Starting phenix.real_space_refine on Tue Jun 17 21:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vao_43097/06_2025/8vao_43097_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vao_43097/06_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_43097/06_2025/8vao_43097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vao_43097/06_2025/8vao_43097.map" model { file = "/net/cci-nas-00/data/ceres_data/8vao_43097/06_2025/8vao_43097_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vao_43097/06_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-5710/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: 16.70, per 1000 atoms: 0.83 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: 5.15 Conformation dependent library (CDL) restraints added in 1.7 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: 1.69 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: 7.37 Time building geometry restraints manager: 6.19 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: 3.800 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: 0.330 Extract box with map and model: 0.680 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 51.760 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.030 ------------------------------------------------------------------------------- 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 : 1.343 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: 2.3270 time to fit residues: 857.3487 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 : 1.810 ------------------------------------------------------------------------------- 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 = 0.120392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104783 restraints weight = 36031.653| |-----------------------------------------------------------------------------| 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: 0.3068 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- 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 : 1.543 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: 0.7733 (mp0) cc_final: 0.7327 (mp0) REVERT: A 772 VAL cc_start: 0.8807 (t) cc_final: 0.8494 (m) REVERT: A 814 LYS cc_start: 0.7503 (mmmm) cc_final: 0.7091 (mmmt) REVERT: A 824 ASN cc_start: 0.8524 (m-40) cc_final: 0.8288 (m110) REVERT: A 873 TYR cc_start: 0.8274 (m-80) cc_final: 0.7952 (m-80) REVERT: A 900 MET cc_start: 0.8348 (mtp) cc_final: 0.8141 (mtp) REVERT: A 934 ILE cc_start: 0.8029 (tp) cc_final: 0.7792 (pt) REVERT: A 992 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7214 (mm110) REVERT: A 1009 THR cc_start: 0.8486 (t) cc_final: 0.8263 (m) REVERT: A 1038 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7865 (mmtm) REVERT: B 737 ASP cc_start: 0.7981 (t0) cc_final: 0.7502 (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: 0.8420 (m-80) cc_final: 0.7806 (m-80) REVERT: B 962 LEU cc_start: 0.8395 (tp) cc_final: 0.8190 (tp) REVERT: B 1117 THR cc_start: 0.8297 (m) cc_final: 0.7906 (p) REVERT: B 1127 ASP cc_start: 0.7280 (m-30) cc_final: 0.7069 (m-30) REVERT: C 725 GLU cc_start: 0.7945 (tt0) cc_final: 0.7741 (tt0) REVERT: C 737 ASP cc_start: 0.8126 (t0) cc_final: 0.7273 (t0) REVERT: C 837 TYR cc_start: 0.8169 (t80) cc_final: 0.7904 (t80) REVERT: C 839 ASP cc_start: 0.7824 (m-30) cc_final: 0.7601 (m-30) REVERT: C 854 LYS cc_start: 0.8156 (tttp) cc_final: 0.7925 (ttmm) REVERT: C 933 LYS cc_start: 0.8190 (mttt) cc_final: 0.7912 (mtpp) REVERT: C 950 ASP cc_start: 0.7575 (m-30) cc_final: 0.7138 (m-30) REVERT: C 992 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7030 (mm110) REVERT: C 1010 GLN cc_start: 0.8067 (tp40) cc_final: 0.7720 (tm-30) REVERT: C 1038 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7993 (mmtm) outliers start: 26 outliers final: 13 residues processed: 340 average time/residue: 2.5577 time to fit residues: 935.4004 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 : 1.555 ------------------------------------------------------------------------------- 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: 0.9990 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 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 = 