Starting phenix.real_space_refine on Wed Aug 7 16:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_43097_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_43097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_43097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_43097_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vao_43097/08_2024/8vao_43097_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 6480 2.51 5 N 1698 2.21 5 O 1977 1.98 5 H 9942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20154 Number of models: 1 Model: "" Number of chains: 6 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: "B" 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: "C" 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 10.01, per 1000 atoms: 0.50 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 B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 15.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 53.1% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.931A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.353A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.556A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.800A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.859A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TRP A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 995 " --> pdb=" O TRP A 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.932A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.352A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.555A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.801A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TRP B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.932A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.533A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.563A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.353A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.773A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.704A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.555A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.777A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.802A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TRP C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 995 " --> pdb=" O TRP C 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 997 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.951A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.951A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA8, first strand: chain 'B' and resid 1094 through 1098 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB3, first strand: chain 'C' and resid 1094 through 1098 516 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.28 Time building geometry restraints manager: 16.69 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: 100.64 - 107.32: 661 107.32 - 113.99: 24181 113.99 - 120.66: 6813 120.66 - 127.33: 5014 127.33 - 134.00: 108 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: 0.00 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: 3.360 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: 0.280 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 66.260 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10428 Z= 0.201 Angle : 0.512 4.714 14205 Z= 0.256 Chirality : 0.040 0.125 1671 Planarity : 0.011 0.232 1836 Dihedral : 13.268 85.356 3900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1305 helix: 0.34 (0.22), residues: 588 sheet: -0.33 (0.36), residues: 150 loop : -1.26 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 886 HIS 0.004 0.001 HIS A1083 PHE 0.009 0.001 PHE C 759 TYR 0.011 0.001 TYR C1067 ARG 0.050 0.005 ARG B1107 *********************** 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 fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.8036 (t0) cc_final: 0.7807 (t0) REVERT: A 748 GLU cc_start: 0.7596 (mp0) cc_final: 0.7309 (mp0) REVERT: A 772 VAL cc_start: 0.8661 (t) cc_final: 0.8386 (m) REVERT: A 814 LYS cc_start: 0.7365 (mmmm) cc_final: 0.7139 (mmpt) REVERT: A 824 ASN cc_start: 0.8361 (m-40) cc_final: 0.8131 (m110) REVERT: A 1009 THR cc_start: 0.8627 (t) cc_final: 0.8351 (m) REVERT: A 1010 GLN cc_start: 0.7966 (tp40) cc_final: 0.7748 (mm-40) REVERT: A 1038 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7832 (mmtm) REVERT: A 1103 PHE cc_start: 0.8059 (m-10) cc_final: 0.7842 (m-80) REVERT: B 737 ASP cc_start: 0.7890 (t0) cc_final: 0.7499 (t0) REVERT: B 748 GLU cc_start: 0.7436 (mp0) cc_final: 0.7235 (mp0) REVERT: B 869 MET cc_start: 0.7596 (mtt) cc_final: 0.7321 (mtm) REVERT: B 950 ASP cc_start: 0.7381 (m-30) cc_final: 0.6908 (m-30) REVERT: B 962 LEU cc_start: 0.8077 (tp) cc_final: 0.7786 (tp) REVERT: B 996 LEU cc_start: 0.7663 (mp) cc_final: 0.7441 (mt) REVERT: B 1009 THR cc_start: 0.8545 (t) cc_final: 0.8240 (m) REVERT: B 1117 THR cc_start: 0.8173 (m) cc_final: 0.7805 (p) REVERT: B 1127 ASP cc_start: 0.7017 (m-30) cc_final: 0.6798 (m-30) REVERT: B 1130 ILE cc_start: 0.8559 (mt) cc_final: 0.8314 (mt) REVERT: C 737 ASP cc_start: 0.8097 (t0) cc_final: 0.7591 (t0) REVERT: C 741 TYR cc_start: 0.8290 (t80) cc_final: 0.8088 (t80) REVERT: C 772 VAL cc_start: 0.8559 (t) cc_final: 0.8352 (m) REVERT: C 836 GLN cc_start: 0.7963 (mt0) cc_final: 0.7703 (mt0) REVERT: C 837 TYR cc_start: 0.8087 (t80) cc_final: 0.7846 (t80) REVERT: C 854 LYS cc_start: 0.7967 (tttp) cc_final: 0.7753 (ttmm) REVERT: C 907 ASN cc_start: 0.7576 (t0) cc_final: 0.7351 (t0) REVERT: C 950 ASP cc_start: 0.7430 (m-30) cc_final: 0.6937 (m-30) REVERT: C 992 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7254 (mm110) REVERT: C 996 LEU cc_start: 0.7822 (mp) cc_final: 0.7568 (mt) REVERT: C 1010 GLN cc_start: 0.7869 (tp40) cc_final: 0.7447 (tm-30) REVERT: C 1038 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7689 (mmtm) outliers start: 0 outliers final: 3 residues processed: 340 average time/residue: 2.3388 time to fit residues: 863.7016 Evaluate side-chains 297 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 805 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 784 GLN A 872 GLN A 992 GLN A1005 GLN B 779 GLN B 784 GLN B 836 GLN B 853 GLN B 895 GLN B 955 ASN B1005 GLN B1101 HIS C 762 GLN C 764 ASN C 784 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10428 Z= 0.391 Angle : 0.600 4.705 14205 Z= 0.319 Chirality : 0.045 0.164 1671 Planarity : 0.005 0.043 1836 Dihedral : 5.840 47.637 1578 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 12.36 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1305 helix: 1.03 (0.21), residues: 606 sheet: -0.15 (0.33), residues: 189 loop : -1.11 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1102 HIS 0.006 0.002 HIS C1064 PHE 0.014 0.002 PHE A 906 TYR 0.017 0.002 TYR C1067 ARG 0.006 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 326 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 747 THR cc_start: 0.8122 (t) cc_final: 0.7909 (p) REVERT: A 748 GLU cc_start: 0.7604 (mp0) cc_final: 0.7184 (mp0) REVERT: A 772 VAL cc_start: 0.8812 (t) cc_final: 0.8476 (m) REVERT: A 814 LYS cc_start: 0.7346 (mmmm) cc_final: 0.7003 (mmmt) REVERT: A 824 ASN cc_start: 0.8494 (m-40) cc_final: 0.8256 (m110) REVERT: A 873 TYR cc_start: 0.8292 (m-80) cc_final: 0.7865 (m-80) REVERT: A 900 MET cc_start: 0.8330 (mtp) cc_final: 0.8107 (mtp) REVERT: A 934 ILE cc_start: 0.8059 (tp) cc_final: 0.7823 (pt) REVERT: A 992 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7206 (mm110) REVERT: A 1009 THR cc_start: 0.8642 (t) cc_final: 0.8412 (m) REVERT: A 1038 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7929 (mmtm) REVERT: B 737 ASP cc_start: 0.7964 (t0) cc_final: 0.7452 (t0) REVERT: B 748 GLU cc_start: 0.7513 (mp0) cc_final: 0.7249 (mp0) REVERT: B 864 LEU cc_start: 0.8174 (tp) cc_final: 0.7913 (tt) REVERT: B 873 TYR cc_start: 0.8415 (m-80) cc_final: 0.7719 (m-80) REVERT: B 1117 THR cc_start: 0.8324 (m) cc_final: 0.7903 (p) REVERT: B 1127 ASP cc_start: 0.7133 (m-30) cc_final: 0.6919 (m-30) REVERT: C 725 GLU cc_start: 0.7921 (tt0) cc_final: 0.7695 (tt0) REVERT: C 737 ASP cc_start: 0.8115 (t0) cc_final: 0.7189 (t0) REVERT: C 837 TYR cc_start: 0.8127 (t80) cc_final: 0.7875 (t80) REVERT: C 839 ASP cc_start: 0.7742 (m-30) cc_final: 0.7514 (m-30) REVERT: C 854 LYS cc_start: 0.8064 (tttp) cc_final: 0.7846 (ttmm) REVERT: C 933 LYS cc_start: 0.8108 (mttt) cc_final: 0.7902 (mtpp) REVERT: C 950 ASP cc_start: 0.7435 (m-30) cc_final: 0.6965 (m-30) REVERT: C 992 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7116 (mm110) REVERT: C 1010 GLN cc_start: 0.8004 (tp40) cc_final: 0.7648 (tm-30) REVERT: C 1038 LYS cc_start: 0.8253 (mmtm) cc_final: 0.8000 (mmtm) outliers start: 26 outliers final: 13 residues processed: 340 average time/residue: 2.4769 time to fit residues: 906.0942 Evaluate side-chains 317 