Starting phenix.real_space_refine on Thu Jan 23 15:12:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vao_43097/01_2025/8vao_43097_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vao_43097/01_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_43097/01_2025/8vao_43097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vao_43097/01_2025/8vao_43097.map" model { file = "/net/cci-nas-00/data/ceres_data/8vao_43097/01_2025/8vao_43097_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vao_43097/01_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-5571/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: 16.64, 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=5, symmetry=0 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 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 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: 5.11 Conformation dependent library (CDL) restraints added in 1.6 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: 1.68 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: 7.46 Time building geometry restraints manager: 6.15 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: 8902 17.07 - 34.14: 522 34.14 - 51.21: 203 51.21 - 68.29: 198 68.29 - 85.36: 9 Dihedral angle restraints: 9834 sinusoidal: 5406 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 9831 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: 1020 2.19 - 2.79: 40843 2.79 - 3.39: 54633 3.39 - 4.00: 71110 4.00 - 4.60: 110931 Nonbonded interactions: 278537 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 278532 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: 3.320 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: 0.380 Extract box with map and model: 0.730 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.530 Find NCS groups from input model: 0.290 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.700 ------------------------------------------------------------------------------- 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 0.033 10428 Z= 0.198 Angle : 0.512 4.714 14205 Z= 0.256 Chirality : 0.040 0.125 1671 Planarity : 0.011 0.232 1836 Dihedral : 13.268 85.356 3900 Min Nonbonded Distance : 1.962 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 *********************** 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 : 1.569 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: 2.4470 time to fit residues: 901.3026 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 : 1.575 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103290 restraints weight = 36771.053| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.89 r_work: 0.3205 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10428 Z= 0.429 Angle : 0.612 4.734 14205 Z= 0.325 Chirality : 0.046 0.177 1671 Planarity : 0.005 0.044 1836 Dihedral : 5.920 48.017 1578 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.40 % Allowed : 12.62 % Favored : 84.98 % 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: -0.00 (0.22), residues: 1305 helix: 1.01 (0.21), residues: 606 sheet: -0.15 (0.32), residues: 189 loop : -1.13 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1102 HIS 0.006 0.002 HIS C1064 PHE 0.014 0.002 PHE A 906 TYR 0.018 0.002 TYR C1067 ARG 0.006 0.001 ARG B1039 *********************** 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 355 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 THR cc_start: 0.8154 (t) cc_final: 0.7951 (p) REVERT: A 748 GLU cc_start: 0.7720 (mp0) cc_final: 0.7316 (mp0) REVERT: A 772 VAL cc_start: 0.8807 (t) cc_final: 0.8492 (m) REVERT: A 814 LYS cc_start: 0.7509 (mmmm) cc_final: 0.7091 (mmmt) REVERT: A 824 ASN cc_start: 0.8532 (m-40) cc_final: 0.8304 (m110) REVERT: A 873 TYR cc_start: 0.8301 (m-80) cc_final: 0.7964 (m-80) REVERT: A 934 ILE cc_start: 0.8052 (tp) cc_final: 0.7802 (pt) REVERT: A 1009 THR cc_start: 0.8488 (t) cc_final: 0.8260 (m) REVERT: A 1038 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7881 (mmtm) REVERT: B 737 ASP cc_start: 0.7979 (t0) cc_final: 0.7497 (t0) REVERT: B 748 GLU cc_start: 0.7613 (mp0) cc_final: 0.7378 (mp0) REVERT: B 873 TYR cc_start: 0.8435 (m-80) cc_final: 0.7826 (m-80) REVERT: B 962 LEU cc_start: 0.8400 (tp) cc_final: 0.8196 (tp) REVERT: B 1116 THR cc_start: 0.8194 (p) cc_final: 0.7784 (p) REVERT: B 1117 THR cc_start: 0.8296 (m) cc_final: 0.7867 (p) REVERT: C 737 ASP cc_start: 0.8114 (t0) cc_final: 0.7288 (t0) REVERT: C 837 TYR cc_start: 0.8201 (t80) cc_final: 0.7916 (t80) REVERT: C 840 CYS cc_start: 0.8300 (t) cc_final: 0.7974 (t) REVERT: C 854 LYS cc_start: 0.8168 (tttp) cc_final: 0.7927 (ttmm) REVERT: C 933 LYS cc_start: 0.8220 (mttt) cc_final: 0.7936 (mtpp) REVERT: C 950 ASP cc_start: 0.7588 (m-30) cc_final: 0.7154 (m-30) REVERT: C 992 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7058 (mm110) REVERT: C 1010 GLN cc_start: 0.8098 (tp40) cc_final: 0.7747 (tm-30) outliers start: 27 outliers final: 14 residues processed: 341 average time/residue: 2.6393 time to fit residues: 967.2336 Evaluate side-chains 321 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 307 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 1073 LYS 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: 2.