0.118212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102493 restraints weight = 36138.943| |-----------------------------------------------------------------------------| 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: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10455 Z= 0.245 Angle : 0.582 5.595 14268 Z= 0.303 Chirality : 0.044 0.176 1671 Planarity : 0.005 0.042 1836 Dihedral : 5.737 48.150 1572 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.84 % Allowed : 14.22 % 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 0.006 0.001 TRP B1102 HIS 0.006 0.002 HIS B1083 PHE 0.013 0.002 PHE A 906 TYR 0.017 0.002 TYR C 904 ARG 0.008 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 9) link_NAG-ASN : angle 2.45857 ( 27) hydrogen bonds : bond 0.05995 ( 516) hydrogen bonds : angle 5.00059 ( 1485) SS BOND : bond 0.00555 ( 18) SS BOND : angle 1.77387 ( 36) covalent geometry : bond 0.00590 (10428) covalent geometry : angle 0.56658 (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 346 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 1.538 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 776 LYS cc_start: 0.8565 (tttm) cc_final: 0.8355 (tttm) REVERT: A 780 GLU cc_start: 0.7746 (tt0) cc_final: 0.7484 (mt-10) REVERT: A 814 LYS cc_start: 0.7499 (mmmm) cc_final: 0.7089 (mmmt) REVERT: A 824 ASN cc_start: 0.8568 (m-40) cc_final: 0.8337 (m110) REVERT: A 934 ILE cc_start: 0.8090 (tp) cc_final: 0.7802 (pt) REVERT: A 992 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7235 (mm110) REVERT: A 1009 THR cc_start: 0.8583 (t) cc_final: 0.8364 (m) REVERT: A 1038 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7984 (mmtm) REVERT: B 748 GLU cc_start: 0.7636 (mp0) cc_final: 0.7382 (mp0) REVERT: B 820 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (t0) REVERT: B 860 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 873 TYR cc_start: 0.8516 (m-80) cc_final: 0.7823 (m-80) REVERT: B 1105 THR cc_start: 0.8592 (p) cc_final: 0.8381 (t) REVERT: B 1117 THR cc_start: 0.8343 (m) cc_final: 0.7873 (p) REVERT: C 737 ASP cc_start: 0.8143 (t0) cc_final: 0.7871 (t0) REVERT: C 835 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7634 (ttmm) REVERT: C 837 TYR cc_start: 0.8176 (t80) cc_final: 0.7888 (t80) REVERT: C 933 LYS cc_start: 0.8178 (mttt) cc_final: 0.7910 (mtpp) REVERT: C 950 ASP cc_start: 0.7608 (m-30) cc_final: 0.7159 (m-30) REVERT: C 983 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7210 (ttm110) REVERT: C 992 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7218 (mm110) REVERT: C 1038 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8052 (mmtm) outliers start: 32 outliers final: 20 residues processed: 327 average time/residue: 2.6786 time to fit residues: 939.7198 Evaluate side-chains 328 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 306 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 961 THR 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 918 GLU 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: 0.9980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 A1005 GLN B 779 GLN B 836 GLN B 895 GLN B 969 ASN B1002 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 = 0.3527 r_free = 0.3527 target = 0.117988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102139 restraints weight = 36359.985| |-----------------------------------------------------------------------------| 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: 0.3023 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4203 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 : 0.548 4.682 14268 Z= 0.282 Chirality : 0.042 0.173 1671 Planarity : 0.005 0.051 1836 Dihedral : 5.680 50.260 1572 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.76 % Allowed : 15.29 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1305 helix: 1.74 (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 0.001 TYR C1067 ARG 0.006 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 9) link_NAG-ASN : angle 2.27483 ( 27) hydrogen bonds : bond 0.05362 ( 516) hydrogen bonds : angle 4.83390 ( 1485) SS BOND : bond 0.00506 ( 18) SS BOND : angle 1.50789 ( 36) covalent geometry : bond 0.00456 (10428) covalent geometry : angle 0.53472 (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 348 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 1.659 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: 0.8745 (t) cc_final: 0.8440 (m) REVERT: A 780 GLU cc_start: 0.7708 (tt0) cc_final: 0.7474 (mt-10) REVERT: A 824 ASN cc_start: 0.8541 (m-40) cc_final: 0.8312 (m110) REVERT: A 1038 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8063 (mmtm) REVERT: B 737 ASP cc_start: 0.7932 (t70) cc_final: 0.7445 (t0) REVERT: B 748 GLU cc_start: 0.7640 (mp0) cc_final: 0.7378 (mp0) REVERT: B 820 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7793 (t0) REVERT: B 860 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 873 TYR cc_start: 0.8559 (m-80) cc_final: 0.7842 (m-80) REVERT: B 1117 THR cc_start: 0.8237 (m) cc_final: 0.7776 (p) REVERT: C 835 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7673 (ttmm) REVERT: C 837 TYR cc_start: 0.8185 (t80) cc_final: 0.7852 (t80) REVERT: C 933 LYS cc_start: 0.8214 (mttt) cc_final: 0.7929 (mtpp) REVERT: C 950 ASP cc_start: 0.7605 (m-30) cc_final: 0.7159 (m-30) REVERT: C 983 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7235 (ttm110) REVERT: C 992 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7270 (mm110) REVERT: C 1038 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8030 (mmtm) outliers start: 31 outliers final: 19 residues processed: 329 average time/residue: 2.6998 time to fit residues: 952.6458 Evaluate side-chains 328 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 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 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 820 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: 0.9980 chunk 124 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 992 GLN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 935 GLN B 955 ASN B 969 ASN 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 = 0.3510 r_free = 0.3510 target = 0.116751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100940 restraints weight = 36471.106| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.91 r_work: 0.3160 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10455 Z= 0.241 Angle : 0.571 5.182 14268 Z= 0.296 Chirality : 0.044 0.179 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.889 52.989 1572 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.29 % Allowed : 14.93 % Favored : 81.78 % 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: 0.77 (0.23), residues: 1305 helix: 1.79 (0.21), residues: 609 sheet: -0.01 (0.34), residues: 189 loop : -0.86 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.005 0.002 HIS A1101 PHE 0.012 0.002 PHE A 888 TYR 0.015 0.002 TYR C1067 ARG 0.006 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 9) link_NAG-ASN : angle 2.48420 ( 27) hydrogen bonds : bond 0.05637 ( 516) hydrogen bonds : angle 4.90365 ( 1485) SS BOND : bond 0.00618 ( 18) SS BOND : angle 1.61248 ( 36) covalent geometry : bond 0.00579 (10428) covalent geometry : angle 0.55636 (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 344 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 1.596 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: 0.8770 (t) cc_final: 0.8458 (m) REVERT: A 780 GLU cc_start: 0.7738 (tt0) cc_final: 0.7523 (mt-10) REVERT: A 824 ASN cc_start: 0.8554 (m-40) cc_final: 0.8324 (m110) REVERT: A 979 ASP cc_start: 0.7556 (m-30) cc_final: 0.7193 (m-30) REVERT: A 1002 GLN cc_start: 0.8230 (mm110) cc_final: 0.7848 (mm110) REVERT: A 1038 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8111 (mmtm) REVERT: B 737 ASP cc_start: 0.7982 (t70) cc_final: 0.7491 (t0) REVERT: B 748 GLU cc_start: 0.7697 (mp0) cc_final: 0.7429 (mp0) REVERT: B 820 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7838 (t0) REVERT: B 860 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8476 (t) REVERT: B 964 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8259 (mtpm) REVERT: C 737 ASP cc_start: 0.8156 (t0) cc_final: 0.7916 (t0) REVERT: C 785 VAL cc_start: 0.7771 (t) cc_final: 0.7548 (p) REVERT: C 837 TYR cc_start: 0.8206 (t80) cc_final: 0.7896 (t80) REVERT: C 933 LYS cc_start: 0.8250 (mttt) cc_final: 0.8007 (mtpp) REVERT: C 992 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7279 (mm110) REVERT: C 1031 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7912 (mt-10) outliers start: 37 outliers final: 27 residues processed: 320 average time/residue: 2.7096 time to fit residues: 930.9220 Evaluate side-chains 324 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 992 GLN B 895 GLN B 935 GLN B 969 ASN B1005 GLN B1074 ASN C 762 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101503 restraints weight = 36417.399| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3170 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10455 Z= 0.175 Angle : 0.544 5.890 14268 Z= 0.277 Chirality : 0.042 0.170 1671 Planarity : 0.005 0.048 1836 Dihedral : 5.798 55.291 1572 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.29 % Allowed : 16.44 % Favored : 80.27 % 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: 0.96 (0.23), residues: 1305 helix: 1.96 (0.21), residues: 609 sheet: -0.00 (0.34), residues: 189 loop : -0.74 (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 0.010 0.001 PHE A 888 TYR 0.012 0.001 TYR C1067 ARG 0.009 0.001 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 9) link_NAG-ASN : angle 2.22265 ( 27) hydrogen bonds : bond 0.05139 ( 516) hydrogen bonds : angle 4.76502 ( 1485) SS BOND : bond 0.00502 ( 18) SS BOND : angle 1.53751 ( 36) covalent geometry : bond 0.00416 (10428) covalent geometry : angle 0.53070 (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 342 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 1.450 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: 0.8743 (t) cc_final: 0.8445 (m) REVERT: A 780 GLU cc_start: 0.7755 (tt0) cc_final: 0.7525 (mt-10) REVERT: A 824 ASN cc_start: 0.8559 (m-40) cc_final: 0.8329 (m110) REVERT: A 979 ASP cc_start: 0.7554 (m-30) cc_final: 0.7197 (m-30) REVERT: A 1002 GLN cc_start: 0.8214 (mm110) cc_final: 0.7920 (mm110) REVERT: A 1038 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8096 (mmtm) REVERT: B 737 ASP cc_start: 0.7983 (t70) cc_final: 0.7463 (t0) REVERT: B 748 GLU cc_start: 0.7664 (mp0) cc_final: 0.7384 (mp0) REVERT: B 780 GLU cc_start: 0.7709 (tt0) cc_final: 0.7470 (tt0) REVERT: B 820 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7750 (t0) REVERT: B 860 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 1002 GLN cc_start: 0.8207 (mm110) cc_final: 0.7934 (mm110) REVERT: C 748 GLU cc_start: 0.7740 (mp0) cc_final: 0.7506 (mp0) REVERT: C 785 VAL cc_start: 0.7776 (t) cc_final: 0.7563 (p) REVERT: C 837 TYR cc_start: 0.8192 (t80) cc_final: 0.7823 (t80) REVERT: C 860 VAL cc_start: 0.8651 (m) cc_final: 0.8365 (t) REVERT: C 933 LYS cc_start: 0.8259 (mttt) cc_final: 0.7980 (mtpp) REVERT: C 983 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7099 (ttm110) REVERT: C 992 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7285 (mm110) REVERT: C 1031 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7875 (mt-10) outliers start: 37 outliers final: 25 residues processed: 320 average time/residue: 2.6337 time to fit residues: 905.5222 Evaluate side-chains 330 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 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 820 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 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 116 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.0870 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 0.0040 chunk 22 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 overall best weight: 0.1048 ------------------------------------------------------------------------------- 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 895 GLN B 955 ASN B 969 ASN B1002 GLN B1005 GLN B1074 ASN C 779 GLN C 969 ASN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104054 restraints weight = 36343.350| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.91 r_work: 0.3213 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10455 Z= 0.097 Angle : 0.498 5.694 14268 Z= 0.250 Chirality : 0.040 0.144 1671 Planarity : 0.004 0.036 1836 Dihedral : 5.506 57.363 1572 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 17.87 % Favored : 80.27 % 