Starting phenix.real_space_refine on Sun Aug 24 01:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5v_42985/08_2025/8v5v_42985.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 10038 2.51 5 N 2652 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15882 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain: "d" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 96} Chain: "g" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 96} Chain: "f" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 978 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "c" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 978 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "e" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 96} Chain: "b" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 978 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.90, per 1000 atoms: 0.25 Number of scatterers: 15882 At special positions: 0 Unit cell: (113.52, 118.8, 146.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 3099 8.00 N 2652 7.00 C 10038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS G 707 " - pdb=" SG CYS E 883 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 788 " - pdb=" SG CYS G 876 " distance=2.03 Simple disulfide: pdb=" SG CYS G 840 " - pdb=" SG CYS G 851 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 707 " - pdb=" SG CYS F 883 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 876 " distance=2.03 Simple disulfide: pdb=" SG CYS E 840 " - pdb=" SG CYS E 851 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 876 " distance=2.03 Simple disulfide: pdb=" SG CYS F 840 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 96 " distance=2.03 Simple disulfide: pdb=" SG CYS f 99 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 99 " - pdb=" SG CYS c 112 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 96 " distance=2.03 Simple disulfide: pdb=" SG CYS b 99 " - pdb=" SG CYS b 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN G1098 " " NAG B 1 " - " ASN E1098 " " NAG C 1 " - " ASN F1098 " " NAG E1301 " - " ASN E 717 " " NAG E1302 " - " ASN E 709 " " NAG E1303 " - " ASN E 801 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E1134 " " NAG F1301 " - " ASN F 717 " " NAG F1302 " - " ASN F 709 " " NAG F1303 " - " ASN F 801 " " NAG F1304 " - " ASN F1074 " " NAG F1305 " - " ASN F1134 " " NAG G1301 " - " ASN G 717 " " NAG G1302 " - " ASN G 709 " " NAG G1303 " - " ASN G 801 " " NAG G1304 " - " ASN G1074 " " NAG G1305 " - " ASN G1134 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 762.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 34 sheets defined 35.0% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'G' and resid 737 through 742 Processing helix chain 'G' and resid 749 through 783 removed outlier: 5.768A pdb=" N SER G 758 " --> pdb=" O LEU G 754 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE G 759 " --> pdb=" O GLN G 755 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS G 760 " --> pdb=" O TYR G 756 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 832 through 842 removed outlier: 4.020A pdb=" N GLY G 842 " --> pdb=" O GLY G 838 " (cutoff:3.500A) Processing helix chain 'G' and resid 847 through 855 removed outlier: 3.758A pdb=" N LYS G 854 " --> pdb=" O ILE G 850 " (cutoff:3.500A) Processing helix chain 'G' and resid 866 through 883 Processing helix chain 'G' and resid 897 through 910 Processing helix chain 'G' and resid 912 through 919 removed outlier: 4.038A pdb=" N LEU G 916 " --> pdb=" O THR G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.593A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 967 Processing helix chain 'G' and resid 976 through 984 removed outlier: 3.534A pdb=" N ILE G 980 " --> pdb=" O VAL G 976 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 981 " --> pdb=" O LEU G 977 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1033 removed outlier: 3.874A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) Processing helix chain 'G' and resid 1140 through 1149 removed outlier: 3.899A pdb=" N GLU G1144 " --> pdb=" O PRO G1140 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE G1148 " --> pdb=" O GLU G1144 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS G1149 " --> pdb=" O LEU G1145 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 749 through 783 removed outlier: 5.774A pdb=" N SER E 758 " --> pdb=" O LEU E 754 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE E 759 " --> pdb=" O GLN E 755 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS E 760 " --> pdb=" O TYR E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 832 through 842 removed outlier: 4.017A pdb=" N GLY E 842 " --> pdb=" O GLY E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 855 removed