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 992 GLN A1005 GLN B 836 GLN B 895 GLN B 955 ASN B 992 GLN B1005 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102325 restraints weight = 36751.392| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10428 Z= 0.341 Angle : 0.550 4.521 14205 Z= 0.289 Chirality : 0.043 0.173 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.692 48.389 1572 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.58 % Allowed : 14.67 % Favored : 82.76 % 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: 0.40 (0.23), residues: 1305 helix: 1.42 (0.21), residues: 612 sheet: -0.02 (0.33), residues: 189 loop : -1.04 (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 B1083 PHE 0.013 0.001 PHE A 906 TYR 0.017 0.002 TYR C 904 ARG 0.011 0.001 ARG B 983 *********************** 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: 29 poor density : 317 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8754 (t) cc_final: 0.8430 (m) REVERT: A 776 LYS cc_start: 0.8601 (tttm) cc_final: 0.8373 (tttm) REVERT: A 780 GLU cc_start: 0.7755 (tt0) cc_final: 0.7472 (mt-10) REVERT: A 814 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7221 (mmpt) REVERT: A 820 ASP cc_start: 0.7895 (t70) cc_final: 0.7597 (t0) REVERT: A 824 ASN cc_start: 0.8563 (m-40) cc_final: 0.8326 (m110) REVERT: A 934 ILE cc_start: 0.8080 (tp) cc_final: 0.7808 (pt) REVERT: A 1002 GLN cc_start: 0.8271 (mm110) cc_final: 0.8069 (mm110) REVERT: A 1009 THR cc_start: 0.8575 (t) cc_final: 0.8353 (m) REVERT: A 1038 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7996 (mmtm) REVERT: B 748 GLU cc_start: 0.7678 (mp0) cc_final: 0.7427 (mp0) REVERT: B 820 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 860 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8433 (t) REVERT: B 873 TYR cc_start: 0.8507 (m-80) cc_final: 0.7816 (m-80) REVERT: B 1002 GLN cc_start: 0.8120 (mm110) cc_final: 0.7812 (mm110) REVERT: B 1105 THR cc_start: 0.8624 (p) cc_final: 0.8410 (t) REVERT: B 1117 THR cc_start: 0.8211 (m) cc_final: 0.7713 (p) REVERT: C 737 ASP cc_start: 0.8143 (t0) cc_final: 0.7862 (t0) REVERT: C 835 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7540 (ttmm) REVERT: C 837 TYR cc_start: 0.8204 (t80) cc_final: 0.7946 (t80) REVERT: C 840 CYS cc_start: 0.8316 (t) cc_final: 0.7887 (t) REVERT: C 933 LYS cc_start: 0.8179 (mttt) cc_final: 0.7903 (mtpp) REVERT: C 950 ASP cc_start: 0.7602 (m-30) cc_final: 0.7154 (m-30) REVERT: C 983 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7193 (ttm110) REVERT: C 992 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7203 (mm110) outliers start: 29 outliers final: 18 residues processed: 327 average time/residue: 2.7712 time to fit residues: 969.8474 Evaluate side-chains 328 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 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 1037 SER Chi-restraints excluded: chain B residue 1072 GLU 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: 0.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 A 992 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 836 GLN B 895 GLN B 969 ASN B1005 GLN B1074 ASN C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101809 restraints weight = 37073.208| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.91 r_work: 0.3173 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10428 Z= 0.280 Angle : 0.528 4.532 14205 Z= 0.274 Chirality : 0.042 0.168 1671 Planarity : 0.005 0.056 1836 Dihedral : 5.631 50.247 1572 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.67 % Allowed : 16.27 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1305 helix: 1.78 (0.21), residues: 612 sheet: -0.02 (0.34), residues: 189 loop : -0.87 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 991 HIS 0.005 0.001 HIS C1064 PHE 0.009 0.001 PHE C 898 TYR 0.014 0.001 TYR C1067 ARG 0.006 0.001 ARG B 983 *********************** 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 349 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7653 (mp0) cc_final: 0.7201 (mp0) REVERT: A 772 VAL cc_start: 0.8731 (t) cc_final: 0.8406 (m) REVERT: A 780 GLU cc_start: 0.7741 (tt0) cc_final: 0.7496 (mt-10) REVERT: A 820 ASP cc_start: 0.7916 (t70) cc_final: 0.7624 (t0) REVERT: A 824 