Starting phenix.real_space_refine on Thu Sep 18 21:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vao_43097/09_2025/8vao_43097_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vao_43097/09_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_43097/09_2025/8vao_43097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vao_43097/09_2025/8vao_43097.map" model { file = "/net/cci-nas-00/data/ceres_data/8vao_43097/09_2025/8vao_43097_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vao_43097/09_2025/8vao_43097_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C Time building chain proxies: 7.13, per 1000 atoms: 0.35 Number of scatterers: 20154 At special positions: 0 Unit cell: (84.6, 87.42, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1977 8.00 N 1698 7.00 C 6480 6.00 H 9942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS B 790 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS C 704 " distance=1.96 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS C 790 " distance=2.10 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 2.08 Conformation dependent library (CDL) restraints added in 596.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.41 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: 5.00 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9942 1.03 - 1.23: 67 1.23 - 1.43: 4238 1.43 - 1.62: 6045 1.62 - 1.82: 78 Bond restraints: 20370 Sorted by residual: bond pdb=" N CYS A 704 " pdb=" CA CYS A 704 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N CYS C 704 " pdb=" CA CYS C 704 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N CYS B 704 " pdb=" CA CYS B 704 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N CYS B 704 " pdb=" H CYS B 704 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N CYS A 704 " pdb=" H CYS A 704 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 20365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 33360 0.94 - 1.89: 3175 1.89 - 2.83: 160 2.83 - 3.77: 55 3.77 - 4.71: 27 Bond angle restraints: 36777 Sorted by residual: angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 126.13 -4.59 1.91e+00 2.74e-01 5.77e+00 angle pdb=" C VAL B1040 " pdb=" N ASP B1041 " pdb=" CA ASP B1041 " ideal model delta sigma weight residual 121.54 125.04 -3.50 1.91e+00 2.74e-01 3.36e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 112.91 -2.21 1.22e+00 6.72e-01 3.29e+00 ... (remaining 36772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8924 17.07 - 34.14: 535 34.14 - 51.21: 207 51.21 - 68.29: 198 68.29 - 85.36: 9 Dihedral angle restraints: 9873 sinusoidal: 5445 harmonic: 4428 Sorted by residual: dihedral pdb=" CD ARG B1107 " pdb=" NE ARG B1107 " pdb=" CZ ARG B1107 " pdb=" NH1 ARG B1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.55 37.55 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CD ARG C1107 " pdb=" NE ARG C1107 " pdb=" CZ ARG C1107 " pdb=" NH1 ARG C1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.43 37.43 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CD ARG A1107 " pdb=" NE ARG A1107 " pdb=" CZ ARG A1107 " pdb=" NH1 ARG A1107 " ideal model delta sinusoidal sigma weight residual 0.00 -37.41 37.41 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 9870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 978 0.025 - 0.050: 372 0.050 - 0.075: 181 0.075 - 0.100: 82 0.100 - 0.125: 58 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA VAL B1065 " pdb=" N VAL B1065 " pdb=" C VAL B1065 " pdb=" CB VAL B1065 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A1065 " pdb=" N VAL A1065 " pdb=" C VAL A1065 " pdb=" CB VAL A1065 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL C1065 " pdb=" N VAL C1065 " pdb=" C VAL C1065 " pdb=" CB VAL C1065 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1668 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1107 " 0.504 9.50e-02 1.11e+02 1.70e-01 4.23e+01 pdb=" NE ARG B1107 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B1107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B1107 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG B1107 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG B1107 