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: 1.30 (0.23), residues: 1305 helix: 2.23 (0.21), residues: 612 sheet: 0.05 (0.34), residues: 189 loop : -0.51 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.002 0.001 HIS C1048 PHE 0.007 0.001 PHE A1121 TYR 0.010 0.001 TYR C 904 ARG 0.004 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.60170 ( 27) hydrogen bonds : bond 0.03968 ( 516) hydrogen bonds : angle 4.44226 ( 1485) SS BOND : bond 0.00273 ( 18) SS BOND : angle 1.16381 ( 36) covalent geometry : bond 0.00222 (10428) covalent geometry : angle 0.49116 (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 321 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8725 (t) cc_final: 0.8417 (m) REVERT: A 824 ASN cc_start: 0.8571 (m-40) cc_final: 0.8333 (m110) REVERT: A 979 ASP cc_start: 0.7536 (m-30) cc_final: 0.7153 (m-30) REVERT: A 1002 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7869 (mm110) REVERT: A 1010 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7428 (tm-30) REVERT: A 1038 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8070 (mmtm) REVERT: A 1091 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7345 (ttp-170) REVERT: B 737 ASP cc_start: 0.7946 (t70) cc_final: 0.7449 (t0) REVERT: B 748 GLU cc_start: 0.7626 (mp0) cc_final: 0.7328 (mp0) REVERT: B 820 ASP cc_start: 0.7953 (t70) cc_final: 0.7735 (t0) REVERT: B 860 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (t) REVERT: B 1002 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7961 (mm110) REVERT: C 837 TYR cc_start: 0.8217 (t80) cc_final: 0.7821 (t80) REVERT: C 860 VAL cc_start: 0.8626 (m) cc_final: 0.8378 (t) REVERT: C 933 LYS cc_start: 0.8231 (mttt) cc_final: 0.7979 (mtpp) REVERT: C 983 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7045 (ttm110) REVERT: C 992 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7186 (mm110) outliers start: 21 outliers final: 13 residues processed: 310 average time/residue: 2.5283 time to fit residues: 843.3051 Evaluate side-chains 309 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 295 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1004 LEU 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: 0.9990 chunk 1 optimal weight: 0.0970 chunk 113 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 895 GLN B 969 ASN B1002 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101959 restraints weight = 36563.209| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.92 r_work: 0.3180 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10455 Z= 0.173 Angle : 0.538 5.127 14268 Z= 0.273 Chirality : 0.042 0.157 1671 Planarity : 0.004 0.035 1836 Dihedral : 5.679 58.995 1572 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 17.78 % 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: 1.23 (0.23), residues: 1305 helix: 2.19 (0.21), residues: 609 sheet: 0.04 (0.34), residues: 189 loop : -0.55 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 998 HIS 0.005 0.001 HIS C1064 PHE 0.009 0.001 PHE A 888 TYR 0.014 0.001 TYR C1067 ARG 0.005 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 9) link_NAG-ASN : angle 2.15892 ( 27) hydrogen bonds : bond 0.04821 ( 516) hydrogen bonds : angle 4.68372 ( 1485) SS BOND : bond 0.00496 ( 18) SS BOND : angle 1.34432 ( 36) covalent geometry : bond 0.00411 (10428) covalent geometry : angle 0.52625 (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 331 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8747 (t) cc_final: 0.8437 (m) REVERT: A 820 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 824 ASN cc_start: 0.8592 (m-40) cc_final: 0.8358 (m110) REVERT: A 979 ASP cc_start: 0.7590 (m-30) cc_final: 0.7204 (m-30) REVERT: A 1010 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7474 (tm-30) REVERT: A 1038 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8068 (mmtm) REVERT: A 1091 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7377 (ttp-170) REVERT: B 737 ASP cc_start: 0.7972 (t70) cc_final: 0.7494 (t0) REVERT: B 748 GLU cc_start: 0.7658 (mp0) cc_final: 0.7382 (mp0) REVERT: B 820 ASP cc_start: 0.8067 (t70) cc_final: 0.7806 (t0) REVERT: B 860 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8453 (t) REVERT: C 785 VAL cc_start: 0.7749 (t) cc_final: 0.7500 (p) REVERT: C 837 TYR cc_start: 0.8225 (t80) cc_final: 0.7842 (t80) REVERT: C 860 VAL cc_start: 0.8608 (m) cc_final: 0.8339 (t) REVERT: C 933 LYS cc_start: 0.8266 (mttt) cc_final: 0.8022 (mtpp) REVERT: C 983 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7133 (ttm110) REVERT: C 1031 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7744 (mt-10) outliers start: 27 outliers final: 18 residues processed: 314 average time/residue: 2.7013 time to fit residues: 907.7064 Evaluate side-chains 323 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 820 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 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG 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 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: 0.9980 chunk 57 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 895 GLN B 955 ASN B 969 ASN B1005 GLN B1074 ASN B1135 ASN C 779 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100425 restraints weight = 36316.840| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.90 r_work: 0.3153 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10455 Z= 0.278 Angle : 0.602 6.779 14268 Z= 0.309 Chirality : 0.045 0.171 1671 Planarity : 0.005 0.039 1836 Dihedral : 6.039 59.819 1572 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.76 % Allowed : 16.98 % Favored : 80.27 % 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: 0.93 (0.23), residues: 1305 helix: 1.91 (0.21), residues: 609 sheet: -0.07 (0.34), residues: 189 loop : -0.69 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 998 HIS 0.005 0.002 HIS B1064 PHE 0.017 0.002 PHE A 888 TYR 0.016 0.002 TYR C1067 ARG 0.004 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 9) link_NAG-ASN : angle 2.51634 ( 27) hydrogen bonds : bond 0.05672 ( 516) hydrogen bonds : angle 4.94403 ( 1485) SS BOND : bond 0.00639 ( 18) SS BOND : angle 1.60900 ( 36) covalent geometry : bond 0.00669 (10428) covalent geometry : angle 0.58807 (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 321 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.535 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 824 ASN cc_start: 0.8613 (m-40) cc_final: 0.8385 (m110) REVERT: A 1002 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 1010 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7542 (tm-30) REVERT: A 1038 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8075 (mmtm) REVERT: B 737 ASP cc_start: 0.8000 (t70) cc_final: 0.7509 (t0) REVERT: B 748 GLU cc_start: 0.7623 (mp0) cc_final: 0.7343 (mp0) REVERT: B 752 LEU cc_start: 0.8326 (mt) cc_final: 0.8107 (mt) REVERT: B 820 ASP cc_start: 0.8144 (t70) cc_final: 0.7874 (t0) REVERT: B 825 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (mptp) REVERT: B 860 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (t) REVERT: C 737 ASP cc_start: 0.8092 (t0) cc_final: 0.7853 (t0) REVERT: C 748 GLU cc_start: 0.7776 (mp0) cc_final: 0.7458 (mp0) REVERT: C 837 TYR cc_start: 0.8228 (t80) cc_final: 0.7875 (t80) REVERT: C 860 VAL cc_start: 0.8629 (m) cc_final: 0.8311 (t) REVERT: C 1031 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7823 (mt-10) outliers start: 31 outliers final: 19 residues processed: 302 average time/residue: 3.1586 time to fit residues: 1022.3820 Evaluate side-chains 308 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 B residue 745 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 995 ARG 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 C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 820 ASP 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 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: 0.7980 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 125 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A 992 GLN B 895 GLN B 914 ASN B1002 GLN B1005 GLN B1074 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101549 restraints weight = 36494.471| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.91 r_work: 0.3170 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5098 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= 0.179 Angle : 0.553 6.120 14268 