ASN cc_start: 0.8552 (m-40) cc_final: 0.8314 (m110) REVERT: A 1002 GLN cc_start: 0.8332 (mm110) cc_final: 0.8035 (mm110) REVERT: A 1038 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8079 (mmtm) REVERT: B 748 GLU cc_start: 0.7680 (mp0) cc_final: 0.7415 (mp0) REVERT: B 820 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 860 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8484 (t) REVERT: B 873 TYR cc_start: 0.8555 (m-80) cc_final: 0.7844 (m-80) REVERT: B 1002 GLN cc_start: 0.8146 (mm110) cc_final: 0.7800 (mm110) REVERT: C 835 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7557 (ttmm) REVERT: C 837 TYR cc_start: 0.8175 (t80) cc_final: 0.7877 (t80) REVERT: C 840 CYS cc_start: 0.8384 (t) cc_final: 0.7937 (t) REVERT: C 933 LYS cc_start: 0.8217 (mttt) cc_final: 0.7928 (mtpp) REVERT: C 950 ASP cc_start: 0.7601 (m-30) cc_final: 0.7153 (m-30) REVERT: C 983 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7229 (ttm110) REVERT: C 992 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7255 (mm110) outliers start: 30 outliers final: 15 residues processed: 330 average time/residue: 2.7309 time to fit residues: 967.8531 Evaluate side-chains 329 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP 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 1037 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL 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: 0.7980 chunk 68 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 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 A 992 GLN A1002 GLN B 895 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100415 restraints weight = 37038.089| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.89 r_work: 0.3153 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10428 Z= 0.384 Angle : 0.552 5.817 14205 Z= 0.290 Chirality : 0.044 0.180 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.871 53.007 1572 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.38 % Allowed : 15.82 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1305 helix: 1.81 (0.21), residues: 609 sheet: -0.01 (0.35), residues: 189 loop : -0.86 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.014 0.002 PHE A 888 TYR 0.015 0.002 TYR C1067 ARG 0.005 0.001 ARG B 983 *********************** 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 347 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 309 time to evaluate : 1.638 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 780 GLU cc_start: 0.7780 (tt0) cc_final: 0.7538 (mt-10) REVERT: A 820 ASP cc_start: 0.8026 (t70) cc_final: 0.7733 (t0) REVERT: A 824 ASN cc_start: 0.8569 (m-40) cc_final: 0.8333 (m110) REVERT: A 979 ASP cc_start: 0.7584 (m-30) cc_final: 0.7202 (m-30) REVERT: A 995 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7694 (mtt180) REVERT: A 1038 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8092 (mmtm) REVERT: B 748 GLU cc_start: 0.7665 (mp0) cc_final: 0.7388 (mp0) REVERT: B 820 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 860 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 964 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8238 (mtpm) REVERT: B 1002 GLN cc_start: 0.8188 (mm110) cc_final: 0.7959 (mm110) REVERT: C 737 ASP cc_start: 0.8129 (t0) cc_final: 0.7384 (t0) REVERT: C 785 VAL cc_start: 0.7751 (t) cc_final: 0.7531 (p) REVERT: C 837 TYR cc_start: 0.8201 (t80) cc_final: 0.7850 (t80) REVERT: C 840 CYS cc_start: 0.8377 (t) cc_final: 0.7897 (t) REVERT: C 933 LYS cc_start: 0.8249 (mttt) cc_final: 0.7975 (mtpp) REVERT: C 992 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7254 (mm110) outliers start: 38 outliers final: 26 residues processed: 322 average time/residue: 2.8023 time to fit residues: 966.5076 Evaluate side-chains 325 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR 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 973 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 Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 853 GLN A 992 GLN B 895 GLN B 935 GLN B 969 ASN B1005 GLN B1074 ASN B1134 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 = 0.3499 r_free = 0.3499 target = 0.115924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100404 restraints weight = 37125.125| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.89 r_work: 0.3153 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10428 Z= 0.353 Angle : 0.556 5.481 14205 Z= 0.287 Chirality : 0.043 0.178 1671 Planarity : 0.005 0.052 1836 Dihedral : 5.915 56.465 1572 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.47 % Allowed : 16.44 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1305 helix: 1.86 (0.21), residues: 609 sheet: -0.04 (0.34), residues: 189 loop : -0.83 