start: 0.7970 (t70) cc_final: 0.7486 (t0) REVERT: B 748 GLU cc_start: 0.7699 (mp0) cc_final: 0.7426 (mp0) REVERT: B 820 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7834 (t0) REVERT: B 860 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 964 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8258 (mtpm) REVERT: C 737 ASP cc_start: 0.8172 (t0) cc_final: 0.7961 (t0) REVERT: C 748 GLU cc_start: 0.7749 (mp0) cc_final: 0.7518 (mp0) REVERT: C 785 VAL cc_start: 0.7774 (t) cc_final: 0.7554 (p) REVERT: C 835 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7625 (ttmm) REVERT: C 837 TYR cc_start: 0.8200 (t80) cc_final: 0.7853 (t80) REVERT: C 933 LYS cc_start: 0.8257 (mttt) cc_final: 0.7986 (mtpp) REVERT: C 992 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7282 (mm110) REVERT: C 1031 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: C 1038 LYS cc_start: 0.8246 (mmtm) cc_final: 0.8036 (mmtm) outliers start: 35 outliers final: 26 residues processed: 317 average time/residue: 2.6880 time to fit residues: 916.8068 Evaluate side-chains 318 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 853 GLN A 935 GLN A 992 GLN A1002 GLN B 836 GLN B 895 GLN B 935 GLN B1005 GLN B1074 ASN C 762 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101355 restraints weight = 36445.836| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.91 r_work: 0.3169 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10455 Z= 0.192 Angle : 0.546 4.656 14268 Z= 0.279 Chirality : 0.042 0.172 1671 Planarity : 0.005 0.047 1836 Dihedral : 5.827 56.000 1572 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.29 % Allowed : 15.91 % Favored : 80.80 % 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: 0.92 (0.23), residues: 1305 helix: 1.91 (0.21), residues: 609 sheet: 0.01 (0.34), residues: 189 loop : -0.75 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 PHE 0.011 0.001 PHE A 888 TYR 0.012 0.001 TYR C1067 ARG 0.005 0.001 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 9) link_NAG-ASN : angle 2.28625 ( 27) hydrogen bonds : bond 0.05241 ( 516) hydrogen bonds : angle 4.79277 ( 1485) SS BOND : bond 0.00524 ( 18) SS BOND : angle 1.57983 ( 36) covalent geometry : bond 0.00456 (10428) covalent geometry : angle 0.53224 (14205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8752 (t) cc_final: 0.8442 (m) REVERT: A 780 GLU cc_start: 0.7765 (tt0) cc_final: 0.7534 (mt-10) REVERT: A 824 ASN cc_start: 0.8571 (m-40) cc_final: 0.8335 (m110) REVERT: A 979 ASP cc_start: 0.7575 (m-30) cc_final: 0.7216 (m-30) REVERT: A 1002 GLN cc_start: 0.8236 (mm110) cc_final: 0.7949 (mm110) REVERT: A 1038 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8084 (mmtm) REVERT: B 737 ASP cc_start: 0.7979 (t70) cc_final: 0.7473 (t0) REVERT: B 748 GLU cc_start: 0.7675 (mp0) cc_final: 0.7409 (mp0) REVERT: B 780 GLU cc_start: 0.7722 (tt0) cc_final: 0.7486 (tt0) REVERT: B 820 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7792 (t0) REVERT: B 860 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8466 (t) REVERT: C 785 VAL cc_start: 0.7788 (t) cc_final: 0.7572 (p) REVERT: C 837 TYR cc_start: 0.8228 (t80) cc_final: 0.7862 (t80) REVERT: C 860 VAL cc_start: 0.8680 (m) cc_final: 0.8371 (t) REVERT: C 933 LYS cc_start: 0.8270 (mttt) cc_final: 0.8027 (mtpp) REVERT: C 983 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7149 (ttm110) REVERT: C 1031 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: C 1038 LYS cc_start: 0.8239 (mmtm) cc_final: 0.8017 (mmtm) outliers start: 37 outliers final: 25 residues processed: 321 average time/residue: 2.6417 time to fit residues: 910.0521 Evaluate side-chains 328 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 116 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 127 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 935 GLN B 955 ASN B1002 GLN B1005 