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B1107 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B1107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1107 " 0.504 9.50e-02 1.11e+02 1.70e-01 4.21e+01 pdb=" NE ARG C1107 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG C1107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG C1107 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C1107 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG C1107 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C1107 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG C1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C1107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1107 " -0.503 9.50e-02 1.11e+02 1.70e-01 4.20e+01 pdb=" NE ARG A1107 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A1107 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A1107 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A1107 " -0.013 2.00e-02 2.50e+03 pdb="HH11 ARG A1107 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1107 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A1107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1107 " 0.012 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1007 2.19 - 2.79: 40843 2.79 - 3.39: 54607 3.39 - 4.00: 71110 4.00 - 4.60: 110931 Nonbonded interactions: 278498 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 786 " pdb=" OE1 GLN C 787 " model vdw 1.586 2.450 nonbonded pdb=" HZ1 LYS A 786 " pdb=" OE1 GLN A 787 " model vdw 1.586 2.450 nonbonded pdb=" HZ1 LYS B 786 " pdb=" OE1 GLN B 787 " model vdw 1.586 2.450 nonbonded pdb=" HH TYR A 741 " pdb=" O LEU A 962 " model vdw 1.611 2.450 nonbonded pdb=" HH TYR B 741 " pdb=" O LEU B 962 " model vdw 1.612 2.450 ... (remaining 278493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10455 Z= 0.138 Angle : 0.517 4.714 14268 Z= 0.257 Chirality : 0.040 0.125 1671 Planarity : 0.011 0.232 1836 Dihedral : 13.268 85.356 3900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.050 0.005 ARG B1107 TYR 0.011 0.001 TYR C1067 PHE 0.009 0.001 PHE C 759 TRP 0.006 0.001 TRP A 886 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00301 (10428) covalent geometry : angle 0.51176 (14205) SS BOND : bond 0.02233 ( 18) SS BOND : angle 0.90221 ( 36) hydrogen bonds : bond 0.21424 ( 516) hydrogen bonds : angle 7.86480 ( 1485) link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 1.49246 ( 27) *********************** 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 : 0.641 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: 1.2213 time to fit residues: 446.9965 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 : 0.525 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN 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 ** 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 = 0.3602 r_free = 0.3602 target = 0.123416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107957 restraints weight = 36108.831| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.88 r_work: 0.3271 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10455 Z= 0.161 Angle : 0.564 4.600 14268 Z= 0.294 Chirality : 0.043 0.174 1671 Planarity : 0.004 0.041 1836 Dihedral : 5.543 45.818 1578 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.13 % Allowed : 12.27 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1305 helix: 1.13 (0.21), residues: 606 sheet: 0.06 (0.34), residues: 189 loop : -1.20 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.018 0.002 TYR A 904 PHE 0.009 0.001 PHE A 906 TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00367 (10428) covalent geometry : angle 0.55530 (14205) SS BOND : bond 0.00709 ( 18) SS BOND : angle 1.19642 ( 36) hydrogen bonds : bond 0.05372 ( 516) hydrogen bonds : angle 4.93675 ( 1485) link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 1.97961 ( 27) *********************** 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 343 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7688 (mp0) cc_final: 0.7332 (mp0) REVERT: A 772 VAL cc_start: 0.8784 (t) cc_final: 0.8513 (m) REVERT: A 814 LYS cc_start: 0.7498 (mmmm) cc_final: 0.7088 (mmmt) REVERT: A 824 ASN cc_start: 0.8494 (m-40) cc_final: 0.8270 (m110) REVERT: A 900 MET cc_start: 0.8297 (mtp) cc_final: 0.8006 (mtp) REVERT: A 1038 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7814 (mmtm) REVERT: A 1116 THR cc_start: 0.8276 (p) cc_final: 0.8050 (p) REVERT: B 737 ASP cc_start: 0.7911 (t0) cc_final: 0.7357 (t0) REVERT: B 748 GLU cc_start: 0.7598 (mp0) cc_final: 0.7378 (mp0) REVERT: B 950 ASP cc_start: 0.7420 (m-30) cc_final: 0.7069 (m-30) REVERT: B 962 LEU cc_start: 0.8362 (tp) cc_final: 0.8111 (tp) REVERT: B 996 LEU cc_start: 0.7676 (mp) cc_final: 0.7442 (mt) REVERT: B 1117 THR cc_start: 0.8265 (m) cc_final: 0.7867 (p) REVERT: B 1130 ILE cc_start: 0.8573 (mt) cc_final: 0.8341 (mt) REVERT: C 737 ASP cc_start: 0.8138 (t0) cc_final: 0.7143 (t0) REVERT: C 772 VAL cc_start: 0.8658 (t) cc_final: 0.8416 (m) REVERT: C 837 TYR cc_start: 0.8085 (t80) cc_final: 0.7810 (t80) REVERT: C 854 LYS cc_start: 0.8160 (tttp) cc_final: 0.7925 (ttmm) REVERT: C 933 LYS cc_start: 0.8123 (mttt) cc_final: 0.7902 (mtpp) REVERT: C 950 ASP cc_start: 0.7484 (m-30) cc_final: 0.7066 (m-30) REVERT: C 1010 GLN cc_start: 0.7958 (tp40) cc_final: 0.7594 (tm-30) outliers start: 24 outliers final: 13 residues processed: 332 average time/residue: 1.2889 time to fit residues: 457.6352 Evaluate side-chains 317 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 918 GLU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 872 GLN A 992 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 992 GLN B1005 GLN C 762 GLN C 992 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101757 restraints weight = 36404.897| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.89 r_work: 0.3169 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10455 Z= 0.299 Angle : 0.620 5.960 14268 Z= 0.326 Chirality : 0.047 0.184 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.833 48.103 1572 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.31 % Allowed : 14.31 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.23), residues: 1305 helix: 1.38 (0.21), residues: 612 sheet: 0.01 (0.33), residues: 189 loop : -1.03 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 983 TYR 0.019 0.002 TYR C1067 PHE 0.017 0.002 PHE A 906 TRP 0.007 0.001 TRP B1102 HIS 0.007 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00727 (10428) covalent geometry : angle 0.60640 (14205) SS BOND : bond 0.00443 ( 18) SS BOND : angle 1.49321 ( 36) hydrogen bonds : bond 0.06428 ( 516) hydrogen bonds : angle 5.10360 ( 1485) link_NAG-ASN : bond 0.00617 ( 9) link_NAG-ASN : angle 2.63641 ( 27) *********************** 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: 26 poor density : 320 time to evaluate : 0.534 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 814 LYS cc_start: 0.7493 (mmmm) cc_final: 0.7185 (mmpt) REVERT: A 824 ASN cc_start: 0.8562 (m-40) cc_final: 0.8326 (m110) REVERT: A 1009 THR cc_start: 0.8548 (t) cc_final: 0.8313 (m) REVERT: A 1038 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7995 (mmtm) REVERT: B 737 ASP cc_start: 0.7984 (t0) cc_final: 0.7504 (t0) REVERT: B 748 GLU cc_start: 0.7664 (mp0) cc_final: 0.7404 (mp0) REVERT: B 820 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7853 (t0) REVERT: B 860 VAL cc_start: 0.8745 (m) cc_final: 0.8436 (t) REVERT: B 864 LEU cc_start: 0.8088 (tp) cc_final: 0.7884 (tt) REVERT: B 873 TYR cc_start: 0.8528 (m-80) cc_final: 0.7810 (m-80) REVERT: B 983 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7431 (ttm110) REVERT: B 1117 THR cc_start: 0.8342 (m) cc_final: 0.7873 (p) REVERT: C 737 ASP cc_start: 0.8164 (t0) cc_final: 0.7888 (t0) REVERT: C 808 ASP cc_start: 0.7476 (p0) cc_final: 0.7267 (p0) REVERT: C 835 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7607 (ttmm) REVERT: C 837 TYR cc_start: 0.8154 (t80) cc_final: 0.7854 (t80) REVERT: C 950 ASP cc_start: 0.7645 (m-30) cc_final: 0.7206 (m-30) REVERT: C 992 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7162 (mm110) REVERT: C 1010 GLN cc_start: 0.8151 (tp40) cc_final: 0.7789 (tm-30) outliers start: 26 outliers final: 15 residues processed: 330 average time/residue: 1.2786 time to fit residues: 