outlier: 3.770A pdb=" N LYS E 854 " --> pdb=" O ILE E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 883 Processing helix chain 'E' and resid 897 through 910 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.036A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.592A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.512A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.875A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1149 removed outlier: 3.897A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E1148 " --> pdb=" O GLU E1144 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E1149 " --> pdb=" O LEU E1145 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 742 Processing helix chain 'F' and resid 749 through 783 removed outlier: 5.759A pdb=" N SER F 758 " --> pdb=" O LEU F 754 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE F 759 " --> pdb=" O GLN F 755 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS F 760 " --> pdb=" O TYR F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 832 through 842 removed outlier: 4.019A pdb=" N GLY F 842 " --> pdb=" O GLY F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 847 through 855 removed outlier: 3.762A pdb=" N LYS F 854 " --> pdb=" O ILE F 850 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 883 Processing helix chain 'F' and resid 897 through 910 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.042A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.591A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 967 Processing helix chain 'F' and resid 976 through 984 removed outlier: 3.569A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.858A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 996 " --> pdb=" O GLN F 992 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1149 removed outlier: 3.901A pdb=" N GLU F1144 " --> pdb=" O PRO F1140 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F1148 " --> pdb=" O GLU F1144 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS F1149 " --> pdb=" O LEU F1145 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 83 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'f' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR f 91 " --> pdb=" O SER f 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 91 removed outlier: 3.997A pdb=" N THR c 91 " --> pdb=" O SER c 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 83 Processing helix chain 'b' and resid 87 through 91 removed outlier: 3.991A pdb=" N THR b 91 " --> pdb=" O SER b 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 711 through 714 removed outlier: 4.148A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 717 through 728 removed outlier: 3.946A pdb=" N MET G1050 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 717 through 728 Processing sheet with id=AA4, first strand: chain 'G' and resid 733 through 735 removed outlier: 4.277A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 796 through 797 Processing sheet with id=AA6, first strand: chain 'G' and resid 1120 through 1122 Processing sheet with id=AA7, first strand: chain 'E' and resid 711 through 714 Processing sheet with id=AA8, first strand: chain 'E' and resid 717 through 728 removed outlier: 3.947A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 717 through 728 Processing sheet with id=AB1, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.277A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 796 through 797 Processing sheet with id=AB3, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'F' and resid 711 through 714 removed outlier: 4.095A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 717 through 728 removed outlier: 3.942A pdb=" N MET F1050 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 717 through 728 Processing sheet with id=AB8, first strand: chain 'F' and resid 733 through 735 removed outlier: 4.275A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 796 through 797 removed outlier: 3.500A pdb=" N PHE F 800 " --> pdb=" O PHE F 797 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'd' and resid 53 through 54 removed outlier: 5.664A pdb=" N LEU d 46 " --> pdb=" O GLN d 37 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN d 37 " --> pdb=" O LEU d 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL d 48 " --> pdb=" O TRP d 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'g' and resid 53 through 54 removed outlier: 5.665A pdb=" N LEU g 46 " --> pdb=" O GLN g 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN g 37 " --> pdb=" O LEU g 46 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL g 48 " --> pdb=" O TRP g 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'f' and resid 10 through 11 removed outlier: 3.802A pdb=" N THR f 124 " --> pdb=" O