Z= 0.281 Chirality : 0.042 0.166 1671 Planarity : 0.004 0.039 1836 Dihedral : 5.851 58.013 1572 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.49 % Allowed : 17.78 % 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: 1.09 (0.23), residues: 1305 helix: 2.01 (0.21), residues: 609 sheet: 0.16 (0.35), residues: 159 loop : -0.60 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 998 HIS 0.004 0.001 HIS C1064 PHE 0.011 0.001 PHE A 888 TYR 0.012 0.001 TYR C 904 ARG 0.005 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 2.21296 ( 27) hydrogen bonds : bond 0.05010 ( 516) hydrogen bonds : angle 4.76918 ( 1485) SS BOND : bond 0.00549 ( 18) SS BOND : angle 1.80412 ( 36) covalent geometry : bond 0.00423 (10428) covalent geometry : angle 0.53810 (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 320 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.694 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 772 VAL cc_start: 0.8769 (t) cc_final: 0.8454 (m) REVERT: A 820 ASP cc_start: 0.7981 (t0) cc_final: 0.7535 (m-30) REVERT: A 824 ASN cc_start: 0.8628 (m-40) cc_final: 0.8380 (m110) REVERT: A 1010 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7499 (tm-30) REVERT: A 1038 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8077 (mmtm) REVERT: A 1045 LYS cc_start: 0.8245 (mmmm) cc_final: 0.8022 (mmmm) REVERT: B 737 ASP cc_start: 0.7980 (t70) cc_final: 0.7470 (t0) REVERT: B 748 GLU cc_start: 0.7600 (mp0) cc_final: 0.7326 (mp0) REVERT: B 752 LEU cc_start: 0.8347 (mt) cc_final: 0.8129 (mt) REVERT: B 820 ASP cc_start: 0.8103 (t70) cc_final: 0.7835 (t0) REVERT: B 825 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8219 (mptp) REVERT: B 860 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (t) REVERT: B 869 MET cc_start: 0.8043 (mtp) cc_final: 0.7825 (mtm) REVERT: C 737 ASP cc_start: 0.8073 (t0) cc_final: 0.7772 (t0) REVERT: C 748 GLU cc_start: 0.7771 (mp0) cc_final: 0.7479 (mp0) REVERT: C 837 TYR cc_start: 0.8239 (t80) cc_final: 0.7934 (t80) REVERT: C 860 VAL cc_start: 0.8621 (m) cc_final: 0.8318 (t) REVERT: C 992 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6896 (mm110) REVERT: C 1031 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7742 (mt-10) outliers start: 28 outliers final: 16 residues processed: 303 average time/residue: 3.2896 time to fit residues: 1071.3374 Evaluate side-chains 311 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 292 time to evaluate : 2.621 ------------------------------------------------------------------------------- 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 1005 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 995 ARG 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 C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE 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 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 914 ASN A 935 GLN A 992 GLN B 895 GLN B 914 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN C 969 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.117354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101669 restraints weight = 36565.757| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.91 r_work: 0.3165 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10455 Z= 0.184 Angle : 0.556 6.644 14268 Z= 0.281 Chirality : 0.042 0.169 1671 Planarity : 0.004 0.040 1836 Dihedral : 5.829 57.038 1572 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.49 % Allowed : 17.78 % 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: 1.10 (0.23), residues: 1305 helix: 2.06 (0.21), residues: 609 sheet: 0.13 (0.36), residues: 159 loop : -0.64 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 PHE 0.011 0.001 PHE A 888 TYR 0.011 0.001 TYR C1067 ARG 0.005 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 9) link_NAG-ASN : angle 2.24599 ( 27) hydrogen bonds : bond 0.04995 ( 516) hydrogen bonds : angle 4.75798 ( 1485) SS BOND : bond 0.00560 ( 18) SS BOND : angle 1.76254 ( 36) covalent geometry : bond 0.00439 (10428) covalent geometry : angle 0.54146 (14205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20371.66 seconds wall clock time: 356 minutes 3.88 seconds (21363.88 seconds total)