GLN B1074 ASN C 779 GLN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102579 restraints weight = 36214.699| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.90 r_work: 0.3187 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10455 Z= 0.128 Angle : 0.521 5.114 14268 Z= 0.263 Chirality : 0.040 0.157 1671 Planarity : 0.004 0.042 1836 Dihedral : 5.689 58.230 1572 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 17.24 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1305 helix: 2.09 (0.21), residues: 609 sheet: 0.02 (0.34), residues: 189 loop : -0.65 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 991 HIS 0.004 0.001 HIS C1064 PHE 0.007 0.001 PHE A 888 TYR 0.010 0.001 TYR C 904 ARG 0.004 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 9) link_NAG-ASN : angle 1.96859 ( 27) hydrogen bonds : bond 0.04620 ( 516) hydrogen bonds : angle 4.63280 ( 1485) SS BOND : bond 0.00388 ( 18) SS BOND : angle 1.31709 ( 36) covalent geometry : bond 0.00298 (10428) covalent geometry : angle 0.51102 (14205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8724 (t) cc_final: 0.8415 (m) REVERT: A 780 GLU cc_start: 0.7734 (tt0) cc_final: 0.7509 (mt-10) REVERT: A 820 ASP cc_start: 0.7924 (t0) cc_final: 0.7616 (m-30) REVERT: A 824 ASN cc_start: 0.8589 (m-40) cc_final: 0.8349 (m110) REVERT: A 979 ASP cc_start: 0.7553 (m-30) cc_final: 0.7170 (m-30) REVERT: A 1002 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 1010 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7483 (tm-30) REVERT: A 1038 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8057 (mmtm) REVERT: A 1091 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7370 (ttp-170) REVERT: B 737 ASP cc_start: 0.7943 (t70) cc_final: 0.7464 (t0) REVERT: B 748 GLU cc_start: 0.7654 (mp0) cc_final: 0.7374 (mp0) REVERT: B 780 GLU cc_start: 0.7648 (tt0) cc_final: 0.7400 (tt0) REVERT: B 820 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7764 (t0) REVERT: B 860 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 1117 THR cc_start: 0.8142 (m) cc_final: 0.7551 (p) REVERT: C 785 VAL cc_start: 0.7759 (t) cc_final: 0.7534 (p) REVERT: C 837 TYR cc_start: 0.8209 (t80) cc_final: 0.7837 (t80) REVERT: C 860 VAL cc_start: 0.8614 (m) cc_final: 0.8324 (t) REVERT: C 933 LYS cc_start: 0.8255 (mttt) cc_final: 0.8008 (mtpp) REVERT: C 983 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7118 (ttm110) REVERT: C 1031 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: C 1038 LYS cc_start: 0.8236 (mmtm) cc_final: 0.8007 (mmtm) outliers start: 30 outliers final: 21 residues processed: 317 average time/residue: 2.6378 time to fit residues: 896.7919 Evaluate side-chains 322 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 298 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 895 GLN B1002 GLN B1074 ASN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101956 restraints weight = 36479.802| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.91 r_work: 0.3172 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10455 Z= 0.157 Angle : 0.536 5.534 14268 Z= 0.271 Chirality : 0.041 0.162 1671 Planarity : 0.004 0.037 1836 Dihedral : 5.720 59.784 1572 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.58 % Allowed : 17.60 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1305 helix: 2.10 (0.21), residues: 609 sheet: 0.05 (0.34), residues: 189 loop : -0.60 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 PHE 0.009 0.001 PHE A 888 TYR 0.011 0.001 TYR C1067 ARG 0.004 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 9) link_NAG-ASN : angle 2.09319 ( 27) hydrogen bonds : bond 0.04786 ( 516) hydrogen bonds : angle 4.69048 ( 1485) SS BOND : bond 0.00455 ( 18) SS BOND : angle 1.35588 ( 36) covalent geometry : bond 0.00371 (10428) covalent geometry : angle 0.52480 (14205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8722 (t) cc_final: 0.8414 (m) REVERT: A 780 GLU cc_start: 0.7744 (tt0) cc_final: 0.7490 (mt-10) REVERT: A 820 ASP cc_start: 0.7962 (t0) cc_final: 0.7635 (m-30) REVERT: A 824 ASN cc_start: 0.8584 (m-40) cc_final: 0.8342 (m110) REVERT: A 1010 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7483 (tm-30) REVERT: A 1038 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8057 (mmtm) REVERT: A 1091 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7377 (ttp-170) REVERT: B 737 ASP cc_start: 0.7963 (t70) cc_final: 0.7478 (t0) REVERT: B 748 GLU cc_start: 0.7644 (mp0) cc_final: 0.7356 (mp0) REVERT: B 780 GLU cc_start: 0.7687 (tt0) cc_final: 0.7425 (tt0) REVERT: B 820 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 860 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (t) REVERT: B 1117 THR cc_start: 0.8153 (m) cc_final: 0.7539 (p) REVERT: C 785 VAL cc_start: 0.7771 (t) cc_final: 0.7515 (p) REVERT: C 837 TYR cc_start: 0.8198 (t80) cc_final: 0.7819 (t80) REVERT: C 860 VAL cc_start: 0.8600 (m) cc_final: 0.8316 (t) REVERT: C 933 LYS cc_start: 0.8248 (mttt) cc_final: 0.8001 (mtpp) REVERT: C 983 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7201 (ttm110) REVERT: C 1031 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7809 (mt-10) outliers start: 29 outliers final: 19 residues processed: 311 average time/residue: 2.7037 time to fit residues: 901.1807 Evaluate side-chains 318 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 895 GLN B1005 GLN B1074 ASN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100663 restraints weight = 36299.748| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.90 r_work: 0.3158 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10455 Z= 0.247 Angle : 0.584 6.395 14268 Z= 0.300 Chirality : 0.044 0.175 1671 Planarity : 0.005 0.039 1836 Dihedral : 5.968 59.200 1572 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.49 % Allowed : 17.16 % Favored : 80.36 % 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: 0.95 (0.23), residues: 1305 helix: 1.93 (0.21), residues: 609 sheet: -0.08 (0.34), residues: 189 loop : -0.67 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.002 HIS B1064 PHE 0.014 0.002 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.004 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 2.45671 ( 27) hydrogen bonds : bond 0.05478 ( 516) hydrogen bonds : angle 4.91424 ( 1485) SS BOND : bond 0.00625 ( 18) SS BOND : angle 1.81416 ( 36) covalent geometry : bond 0.00592 (10428) covalent geometry : angle 0.56771 (14205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7751 (tt0) cc_final: 0.7512 (mt-10) REVERT: A 820 ASP cc_start: 0.7982 (t0) cc_final: 0.7661 (m-30) REVERT: A 824 ASN cc_start: 0.8631 (m-40) cc_final: 0.8376 (m110) REVERT: A 1002 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8046 (mm110) REVERT: A 1010 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7515 (tm-30) REVERT: A 1038 LYS cc_start: 0.8337 (mmtm) cc_final: 0.8073 (mmtm) REVERT: B 737 ASP cc_start: 0.8002 (t70) cc_final: 0.7507 (t0) REVERT: B 748 GLU cc_start: 0.7619 (mp0) cc_final: 0.7341 (mp0) REVERT: B 780 GLU cc_start: 0.7769 (tt0) cc_final: 0.7509 (tt0) REVERT: B 820 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7831 (t0) REVERT: B 860 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (t) REVERT: B 980 ILE cc_start: 0.7453 (pt) cc_final: 0.7193 (mt) REVERT: C 748 GLU cc_start: 0.7754 (mp0) cc_final: 0.7429 (mp0) REVERT: C 785 VAL cc_start: 0.7840 (t) cc_final: 0.7630 (p) REVERT: C 837 TYR cc_start: 0.8236 (t80) cc_final: 0.7898 (t80) REVERT: C 860 VAL cc_start: 0.8611 (m) cc_final: 0.8306 (t) REVERT: C 1031 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (mt-10) outliers start: 28 outliers final: 18 residues processed: 305 average time/residue: 2.7070 time to fit residues: 884.8871 Evaluate