451.3056 Evaluate side-chains 321 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 305 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 734 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 124 optimal weight: 0.3980 chunk 119 optimal weight: 0.2980 chunk 126 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 58 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 A1005 GLN B 779 GLN B 836 GLN B 955 ASN B 969 ASN B1002 GLN B1005 GLN B1074 ASN C 762 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104411 restraints weight = 36450.253| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.92 r_work: 0.3214 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10455 Z= 0.106 Angle : 0.514 4.437 14268 Z= 0.261 Chirality : 0.040 0.154 1671 Planarity : 0.004 0.050 1836 Dihedral : 5.419 48.915 1572 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.04 % Allowed : 16.00 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.23), residues: 1305 helix: 1.86 (0.21), residues: 615 sheet: 0.49 (0.38), residues: 159 loop : -0.70 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.011 0.001 TYR C 904 PHE 0.006 0.001 PHE B1089 TRP 0.008 0.001 TRP B 991 HIS 0.002 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00239 (10428) covalent geometry : angle 0.50590 (14205) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.30149 ( 36) hydrogen bonds : bond 0.04501 ( 516) hydrogen bonds : angle 4.58634 ( 1485) link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 1.69159 ( 27) *********************** 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 333 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8733 (t) cc_final: 0.8429 (m) REVERT: A 814 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7125 (mmmt) REVERT: A 824 ASN cc_start: 0.8546 (m-40) cc_final: 0.8313 (m110) REVERT: A 1038 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8065 (mmtm) REVERT: B 737 ASP cc_start: 0.7954 (t0) cc_final: 0.7522 (t0) REVERT: B 748 GLU cc_start: 0.7585 (mp0) cc_final: 0.7324 (mp0) REVERT: B 820 ASP cc_start: 0.7867 (t70) cc_final: 0.7647 (t0) REVERT: B 860 VAL cc_start: 0.8711 (m) cc_final: 0.8443 (t) REVERT: B 873 TYR cc_start: 0.8516 (m-10) cc_final: 0.7859 (m-80) REVERT: B 1117 THR cc_start: 0.8216 (m) cc_final: 0.7683 (p) REVERT: C 737 ASP cc_start: 0.8144 (t0) cc_final: 0.7871 (t0) REVERT: C 808 ASP cc_start: 0.7455 (p0) cc_final: 0.7241 (p0) REVERT: C 835 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7678 (ttmm) REVERT: C 837 TYR cc_start: 0.8125 (t80) cc_final: 0.7811 (t80) REVERT: C 860 VAL cc_start: 0.8639 (m) cc_final: 0.8345 (t) REVERT: C 950 ASP cc_start: 0.7582 (m-30) cc_final: 0.7133 (m-30) REVERT: C 983 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7174 (ttm110) REVERT: C 992 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7049 (mm110) outliers start: 23 outliers final: 11 residues processed: 320 average time/residue: 1.2076 time to fit residues: 415.9402 Evaluate side-chains 303 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 745 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 119 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 872 GLN A 935 GLN A 992 GLN B 762 GLN B1002 GLN B1005 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102556 restraints weight = 36399.170| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.90 r_work: 0.3187 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10455 Z= 0.168 Angle : 0.535 5.930 14268 Z= 0.273 Chirality : 0.042 0.161 1671 Planarity : 0.004 0.037 1836 Dihedral : 5.502 50.304 1572 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 16.62 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.23), residues: 1305 helix: 2.00 (0.21), residues: 612 sheet: 0.09 (0.34), residues: 189 loop : -0.59 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1039 TYR 0.014 0.001 TYR C1067 PHE 0.010 0.001 PHE A 906 TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00400 (10428) covalent geometry : angle 0.52346 (14205) SS BOND : bond 0.00508 ( 18) SS BOND : angle 1.44456 ( 36) hydrogen bonds : bond 0.04992 ( 516) hydrogen bonds : angle 4.67176 ( 1485) link_NAG-ASN : bond 0.00345 ( 9) link_NAG-ASN : angle 2.12844 ( 27) *********************** 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 331 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7658 (mp0) cc_final: 0.7198 (mp0) REVERT: A 772 VAL cc_start: 0.8748 (t) cc_final: 0.8429 (m) REVERT: A 814 LYS cc_start: 0.7529 (mmmm) cc_final: 0.7111 (mmmt) REVERT: A 824 ASN cc_start: 0.8556 (m-40) cc_final: 0.8314 (m110) REVERT: A 979 ASP cc_start: 0.7258 (m-30) cc_final: 0.6905 (m-30) REVERT: A 1038 LYS cc_start: 0.8285 (mmtm) cc_final: 0.8068 (mmtm) REVERT: B 737 ASP cc_start: 0.7975 (t0) cc_final: 0.7494 (t0) REVERT: B 748 GLU cc_start: 0.7674 (mp0) cc_final: 0.7409 (mp0) REVERT: B 820 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7753 (t0) REVERT: B 860 VAL cc_start: 0.8720 (m) cc_final: 0.8465 (t) REVERT: B 873 TYR cc_start: 0.8561 (m-80) cc_final: 0.7815 (m-80) REVERT: C 737 ASP cc_start: 0.8134 (t0) cc_final: 0.7871 (t0) REVERT: C 808 ASP cc_start: 0.7455 (p0) cc_final: 0.7253 (p0) REVERT: C 835 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7671 (ttmm) REVERT: C 837 TYR cc_start: 0.8175 (t80) cc_final: 0.7807 (t80) REVERT: C 860 VAL cc_start: 0.8663 (m) cc_final: 0.8364 (t) REVERT: C 950 ASP cc_start: 0.7626 (m-30) cc_final: 0.7186 (m-30) outliers start: 25 outliers final: 17 residues processed: 318 average time/residue: 1.2952 time to fit residues: 441.1686 Evaluate side-chains 312 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 294 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 1126 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 779 GLN A 935 GLN B 955 ASN B1002 GLN B1005 GLN B1010 GLN C 762 GLN C 901 GLN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101900 restraints weight = 36385.517| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.90 r_work: 0.3176 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10455 Z= 0.195 Angle : 0.553 5.019 14268 Z= 0.282 Chirality : 0.042 0.162 1671 Planarity : 0.004 0.042 1836 Dihedral : 5.639 52.219 1572 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.93 % Allowed : 16.09 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.23), residues: 1305 helix: 1.97 (0.21), residues: 612 sheet: 0.08 (0.35), residues: 189 loop : -0.62 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 765 TYR 0.013 0.001 TYR C1067 PHE 0.010 0.001 PHE A 888 TRP 0.005 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00465 (10428) covalent geometry : angle 0.53969 (14205) SS BOND : bond 0.00531 ( 18) SS BOND : angle 1.52221 ( 36) hydrogen bonds : bond 0.05190 ( 516) hydrogen bonds : angle 4.74500 ( 1485) link_NAG-ASN : bond 0.00381 ( 9) link_NAG-ASN : angle 2.23563 ( 27) *********************** 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 332 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 0.513 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 814 LYS cc_start: 0.7513 (mmmm) cc_final: 0.7096 (mmmt) REVERT: A 824 ASN cc_start: 0.8541 (m-40) cc_final: 0.8303 (m110) REVERT: A 979 ASP cc_start: 0.7322 (m-30) cc_final: 0.6930 (m-30) REVERT: A 995 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7584 (mtt180) REVERT: A 1038 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8084 (mmtm) REVERT: B 748 GLU cc_start: 0.7675 (mp0) cc_final: 0.7393 (mp0) REVERT: B 820 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7808 (t0) REVERT: B 860 VAL cc_start: 0.8728 (m) cc_final: 0.8471 (t) REVERT: C 785 VAL cc_start: 0.7710 (t) cc_final: 0.7492 (p) REVERT: C 835 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7605 (ttmm) REVERT: C 837 TYR cc_start: 0.8167 (t80) cc_final: 0.7787 (t80) REVERT: C 860 VAL cc_start: 0.8636 (m) cc_final: 0.8350 (t) REVERT: C 1031 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7802 (mt-10) outliers start: 33 outliers final: 24 residues processed: 312 average time/residue: 1.3499 time to fit residues: 449.8648 Evaluate side-chains 322 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 860 VAL 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 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 820 ASP 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 1068 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 779 GLN A 935 GLN A 992 GLN B 872 GLN B 935 GLN B 969 ASN B1002 GLN B1005 GLN B1074 ASN B1106 GLN C 779 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100927 restraints weight = 36452.855| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.89 r_work: 0.3161 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10455 Z= 0.250 Angle : 0.584 5.319 14268 Z= 0.299 Chirality : 0.044 0.180 1671 Planarity : 0.005 0.044 1836 Dihedral : 5.865 52.871 1572 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.47 % Allowed : 16.