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.013 0.001 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.005 0.001 ARG C 765 *********************** 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 345 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 1.654 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 780 GLU cc_start: 0.7799 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 824 ASN cc_start: 0.8576 (m-40) cc_final: 0.8335 (m110) REVERT: A 979 ASP cc_start: 0.7537 (m-30) cc_final: 0.7169 (m-30) REVERT: A 995 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7661 (mtt180) REVERT: A 1002 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7907 (mm110) REVERT: A 1038 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8068 (mmtm) REVERT: B 748 GLU cc_start: 0.7646 (mp0) cc_final: 0.7374 (mp0) REVERT: B 820 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7779 (t0) REVERT: B 860 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8471 (t) REVERT: B 964 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8236 (mtpm) REVERT: B 1002 GLN cc_start: 0.8258 (mm110) cc_final: 0.8043 (mm110) REVERT: B 1117 THR cc_start: 0.8204 (m) cc_final: 0.7627 (p) REVERT: C 737 ASP cc_start: 0.8150 (t0) cc_final: 0.7929 (t0) REVERT: C 748 GLU cc_start: 0.7723 (mp0) cc_final: 0.7506 (mp0) REVERT: C 785 VAL cc_start: 0.7800 (t) cc_final: 0.7555 (p) REVERT: C 837 TYR cc_start: 0.8225 (t80) cc_final: 0.7889 (t80) REVERT: C 840 CYS cc_start: 0.8373 (t) cc_final: 0.7925 (t) REVERT: C 873 TYR cc_start: 0.8412 (m-80) cc_final: 0.8207 (m-80) REVERT: C 933 LYS cc_start: 0.8277 (mttt) cc_final: 0.8033 (mtpp) REVERT: C 983 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7204 (ttm110) REVERT: C 992 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7276 (mm110) outliers start: 39 outliers final: 27 residues processed: 320 average time/residue: 2.7940 time to fit residues: 957.6837 Evaluate side-chains 328 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL 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: 0.0270 chunk 116 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 872 GLN B 895 GLN B 935 GLN B 955 ASN B 969 ASN B1074 ASN B1135 ASN C 969 ASN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101079 restraints weight = 36963.620| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.89 r_work: 0.3162 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10428 Z= 0.273 Angle : 0.528 5.125 14205 Z= 0.271 Chirality : 0.042 0.170 1671 Planarity : 0.004 0.042 1836 Dihedral : 5.846 59.746 1572 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.02 % Allowed : 17.33 % Favored : 79.64 % 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: 0.94 (0.23), residues: 1305 helix: 1.96 (0.21), residues: 609 sheet: -0.00 (0.34), residues: 189 loop : -0.79 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 *********************** 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 338 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8752 (t) cc_final: 0.8440 (m) REVERT: A 780 GLU cc_start: 0.7808 (tt0) cc_final: 0.7561 (mt-10) REVERT: A 820 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: A 824 ASN cc_start: 0.8577 (m-40) cc_final: 0.8349 (m110) REVERT: A 995 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7643 (mtt180) REVERT: A 1002 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7981 (mm110) REVERT: A 1010 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7495 (tm-30) REVERT: A 1038 LYS cc_start: 0.8306 (mmtm) cc_final: 0.8057 (mmtm) REVERT: B 737 ASP cc_start: 0.7972 (t0) cc_final: 0.7717 (t0) REVERT: B 748 GLU cc_start: 0.7656 (mp0) cc_final: 0.7366 (mp0) REVERT: B 820 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7791 (t0) REVERT: B 860 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8459 (t) REVERT: B 1002 GLN cc_start: 0.8229 (mm110) cc_final: 0.7938 (mm-40) REVERT: C 785 VAL cc_start: 0.7821 (t) cc_final: 0.7578 (p) REVERT: C 837 TYR cc_start: 0.8247 (t80) cc_final: 0.7917 (t80) REVERT: C 840 CYS cc_start: 0.8391 (t) cc_final: 0.7925 (t) REVERT: C 860 VAL cc_start: 0.8659 (m) cc_final: 0.8368 (t) REVERT: C 933 LYS cc_start: 0.8302 (mttt) cc_final: 0.8049 (mtpp) REVERT: C 983 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7207 (ttm110) REVERT: C 992 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7249 (mm110) REVERT: C 1031 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: C 1118 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6783 (p0) outliers start: 34 outliers final: 23 residues processed: 316 average time/residue: 2.7711 time to fit residues: 938.2874 Evaluate side-chains 327 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 1005 GLN 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 