side-chains 312 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 895 GLN B 955 ASN B1002 GLN B1005 GLN B1074 ASN B1134 ASN C 779 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102136 restraints weight = 36474.084| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10455 Z= 0.139 Angle : 0.538 6.257 14268 Z= 0.272 Chirality : 0.041 0.161 1671 Planarity : 0.004 0.036 1836 Dihedral : 5.744 57.468 1572 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.31 % Allowed : 17.60 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1305 helix: 2.08 (0.21), residues: 609 sheet: -0.04 (0.34), residues: 189 loop : -0.63 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 998 HIS 0.003 0.001 HIS C1064 PHE 0.008 0.001 PHE A 888 TYR 0.011 0.001 TYR C 904 ARG 0.003 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 9) link_NAG-ASN : angle 2.03678 ( 27) hydrogen bonds : bond 0.04688 ( 516) hydrogen bonds : angle 4.70970 ( 1485) SS BOND : bond 0.00494 ( 18) SS BOND : angle 1.62203 ( 36) covalent geometry : bond 0.00324 (10428) covalent geometry : angle 0.52532 (14205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8717 (t) cc_final: 0.8410 (m) REVERT: A 780 GLU cc_start: 0.7754 (tt0) cc_final: 0.7528 (mt-10) REVERT: A 820 ASP cc_start: 0.7984 (t0) cc_final: 0.7664 (m-30) REVERT: A 824 ASN cc_start: 0.8615 (m-40) cc_final: 0.8373 (m110) REVERT: A 1002 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8036 (mm110) REVERT: A 1010 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7482 (tm-30) REVERT: A 1038 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8063 (mmtm) REVERT: B 737 ASP cc_start: 0.7970 (t70) cc_final: 0.7473 (t0) REVERT: B 748 GLU cc_start: 0.7583 (mp0) cc_final: 0.7290 (mp0) REVERT: B 780 GLU cc_start: 0.7709 (tt0) cc_final: 0.7447 (tt0) REVERT: B 820 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7786 (t0) REVERT: B 825 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8201 (mptp) REVERT: B 860 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8434 (t) REVERT: B 980 ILE cc_start: 0.7427 (pt) cc_final: 0.7154 (mt) REVERT: C 737 ASP cc_start: 0.8141 (t0) cc_final: 0.7903 (t0) REVERT: C 748 GLU cc_start: 0.7716 (mp0) cc_final: 0.7429 (mp0) REVERT: C 785 VAL cc_start: 0.7825 (t) cc_final: 0.7618 (p) REVERT: C 837 TYR cc_start: 0.8244 (t80) cc_final: 0.7845 (t80) REVERT: C 860 VAL cc_start: 0.8602 (m) cc_final: 0.8331 (t) REVERT: C 1031 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7784 (mt-10) outliers start: 26 outliers final: 20 residues processed: 301 average time/residue: 2.7162 time to fit residues: 875.8716 Evaluate side-chains 311 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 895 GLN B1002 GLN B1074 ASN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101648 restraints weight = 36538.992| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.90 r_work: 0.3172 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10455 Z= 0.174 Angle : 0.549 6.416 14268 Z= 0.278 Chirality : 0.042 0.162 1671 Planarity : 0.004 0.039 1836 Dihedral : 5.780 57.060 1572 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 17.87 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1305 helix: 2.09 (0.21), residues: 609 sheet: 0.11 (0.36), residues: 159 loop : -0.56 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 998 HIS 0.004 0.001 HIS C1064 PHE 0.011 0.001 PHE A 888 TYR 0.011 0.001 TYR C1067 ARG 0.003 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 9) link_NAG-ASN : angle 2.19855 ( 27) hydrogen bonds : bond 0.04908 ( 516) hydrogen bonds : angle 4.74050 ( 1485) SS BOND : bond 0.00522 ( 18) SS BOND : angle 1.65964 ( 36) covalent geometry : bond 0.00414 (10428) covalent geometry : angle 0.53582 (14205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17560.81 seconds wall clock time: 300 minutes 6.94 seconds (18006.94 seconds total)