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 304 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 872 GLN A1005 GLN B 836 GLN B 895 GLN B 955 ASN B 992 GLN B1005 GLN B1106 GLN C 762 GLN C 914 ASN C 969 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10428 Z= 0.402 Angle : 0.574 4.791 14205 Z= 0.303 Chirality : 0.044 0.178 1671 Planarity : 0.005 0.043 1836 Dihedral : 5.766 48.227 1572 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.76 % Allowed : 14.31 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1305 helix: 1.37 (0.21), residues: 612 sheet: 0.03 (0.33), residues: 189 loop : -1.08 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.006 0.002 HIS B1083 PHE 0.015 0.002 PHE A 906 TYR 0.017 0.002 TYR C 904 ARG 0.007 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 316 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8412 (tttm) cc_final: 0.8111 (tttm) REVERT: A 780 GLU cc_start: 0.7423 (tt0) cc_final: 0.7166 (mt-10) REVERT: A 814 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7137 (mmpt) REVERT: A 824 ASN cc_start: 0.8534 (m-40) cc_final: 0.8290 (m110) REVERT: A 873 TYR cc_start: 0.8376 (m-80) cc_final: 0.8135 (m-80) REVERT: A 934 ILE cc_start: 0.8112 (tp) cc_final: 0.7832 (pt) REVERT: A 954 GLN cc_start: 0.8224 (mt0) cc_final: 0.8017 (mt0) REVERT: A 992 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7187 (mm110) REVERT: A 1009 THR cc_start: 0.8719 (t) cc_final: 0.8487 (m) REVERT: A 1038 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8024 (mmtm) REVERT: B 748 GLU cc_start: 0.7517 (mp0) cc_final: 0.7240 (mp0) REVERT: B 820 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 860 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8386 (t) REVERT: B 873 TYR cc_start: 0.8503 (m-80) cc_final: 0.7826 (m-80) REVERT: B 1117 THR cc_start: 0.8365 (m) cc_final: 0.7866 (p) REVERT: C 737 ASP cc_start: 0.8140 (t0) cc_final: 0.7873 (t0) REVERT: C 835 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7477 (ttmm) REVERT: C 837 TYR cc_start: 0.8124 (t80) cc_final: 0.7826 (t80) REVERT: C 933 LYS cc_start: 0.8133 (mttt) cc_final: 0.7928 (mtpp) REVERT: C 950 ASP cc_start: 0.7489 (m-30) cc_final: 0.7009 (m-30) REVERT: C 983 ARG cc_start: 0.7295 (ttm110) cc_final: 0.7073 (ttm110) REVERT: C 992 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7205 (mm110) REVERT: C 1038 LYS cc_start: 0.8288 (mmtm) cc_final: 0.8051 (mmtm) outliers start: 31 outliers final: 19 residues processed: 328 average time/residue: 2.5973 time to fit residues: 915.0317 Evaluate side-chains 328 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 307 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 124 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 779 GLN B 836 GLN B 895 GLN B 969 ASN B1005 GLN B1074 ASN C 762 GLN C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10428 Z= 0.376 Angle : 0.560 4.928 14205 Z= 0.294 Chirality : 0.044 0.182 1671 Planarity : 0.005 0.050 1836 Dihedral : 5.850 51.549 1572 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.20 % Allowed : 14.76 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1305 helix: 1.66 (0.21), residues: 609 sheet: -0.03 (0.34), residues: 189 loop : -0.98 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.002 HIS B1083 PHE 0.013 0.002 PHE A 906 TYR 0.016 0.002 TYR C1067 ARG 0.008 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 315 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8788 (t) cc_final: 0.8443 (m) REVERT: A 776 LYS cc_start: 0.8456 (tttm) cc_final: 0.8174 (tttm) REVERT: A 780 GLU cc_start: 0.7424 (tt0) cc_final: 0.7188 (mt-10) REVERT: A 824 ASN cc_start: 0.8519 (m-40) cc_final: 0.8286 (m110) REVERT: A 954 GLN cc_start: 0.8235 (mt0) cc_final: 0.8031 (mt0) REVERT: A 992 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7237 (mm110) REVERT: A 1009 THR cc_start: 0.8673 (t) cc_final: 0.8461 (m) REVERT: A 1013 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8027 (mt) REVERT: A 1038 LYS cc_start: 0.8356 (mmtm) cc_final: 0.8110 (mmtm) REVERT: A 1091 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7395 (ttp-170) REVERT: B 737 ASP cc_start: 0.8030 (t70) cc_final: 0.7460 (t0) REVERT: B 748 GLU cc_start: 0.7512 (mp0) cc_final: 0.7219 (mp0) REVERT: B 820 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7711 (t0) REVERT: B 860 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8419 (t) REVERT: B 873 TYR cc_start: 0.8561 (m-80) cc_final: 0.7839 (m-80) REVERT: B 1002 GLN cc_start: 0.8138 (mm110) cc_final: 0.7877 (mm110) REVERT: B 1117 THR cc_start: 0.8263 (m) cc_final: 0.7722 (p) REVERT: C 785 VAL cc_start: 0.7665 (t) cc_final: 0.7433 (p) REVERT: C 835 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7529 (ttmm) REVERT: C 837 TYR cc_start: 0.8132 (t80) cc_final: 0.7854 (t80) REVERT: C 933 LYS cc_start: 0.8169 (mttt) cc_final: 0.7962 (mtpp) REVERT: C 992 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7210 (mm110) REVERT: C 1038 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8059 (mmtm) outliers start: 36 outliers final: 23 residues processed: 329 average time/residue: 2.6137 time to fit residues: 922.6026 Evaluate side-chains 333 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 1013 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.0060 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 853 GLN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 955 ASN B 969 ASN B1002 GLN B1005 GLN B1074 ASN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10428 Z= 0.371 Angle : 0.552 4.509 14205 Z= 0.288 Chirality : 0.044 0.180 1671 Planarity : 0.005 0.046 1836 Dihedral : 5.931 54.157 1572 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.64 % Allowed : 14.58 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1305 helix: 1.77 (0.21), residues: 609 sheet: 0.02 (0.34), residues: 189 loop : -0.88 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS B1064 PHE 0.013 0.002 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.005 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 304 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8795 (t) cc_final: 0.8440 (m) REVERT: A 776 LYS cc_start: 0.8443 (tttm) cc_final: 0.8186 (tttm) REVERT: A 780 GLU cc_start: 0.7409 (tt0) cc_final: 0.7189 (mt-10) REVERT: A 824 ASN cc_start: 0.8526 (m-40) cc_final: 0.8281 (m110) REVERT: A 979 ASP cc_start: 0.7660 (m-30) cc_final: 0.7281 (m-30) REVERT: A 992 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7250 (mm110) REVERT: A 1009 THR cc_start: 0.8668 (t) cc_final: 0.8460 (m) REVERT: A 1013 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 1038 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8102 (mmtm) REVERT: B 737 ASP cc_start: 0.8051 (t70) cc_final: 0.7499 (t0) REVERT: B 748 GLU cc_start: 0.7509 (mp0) cc_final: 0.7202 (mp0) REVERT: B 820 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7700 (t0) REVERT: B 860 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (t) REVERT: C 748 GLU cc_start: 0.7561 (mp0) cc_final: 0.7320 (mp0) REVERT: C 785 VAL cc_start: 0.7697 (t) cc_final: 0.7483 (p) REVERT: C 837 TYR cc_start: 0.8165 (t80) cc_final: 0.7800 (t80) REVERT: C 983 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7013 (ttm110) REVERT: C 992 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7312 (mm110) REVERT: C 1031 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8085 (mt-10) outliers start: 41 outliers final: 27 residues processed: 319 average time/residue: 2.6722 time to fit residues: 914.2829 Evaluate side-chains 328 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 297 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 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 1013 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL 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 41 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 779 GLN A1002 GLN B 836 GLN B 895 GLN B 935 GLN B1002 GLN B1005 GLN B1074 ASN B1135 ASN C 762 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10428 Z= 0.441 Angle : 0.583 5.737 14205 Z= 0.303 Chirality : 0.045 0.194 1671 Planarity : 0.005 0.058 1836 Dihedral : 6.095 58.772 1572 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.18 % Allowed : 14.93 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1305 helix: 1.71 (0.21), residues: 618 sheet: -0.04 (0.34), residues: 189 loop : -0.84 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.015 0.002 PHE A 888 TYR 0.015 0.002 TYR C1067 ARG 0.009 0.001 ARG B 983 *********************** 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 350 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 303 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8447 (tttm) cc_final: 0.8145 (tttm) REVERT: A 780 GLU cc_start: 0.7422 (tt0) cc_final: 0.7150 (mt-10) REVERT: A 824 ASN cc_start: 0.8572 (m-40) cc_final: 0.8337 (m110) REVERT: A 979 ASP cc_start: 0.7686 (m-30) cc_final: 0.7286 (m-30) REVERT: A 992 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7241 (mm110) REVERT: A 1009 THR cc_start: 0.8691 (t) cc_final: 0.8436 (m) REVERT: A 1013 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 1038 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8068 (mmtm) REVERT: B 737 ASP cc_start: 0.8062 (t70) cc_final: 0.7512 (t0) REVERT: B 748 GLU cc_start: 0.7470 (mp0) cc_final: 0.7181 (mp0) REVERT: B 780 GLU cc_start: 0.7410 (tt0) cc_final: 0.7165 (tt0) REVERT: B 820 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7706 (t0) REVERT: B 825 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8183 (mptp) REVERT: B 860 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 1118 ASP cc_start: 0.7376 (p0) cc_final: 0.7169 (p0) REVERT: C 785 VAL cc_start: 0.7790 (t) cc_final: 0.7561 (p) REVERT: C 837 TYR cc_start: 0.8188 (t80) cc_final: 0.7852 (t80) REVERT: C 873 TYR cc_start: 0.8400 (m-80) cc_final: 0.8162 (m-80) REVERT: C 983 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7106 (ttm110) REVERT: C 992 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7319 (mm110) REVERT: C 1031 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8110 (mt-10) outliers start: 47 outliers final: 31 residues processed: 322 average time/residue: 2.7452 time to fit residues: 947.5513 Evaluate side-chains 335 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 299 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 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 1013 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL 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 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 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 935 GLN A 969 ASN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 914 ASN B 935 GLN B 955 ASN B1002 GLN B1005 GLN B1074 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10428 Z= 0.317 Angle : 0.545 5.288 14205 Z= 0.280 Chirality : 0.042 0.177 1671 Planarity : 0.005 0.044 1836 Dihedral : 5.991 59.844 1572 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.64 % Allowed : 16.62 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1305 helix: 1.89 (0.21), residues: 609 sheet: -0.00 (0.34), residues: 189 loop : -0.80 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 PHE 0.012 0.001 PHE A 888 TYR 0.012 0.001 TYR C 904 ARG 0.005 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 299 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 VAL cc_start: 0.8796 (t) cc_final: 0.8455 (m) REVERT: A 776 LYS cc_start: 0.8439 (tttm) cc_final: 0.8198 (tttm) REVERT: A 780 GLU cc_start: 0.7414 (tt0) cc_final: 0.7175 (mt-10) REVERT: A 824 ASN cc_start: 0.8583 (m-40) cc_final: 0.8342 (m110) REVERT: A 992 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7259 (mm110) REVERT: A 1009 THR cc_start: 0.8685 (t) cc_final: 0.8475 (m) REVERT: A 1013 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 1038 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8067 (mmtm) REVERT: B 748 GLU cc_start: 0.7473 (mp0) cc_final: 0.7150 (mp0) REVERT: B 780 GLU cc_start: 0.7336 (tt0) cc_final: 0.7086 (tt0) REVERT: B 820 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7659 (t0) REVERT: B 825 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8155 (mptp) REVERT: B 860 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8382 (t) REVERT: B 1118 ASP cc_start: 0.7385 (p0) cc_final: 0.7115 (p0) REVERT: C 748 GLU cc_start: 0.7570 (mp0) cc_final: 0.7275 (mp0) REVERT: C 837 TYR cc_start: 0.8211 (t80) cc_final: 0.7902 (t80) REVERT: C 860 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8253 (t) REVERT: C 873 TYR cc_start: 0.8389 (m-80) cc_final: 0.8157 (m-80) REVERT: C 992 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7342 (mm110) REVERT: C 1031 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8049 (mt-10) outliers start: 41 outliers final: 27 residues processed: 314 average time/residue: 2.6694 time to fit residues: 899.6796 Evaluate side-chains 328 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 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 745 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL 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 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN B 895 GLN B 914 ASN B1002 GLN B1074 ASN C 779 