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 950 ASP 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 1105 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 895 GLN B 969 ASN B1005 GLN B1074 ASN C 779 GLN C 969 ASN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100739 restraints weight = 37190.233| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.90 r_work: 0.3157 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10428 Z= 0.313 Angle : 0.543 5.634 14205 Z= 0.279 Chirality : 0.042 0.174 1671 Planarity : 0.004 0.043 1836 Dihedral : 5.888 59.326 1572 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.47 % Allowed : 17.07 % Favored : 79.47 % 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: 0.94 (0.23), residues: 1305 helix: 1.98 (0.21), residues: 609 sheet: -0.06 (0.34), residues: 189 loop : -0.77 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 PHE 0.012 0.001 PHE A 888 TYR 0.012 0.001 TYR C1067 ARG 0.004 0.001 ARG B 765 *********************** 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 336 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8755 (t) cc_final: 0.8451 (m) REVERT: A 780 GLU cc_start: 0.7783 (tt0) cc_final: 0.7556 (mt-10) REVERT: A 824 ASN cc_start: 0.8622 (m-40) cc_final: 0.8392 (m110) REVERT: A 1002 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7949 (mm110) REVERT: A 1038 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8064 (mmtm) REVERT: B 737 ASP cc_start: 0.7977 (t0) cc_final: 0.7646 (t0) REVERT: B 748 GLU cc_start: 0.7652 (mp0) cc_final: 0.7376 (mp0) REVERT: B 820 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7829 (t0) REVERT: B 825 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8198 (mptp) REVERT: B 860 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8454 (t) REVERT: B 980 ILE cc_start: 0.7503 (pt) cc_final: 0.7245 (mt) REVERT: B 1002 GLN cc_start: 0.8239 (mm110) cc_final: 0.7993 (mm110) REVERT: C 748 GLU cc_start: 0.7725 (mp0) cc_final: 0.7510 (mp0) REVERT: C 785 VAL cc_start: 0.7850 (t) cc_final: 0.7630 (p) REVERT: C 837 TYR cc_start: 0.8257 (t80) cc_final: 0.7927 (t80) REVERT: C 840 CYS cc_start: 0.8394 (t) cc_final: 0.7947 (t) REVERT: C 860 VAL cc_start: 0.8652 (m) cc_final: 0.8355 (t) REVERT: C 933 LYS cc_start: 0.8292 (mttt) cc_final: 0.8044 (mtpp) REVERT: C 992 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7254 (mm110) REVERT: C 1031 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7772 (mt-10) outliers start: 39 outliers final: 25 residues processed: 311 average time/residue: 2.7137 time to fit residues: 904.9649 Evaluate side-chains 326 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 934 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 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 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 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 992 GLN B 895 GLN B 955 ASN B1074 ASN C 969 ASN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100165 restraints weight = 36955.175| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.90 r_work: 0.3150 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10428 Z= 0.372 Angle : 0.555 4.936 14205 Z= 0.287 Chirality : 0.044 0.179 1671 Planarity : 0.005 0.041 1836 Dihedral : 5.971 57.960 1572 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 17.16 % 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: 0.90 (0.23), residues: 1305 helix: 1.92 (0.21), residues: 609 sheet: 0.09 (0.35), residues: 159 loop : -0.80 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 998 HIS 0.005 0.001 HIS B1064 PHE 0.014 0.002 PHE A 888 TYR 0.013 0.002 TYR C1067 ARG 0.004 0.001 ARG B 983 *********************** 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 326 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 1.578 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 780 GLU cc_start: 0.7781 (tt0) cc_final: 0.7567 (mt-10) REVERT: A 820 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: A 824 ASN cc_start: 0.8627 (m-40) cc_final: 0.8386 (m110) REVERT: A 1002 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7960 (mm110) REVERT: A 1010 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7509 (tm-30) REVERT: A 1038 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8069 (mmtm) REVERT: A 1045 LYS cc_start: 0.8250 (mmmm) cc_final: 0.8028 (mmmm) REVERT: A 1091 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7425 (ttp-170) REVERT: B 737 ASP cc_start: 0.7989 (t0) cc_final: 0.7676 (t0) REVERT: B 748 GLU cc_start: 0.7671 (mp0) cc_final: 0.7323 (mp0) REVERT: B 820 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 825 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (mptp) REVERT: B 860 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8450 (t) REVERT: B 1002 GLN cc_start: 0.8227 (mm110) cc_final: 0.8001 (mm110) REVERT: C 837 TYR cc_start: 0.8272 (t80) cc_final: 0.7894 (t80) REVERT: C 840 CYS cc_start: 0.8412 (t) cc_final: 0.7983 (t) REVERT: C 992 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7185 (mm110) REVERT: C 1031 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7817 (mt-10) outliers start: 35 outliers final: 26 residues processed: 305 average time/residue: 2.8359 time to fit residues: 925.3710 Evaluate side-chains 316 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 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 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 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 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 872 GLN B 895 GLN B 914 ASN B1074 ASN C 969 ASN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100169 restraints weight = 37109.614| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.91 r_work: 0.3150 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10428 Z= 0.345 Angle : 0.547 4.544 14205 Z= 0.283 Chirality : 0.043 0.178 1671 Planarity : 0.005 0.040 1836 Dihedral : 5.939 56.722 1572 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 17.69 % Favored : 79.20 % 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: 0.89 (0.23), residues: 1305 helix: 1.92 (0.21), residues: 609 sheet: 0.10 (0.36), residues: 159 loop : -0.81 (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 0.014 0.001 PHE A 888 TYR 0.013 0.001 TYR C1067 ARG 0.006 0.001 ARG B 765 ********************** 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 324 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 1.591 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: A 780 GLU cc_start: 0.7788 (tt0) cc_final: 0.7569 (mt-10) REVERT: A 820 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: A 824 ASN cc_start: 0.8626 (m-40) cc_final: 0.8382 (m110) REVERT: A 995 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7655 (mtt180) REVERT: A 1002 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7948 (mm110) REVERT: A 1010 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7489 (tm-30) REVERT: A 1038 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8077 (mmtm) REVERT: A 1045 LYS cc_start: 0.8265 (mmmm) cc_final: 0.8039 (mmmm) REVERT: A 1091 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7408 (ttp-170) REVERT: B 737 ASP cc_start: 0.7986 (t0) cc_final: 0.7774 (t0) REVERT: B 748 GLU cc_start: 0.7680 (mp0) cc_final: 0.7340 (mp0) REVERT: B 780 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 820 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7814 (t0) REVERT: B 825 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8231 (mptp) REVERT: B 860 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8436 (t) REVERT: B 1002 GLN cc_start: 0.8241 (mm110) cc_final: 0.8002 (mm110) REVERT: C 837 TYR cc_start: 0.8300 (t80) cc_final: 0.7959 (t80) REVERT: C 840 CYS cc_start: 0.8466 (t) cc_final: 0.8067 (t) REVERT: C 951 VAL cc_start: 0.8229 (m) cc_final: 0.7939 (t) REVERT: C 992 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7086 (mm110) REVERT: C 1031 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7808 (mt-10) outliers start: 35 outliers final: 24 residues processed: 301 average time/residue: 2.8950 time to fit residues: 936.5258 Evaluate side-chains 318 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 934 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 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU 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 1031 GLU Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 39 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A 992 GLN B 895 GLN B 914 ASN B 955 ASN B1074 ASN C 969 ASN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101094 restraints weight = 37170.806| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.91 r_work: 0.3167 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10428 Z= 0.228 Angle : 0.515 5.779 14205 Z= 0.264 Chirality : 0.041 0.164 1671 Planarity : 0.005 0.096 1836 Dihedral : 5.787 55.491 1572 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 17.69 % Favored : 79.56 % 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: 1.06 (0.23), residues: 1305 helix: 2.09 (0.21), residues: 609 sheet: 0.17 (0.36), residues: 159 loop : -0.76 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 991 HIS 0.004 0.001 HIS C1064 PHE 0.010 0.001 PHE A 888 TYR 0.010 0.001 TYR C 904 ARG 0.014 0.001 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17079.02 seconds wall clock time: 299 minutes 46.24 seconds (17986.24 seconds total)