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.23), residues: 1305 helix: 1.85 (0.21), residues: 609 sheet: 0.03 (0.35), residues: 189 loop : -0.71 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1019 TYR 0.015 0.002 TYR C1067 PHE 0.014 0.002 PHE A 888 TRP 0.005 0.001 TRP B1102 HIS 0.005 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00601 (10428) covalent geometry : angle 0.56964 (14205) SS BOND : bond 0.00589 ( 18) SS BOND : angle 1.61163 ( 36) hydrogen bonds : bond 0.05565 ( 516) hydrogen bonds : angle 4.87545 ( 1485) link_NAG-ASN : bond 0.00569 ( 9) link_NAG-ASN : angle 2.47881 ( 27) *********************** 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 344 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 824 ASN cc_start: 0.8560 (m-40) cc_final: 0.8332 (m110) REVERT: A 979 ASP cc_start: 0.7325 (m-30) cc_final: 0.6917 (m-30) REVERT: A 1038 LYS cc_start: 0.8289 (mmtm) cc_final: 0.8061 (mmtm) REVERT: B 748 GLU cc_start: 0.7680 (mp0) cc_final: 0.7400 (mp0) REVERT: B 820 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7821 (t0) REVERT: B 860 VAL cc_start: 0.8729 (m) cc_final: 0.8470 (t) REVERT: C 748 GLU cc_start: 0.7759 (mp0) cc_final: 0.7525 (mp0) REVERT: C 785 VAL cc_start: 0.7820 (t) cc_final: 0.7579 (p) REVERT: C 835 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7627 (ttmm) REVERT: C 837 TYR cc_start: 0.8194 (t80) cc_final: 0.7876 (t80) REVERT: C 860 VAL cc_start: 0.8654 (m) cc_final: 0.8373 (t) REVERT: C 873 TYR cc_start: 0.8401 (m-80) cc_final: 0.8193 (m-80) REVERT: C 983 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7167 (ttm110) REVERT: C 1031 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7873 (mt-10) outliers start: 39 outliers final: 27 residues processed: 321 average time/residue: 1.3288 time to fit residues: 455.6300 Evaluate side-chains 329 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 976 VAL Chi-restraints excluded: chain B residue 993 ILE 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 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 1068 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 779 GLN A 853 GLN A 935 GLN A 969 ASN B 872 GLN B 895 GLN B 935 GLN B 955 ASN B 969 ASN B1002 GLN B1074 ASN C 969 ASN C 992 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101293 restraints weight = 36603.516| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.91 r_work: 0.3167 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10455 Z= 0.212 Angle : 0.570 5.765 14268 Z= 0.290 Chirality : 0.043 0.173 1671 Planarity : 0.005 0.092 1836 Dihedral : 5.863 55.313 1572 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.02 % Allowed : 17.07 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.23), residues: 1305 helix: 1.86 (0.21), residues: 609 sheet: 0.09 (0.34), residues: 189 loop : -0.72 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1091 TYR 0.013 0.001 TYR C1067 PHE 0.012 0.001 PHE A 888 TRP 0.005 0.001 TRP A 998 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00505 (10428) covalent geometry : angle 0.55533 (14205) SS BOND : bond 0.00567 ( 18) SS BOND : angle 1.68184 ( 36) hydrogen bonds : bond 0.05275 ( 516) hydrogen bonds : angle 4.82034 ( 1485) link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 2.34013 ( 27) *********************** 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 333 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.524 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 752 LEU cc_start: 0.8436 (mt) cc_final: 0.8232 (mp) REVERT: A 755 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7730 (mm110) REVERT: A 772 VAL cc_start: 0.8767 (t) cc_final: 0.8446 (m) REVERT: A 805 ILE cc_start: 0.8253 (mm) cc_final: 0.8009 (OUTLIER) REVERT: A 824 ASN cc_start: 0.8587 (m-40) cc_final: 0.8348 (m110) REVERT: A 979 ASP cc_start: 0.7361 (m-30) cc_final: 0.6982 (m-30) REVERT: A 1038 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8060 (mmtm) REVERT: B 748 GLU cc_start: 0.7620 (mp0) cc_final: 0.7334 (mp0) REVERT: B 765 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7606 (ttm-80) REVERT: B 820 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7784 (t0) REVERT: B 860 VAL cc_start: 0.8719 (m) cc_final: 0.8469 (t) REVERT: C 785 VAL cc_start: 0.7848 (t) cc_final: 0.7607 (p) REVERT: C 835 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7611 (ttmm) REVERT: C 837 TYR cc_start: 0.8221 (t80) cc_final: 0.7836 (t80) REVERT: C 860 VAL cc_start: 0.8635 (m) cc_final: 0.8335 (t) REVERT: C 983 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7193 (ttm110) REVERT: C 1031 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7825 (mt-10) outliers start: 34 outliers final: 26 residues processed: 313 average time/residue: 1.3601 time to fit residues: 454.7427 Evaluate side-chains 325 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 1122 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE 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 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 Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 779 GLN A 935 GLN B1002 GLN B1005 GLN B1074 ASN B1135 ASN C 779 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101733 restraints weight = 36387.621| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.90 r_work: 0.3174 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10455 Z= 0.169 Angle : 0.547 5.778 14268 Z= 0.276 Chirality : 0.042 0.167 1671 Planarity : 0.005 0.081 1836 Dihedral : 5.796 57.362 1572 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.49 % Allowed : 17.60 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.23), residues: 1305 helix: 2.01 (0.21), residues: 609 sheet: 0.08 (0.35), residues: 189 loop : -0.66 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1091 TYR 0.011 0.001 TYR C 904 PHE 0.010 0.001 PHE A 888 TRP 0.005 0.001 TRP A 998 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00400 (10428) covalent geometry : angle 0.53381 (14205) SS BOND : bond 0.00500 ( 18) SS BOND : angle 1.58024 ( 36) hydrogen bonds : bond 0.04939 ( 516) hydrogen bonds : angle 4.74006 ( 1485) link_NAG-ASN : bond 0.00344 ( 9) link_NAG-ASN : angle 2.17325 ( 27) *********************** 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 320 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8750 (t) cc_final: 0.8439 (m) REVERT: A 805 ILE cc_start: 0.8268 (mm) cc_final: 0.8014 (mp) REVERT: A 820 ASP cc_start: 0.7944 (t0) cc_final: 0.7490 (m-30) REVERT: A 824 ASN cc_start: 0.8607 (m-40) cc_final: 0.8362 (m110) REVERT: A 979 ASP cc_start: 0.7358 (m-30) cc_final: 0.6979 (m-30) REVERT: A 1010 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7494 (tm-30) REVERT: A 1038 LYS cc_start: 0.8294 (mmtm) cc_final: 0.8060 (mmtm) REVERT: B 748 GLU cc_start: 0.7592 (mp0) cc_final: 0.7311 (mp0) REVERT: B 820 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 860 VAL cc_start: 0.8689 (m) cc_final: 0.8451 (t) REVERT: C 748 GLU cc_start: 0.7744 (mp0) cc_final: 0.7465 (mp0) REVERT: C 785 VAL cc_start: 0.7834 (t) cc_final: 0.7621 (p) REVERT: C 835 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7637 (ttmm) REVERT: C 837 TYR cc_start: 0.8206 (t80) cc_final: 0.7865 (t80) REVERT: C 860 VAL cc_start: 0.8618 (m) cc_final: 0.8344 (t) outliers start: 28 outliers final: 22 residues processed: 302 average time/residue: 1.3716 time to fit residues: 443.3852 Evaluate side-chains 316 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1122 VAL 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 864 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 995 ARG 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 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 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 779 GLN B 895 GLN B 955 ASN B1002 GLN B1074 ASN C 969 ASN C 992 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101364 restraints weight = 36580.007| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3169 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10455 Z= 0.204 Angle : 0.572 7.008 14268 Z= 0.289 Chirality : 0.043 0.172 1671 Planarity : 0.005 0.081 1836 Dihedral : 5.905 59.382 1572 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.58 % Allowed : 17.