GLU f 10 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE f 34 " --> pdb=" O TRP f 50 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP f 50 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP f 36 " --> pdb=" O MET f 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 10 through 11 removed outlier: 3.802A pdb=" N THR f 124 " --> pdb=" O GLU f 10 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE f 116 " --> pdb=" O ARG f 98 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY f 100 " --> pdb=" O PHE f 114 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE f 114 " --> pdb=" O GLY f 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'c' and resid 10 through 11 removed outlier: 3.783A pdb=" N THR c 124 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE c 34 " --> pdb=" O TRP c 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP c 50 " --> pdb=" O ILE c 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP c 36 " --> pdb=" O MET c 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 10 through 11 removed outlier: 3.783A pdb=" N THR c 124 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE c 116 " --> pdb=" O ARG c 98 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY c 100 " --> pdb=" O PHE c 114 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE c 114 " --> pdb=" O GLY c 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'e' and resid 53 through 54 removed outlier: 3.514A pdb=" N THR e 53 " --> pdb=" O TYR e 49 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU e 46 " --> pdb=" O GLN e 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN e 37 " --> pdb=" O LEU e 46 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL e 48 " --> pdb=" O TRP e 35 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'b' and resid 10 through 11 removed outlier: 3.791A pdb=" N THR b 124 " --> pdb=" O GLU b 10 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE b 34 " --> pdb=" O TRP b 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP b 50 " --> pdb=" O ILE b 34 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP b 36 " --> pdb=" O MET b 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 10 through 11 removed outlier: 3.791A pdb=" N THR b 124 " --> pdb=" O GLU b 10 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE b 116 " --> pdb=" O ARG b 98 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLY b 100 " --> pdb=" O PHE b 114 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE b 114 " --> pdb=" O GLY b 100 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2229 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: 3.13 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5121 1.34 - 1.46: 3945 1.46 - 1.58: 7047 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 16239 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 NAG E1304 " pdb=" O5 NAG E1304 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG F1304 " pdb=" O5 NAG F1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 16234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 21776 1.54 - 3.09: 282 3.09 - 4.63: 27 4.63 - 6.18: 9 6.18 - 7.72: 1 Bond angle restraints: 22095 Sorted by residual: angle pdb=" CA LEU F1001 " pdb=" CB LEU F1001 " pdb=" CG LEU F1001 " ideal model delta sigma weight residual 116.30 124.02 -7.72 3.50e+00 8.16e-02 4.87e+00 angle pdb=" N ILE c 76 " pdb=" CA ILE c 76 " pdb=" C ILE c 76 " ideal model delta sigma weight residual 113.10 110.98 2.12 9.70e-01 1.06e+00 4.80e+00 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" C PRO g 96 " ideal model delta sigma weight residual 110.70 113.21 -2.51 1.22e+00 6.72e-01 4.22e+00 angle pdb=" N PRO d 96 " pdb=" CA PRO d 96 " pdb=" C PRO d 96 " ideal model delta sigma weight residual 110.70 113.18 -2.48 1.22e+00 6.72e-01 4.12e+00 angle pdb=" N PRO e 96 " pdb=" CA PRO e 96 " pdb=" C PRO e 96 " ideal model delta sigma weight residual 110.70 113.15 -2.45 1.22e+00 6.72e-01 4.05e+00 ... (remaining 22090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 9075 15.86 - 31.73: 693 31.73 - 47.59: 174 47.59 - 63.46: 36 63.46 - 79.32: 12 Dihedral angle restraints: 9990 sinusoidal: 4143 harmonic: 5847 Sorted by residual: dihedral pdb=" CB CYS e 23 " pdb=" SG CYS e 23 " pdb=" SG CYS e 88 " pdb=" CB CYS e 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.97 -48.97 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS d 23 " pdb=" SG CYS d 23 " pdb=" SG CYS d 88 " pdb=" CB CYS d 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.88 -48.88 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS g 23 " pdb=" SG CYS g 23 " pdb=" SG CYS g 88 " pdb=" CB CYS g 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.85 -48.85 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 