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10428 Z= 0.390 Angle : 0.571 5.914 14205 Z= 0.295 Chirality : 0.044 0.186 1671 Planarity : 0.005 0.043 1836 Dihedral : 6.031 58.926 1572 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.64 % Allowed : 16.89 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1305 helix: 1.79 (0.21), residues: 618 sheet: 0.14 (0.36), residues: 159 loop : -0.71 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.014 0.002 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.004 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 294 time to evaluate : 1.524 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: symmetry clash REVERT: A 776 LYS cc_start: 0.8444 (tttm) cc_final: 0.8182 (tttm) REVERT: A 780 GLU cc_start: 0.7422 (tt0) cc_final: 0.7172 (mt-10) REVERT: A 820 ASP cc_start: 0.7922 (t0) cc_final: 0.7523 (m-30) REVERT: A 824 ASN cc_start: 0.8602 (m-40) cc_final: 0.8356 (m110) REVERT: A 992 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7253 (mm110) REVERT: A 1009 THR cc_start: 0.8670 (t) cc_final: 0.8441 (m) REVERT: A 1013 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 1038 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8070 (mmtm) REVERT: A 1045 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7970 (mmmm) REVERT: B 748 GLU cc_start: 0.7482 (mp0) cc_final: 0.7176 (mp0) REVERT: B 780 GLU cc_start: 0.7342 (tt0) cc_final: 0.7093 (tt0) REVERT: B 820 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 825 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8166 (mptp) REVERT: B 860 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (t) REVERT: B 1118 ASP cc_start: 0.7373 (p0) cc_final: 0.7102 (p0) REVERT: C 748 GLU cc_start: 0.7573 (mp0) cc_final: 0.7226 (mp0) REVERT: C 837 TYR cc_start: 0.8222 (t80) cc_final: 0.7901 (t80) REVERT: C 860 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8286 (t) REVERT: C 873 TYR cc_start: 0.8391 (m-80) cc_final: 0.8180 (m-80) REVERT: C 992 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7055 (mm110) REVERT: C 1031 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8081 (mt-10) outliers start: 41 outliers final: 25 residues processed: 309 average time/residue: 2.7434 time to fit residues: 912.3581 Evaluate side-chains 321 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 290 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 901 GLN A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN B 895 GLN B 914 ASN B 955 ASN B1002 GLN B1005 GLN B1074 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10428 Z= 0.453 Angle : 0.588 4.585 14205 Z= 0.305 Chirality : 0.045 0.188 1671 Planarity : 0.005 0.044 1836 Dihedral : 6.123 57.682 1572 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.64 % Allowed : 17.24 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1305 helix: 1.75 (0.21), residues: 618 sheet: 0.17 (0.35), residues: 159 loop : -0.81 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.016 0.002 PHE A 888 TYR 0.014 0.002 TYR C1067 ARG 0.004 0.001 ARG B 765 *********************** 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 331 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 290 time to evaluate : 1.532 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 776 LYS cc_start: 0.8445 (tttm) cc_final: 0.8167 (tttm) REVERT: A 780 GLU cc_start: 0.7422 (tt0) cc_final: 0.7157 (mt-10) REVERT: A 824 ASN cc_start: 0.8604 (m-40) cc_final: 0.8363 (m110) REVERT: A 992 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7247 (mm110) REVERT: A 1009 THR cc_start: 0.8683 (t) cc_final: 0.8449 (m) REVERT: A 1013 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 1038 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8079 (mmtm) REVERT: A 1045 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7985 (mmmm) REVERT: B 748 GLU cc_start: 0.7485 (mp0) cc_final: 0.7179 (mp0) REVERT: B 780 GLU cc_start: 0.7340 (tt0) cc_final: 0.7097 (tt0) REVERT: B 820 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7742 (t0) REVERT: B 825 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8166 (mptp) REVERT: B 860 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8378 (t) REVERT: B 1118 ASP cc_start: 0.7355 (p0) cc_final: 0.7060 (p0) REVERT: C 737 ASP cc_start: 0.8144 (t0) cc_final: 0.7807 (t0) REVERT: C 748 GLU cc_start: 0.7570 (mp0) cc_final: 0.7247 (mp0) REVERT: C 837 TYR cc_start: 0.8221 (t80) cc_final: 0.7866 (t80) REVERT: C 918 