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1305 helix: 1.89 (0.21), residues: 618 sheet: 0.03 (0.35), residues: 189 loop : -0.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1091 TYR 0.012 0.001 TYR C1067 PHE 0.013 0.001 PHE A 888 TRP 0.005 0.001 TRP C 991 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00487 (10428) covalent geometry : angle 0.55827 (14205) SS BOND : bond 0.00545 ( 18) SS BOND : angle 1.64739 ( 36) hydrogen bonds : bond 0.05152 ( 516) hydrogen bonds : angle 4.80389 ( 1485) link_NAG-ASN : bond 0.00435 ( 9) link_NAG-ASN : angle 2.31009 ( 27) ********************** 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 321 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8766 (t) cc_final: 0.8445 (m) REVERT: A 805 ILE cc_start: 0.8293 (mm) cc_final: 0.8051 (mp) REVERT: A 820 ASP cc_start: 0.7972 (t0) cc_final: 0.7566 (m-30) REVERT: A 824 ASN cc_start: 0.8624 (m-40) cc_final: 0.8375 (m110) REVERT: A 979 ASP cc_start: 0.7405 (m-30) cc_final: 0.7006 (m-30) REVERT: A 1010 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7498 (tm-30) REVERT: A 1038 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8056 (mmtm) REVERT: A 1045 LYS cc_start: 0.8254 (mmmm) cc_final: 0.8018 (mmmm) REVERT: B 748 GLU cc_start: 0.7618 (mp0) cc_final: 0.7340 (mp0) REVERT: B 765 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7593 (ttm-80) REVERT: B 820 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7787 (t0) REVERT: B 860 VAL cc_start: 0.8685 (m) cc_final: 0.8443 (t) REVERT: C 748 GLU cc_start: 0.7748 (mp0) cc_final: 0.7468 (mp0) REVERT: C 835 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7611 (ttmm) REVERT: C 837 TYR cc_start: 0.8228 (t80) cc_final: 0.7847 (t80) REVERT: C 860 VAL cc_start: 0.8619 (m) cc_final: 0.8322 (t) REVERT: C 1031 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7823 (mt-10) outliers start: 29 outliers final: 24 residues processed: 302 average time/residue: 1.4869 time to fit residues: 479.3420 Evaluate side-chains 314 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1122 VAL 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 864 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 995 ARG 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 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 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 779 GLN A 935 GLN B 872 GLN B 895 GLN B 914 ASN B1002 GLN B1005 GLN B1074 ASN 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 = 0.3509 r_free = 0.3509 target = 0.116825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101182 restraints weight = 36568.322| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.88 r_work: 0.3164 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10455 Z= 0.218 Angle : 0.570 4.999 14268 Z= 0.291 Chirality : 0.043 0.173 1671 Planarity : 0.005 0.077 1836 Dihedral : 5.968 59.669 1572 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.84 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1305 helix: 1.88 (0.21), residues: 618 sheet: 0.25 (0.36), residues: 159 loop : -0.65 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1091 TYR 0.013 0.001 TYR C1067 PHE 0.013 0.001 PHE A 888 TRP 0.005 0.001 TRP C 991 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00521 (10428) covalent geometry : angle 0.55600 (14205) SS BOND : bond 0.00560 ( 18) SS BOND : angle 1.69159 ( 36) hydrogen bonds : bond 0.05251 ( 516) hydrogen bonds : angle 4.84168 ( 1485) link_NAG-ASN : bond 0.00472 ( 9) link_NAG-ASN : angle 2.35301 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8852.74 seconds wall clock time: 150 minutes 6.54 seconds (9006.54 seconds total)