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7285 (mt-10) REVERT: C 992 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7273 (mm110) REVERT: C 1031 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8106 (mt-10) outliers start: 41 outliers final: 26 residues processed: 305 average time/residue: 2.7408 time to fit residues: 895.6181 Evaluate side-chains 320 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 289 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 109 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 969 ASN A1002 GLN B 836 GLN B 895 GLN B 914 ASN B1074 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10428 Z= 0.242 Angle : 0.528 4.359 14205 Z= 0.270 Chirality : 0.041 0.170 1671 Planarity : 0.004 0.042 1836 Dihedral : 5.880 56.463 1572 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.11 % Allowed : 17.60 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1305 helix: 2.01 (0.21), residues: 609 sheet: 0.20 (0.35), residues: 159 loop : -0.76 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 991 HIS 0.003 0.001 HIS C1064 PHE 0.011 0.001 PHE C1121 TYR 0.011 0.001 TYR C 904 ARG 0.004 0.001 ARG C 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 296 time to evaluate : 1.603 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 748 GLU cc_start: 0.7489 (mp0) cc_final: 0.7074 (mp0) REVERT: A 772 VAL cc_start: 0.8787 (t) cc_final: 0.8435 (m) REVERT: A 776 LYS cc_start: 0.8433 (tttm) cc_final: 0.8164 (tttm) REVERT: A 780 GLU cc_start: 0.7380 (tt0) cc_final: 0.7141 (mt-10) REVERT: A 820 ASP cc_start: 0.7877 (t0) cc_final: 0.7437 (m-30) REVERT: A 824 ASN cc_start: 0.8610 (m-40) cc_final: 0.8356 (m110) REVERT: A 992 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7270 (mm110) REVERT: A 993 ILE cc_start: 0.8171 (tt) cc_final: 0.7928 (mm) REVERT: A 1002 GLN cc_start: 0.8254 (mm110) cc_final: 0.7931 (mm110) REVERT: A 1013 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 1038 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8069 (mmtm) REVERT: A 1045 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7992 (mmmm) REVERT: B 748 GLU cc_start: 0.7446 (mp0) cc_final: 0.7138 (mp0) REVERT: B 780 GLU cc_start: 0.7333 (tt0) cc_final: 0.7070 (tt0) REVERT: B 820 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7671 (t0) REVERT: B 825 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8154 (mptp) REVERT: B 860 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 1118 ASP cc_start: 0.7340 (p0) cc_final: 0.7041 (p0) REVERT: C 737 ASP cc_start: 0.8106 (t0) cc_final: 0.7861 (t0) REVERT: C 748 GLU cc_start: 0.7556 (mp0) cc_final: 0.7209 (mp0) REVERT: C 837 TYR cc_start: 0.8224 (t80) cc_final: 0.7831 (t80) REVERT: C 918 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7219 (mt-10) REVERT: C 992 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7291 (mm110) REVERT: C 1031 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7990 (mt-10) outliers start: 35 outliers final: 23 residues processed: 308 average time/residue: 2.6309 time to fit residues: 870.1466 Evaluate side-chains 322 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 294 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE 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 825 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 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 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 0.0670 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 935 GLN A1002 GLN B 836 GLN B 872 GLN B 895 GLN B 914 ASN B 955 ASN B1002 GLN C 969 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101759 restraints weight = 36531.528| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.90 r_work: 0.3170 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10428 Z= 0.240 Angle : 0.523 4.788 14205 Z= 0.268 Chirality : 0.041 0.167 1671 Planarity : 0.005 0.099 1836 Dihedral : 5.815 55.888 1572 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.67 % Allowed : 18.22 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1305 helix: 2.14 (0.21), residues: 609 sheet: 0.25 (0.35), residues: 159 loop : -0.71 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 991 HIS 0.004 0.001 HIS C1064 PHE 0.010 0.001 PHE C1121 TYR 0.011 0.001 TYR C 904 ARG 0.014 0.001 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12439.78 seconds wall clock time: 213 minutes 35.94 seconds (12815.94 seconds total)