9987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1609 0.027 - 0.053: 540 0.053 - 0.080: 182 0.080 - 0.106: 179 0.106 - 0.133: 34 Chirality restraints: 2544 Sorted by residual: chirality pdb=" C1 NAG E1304 " pdb=" ND2 ASN E1074 " pdb=" C2 NAG E1304 " pdb=" O5 NAG E1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE G1081 " pdb=" N ILE G1081 " pdb=" C ILE G1081 " pdb=" CB ILE G1081 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE E1081 " pdb=" N ILE E1081 " pdb=" C ILE E1081 " pdb=" CB ILE E1081 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 2541 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 896 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO E 897 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 897 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 897 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 896 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO F 897 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 897 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 897 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 896 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO G 897 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 897 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 897 " -0.019 5.00e-02 4.00e+02 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3879 2.80 - 3.33: 14140 3.33 - 3.85: 26280 3.85 - 4.38: 28924 4.38 - 4.90: 51244 Nonbonded interactions: 124467 Sorted by model distance: nonbonded pdb=" OH TYR F 837 " pdb=" OD1 ASP F 848 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR E 837 " pdb=" OD1 ASP E 848 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR G 837 " pdb=" OD1 ASP G 848 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR G1116 " pdb=" OD1 ASP G1118 " model vdw 2.355 3.040 nonbonded pdb=" OG1 THR F1116 " pdb=" OD1 ASP F1118 " model vdw 2.357 3.040 ... (remaining 124462 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'f' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'g' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.002 0.041 16289 Z= 0.123 Angle : 0.504 9.537 22216 Z= 0.242 Chirality : 0.039 0.133 2544 Planarity : 0.003 0.037 2835 Dihedral : 12.046 79.322 6159 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.19), residues: 2007 helix: 2.74 (0.21), residues: 609 sheet: 0.65 (0.23), residues: 531 loop : -0.50 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G1014 TYR 0.008 0.001 TYR E1067 PHE 0.009 0.001 PHE F 906 TRP 0.005 0.001 TRP b 50 HIS 0.001 0.000 HIS c 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (16239) covalent geometry : angle 0.44626 (22095) SS BOND : bond 0.00147 ( 29) SS BOND : angle 0.35143 ( 58) hydrogen bonds : bond 0.12059 ( 767) hydrogen bonds : angle 4.61163 ( 2229) link_BETA1-4 : bond 0.01826 ( 3) link_BETA1-4 : angle 6.24876 ( 9) link_NAG-ASN : bond 0.00044 ( 18) link_NAG-ASN : angle 4.05515 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.758 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: E 869 MET cc_start: 0.9223 (mtt) cc_final: 0.8792 (mpp) REVERT: F 888 PHE cc_start: 0.9073 (t80) cc_final: 0.8668 (t80) REVERT: d 93 ASN cc_start: 0.8318 (t0) cc_final: 0.8066 (m110) REVERT: f 70 MET cc_start: 0.8618 (mtt) cc_final: 0.8174 (mtt) REVERT: f 83 LEU cc_start: 0.9072 (mt) cc_final: 0.8858 (tm) REVERT: f 87 THR cc_start: 0.8478 (m) cc_final: 0.7529 (p) REVERT: f 90 ASP cc_start: 0.7844 (m-30) cc_final: 0.6794 (m-30) REVERT: f 110 ASP cc_start: 0.8085 (t0) cc_final: 0.7602 (t0) REVERT: c 70 MET cc_start: 0.8817 (mtt) cc_final: 0.8409 (mtp) REVERT: c 86 LEU cc_start: 0.8912 (tp) cc_final: 0.8279 (tt) REVERT: c 87 THR cc_start: 0.8646 (m) cc_final: 0.8311 (p) REVERT: e 78 LEU cc_start: 0.8153 (tp) cc_final: 0.7848 (mp) REVERT: b 70 MET cc_start: 0.8957 (mtt) cc_final: 0.8537 (mtp) REVERT: b 86 LEU cc_start: 0.9052 (tp) cc_final: 0.8552 (tt) REVERT: b 110 ASP cc_start: 0.8199 (t0) cc_final: 0.7666 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.9016 time to fit residues: 207.8246 Evaluate side-chains 86 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1002 GLN F1142 GLN d 42 GLN f 59 ASN c 59 ASN e 93 ASN b 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.056429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.040569 restraints weight = 81074.197| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.28 r_work: 0.2937 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16289 Z= 0.128 Angle : 0.575 7.900 22216 Z= 0.288 Chirality : 0.041 0.145 2544 Planarity : 0.004 0.047 2835 Dihedral : 3.443 36.039 2616 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.11 % Allowed : 9.37 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.19), residues: 2007 helix: 2.59 (0.21), residues: 630 sheet: 0.65 (0.22), residues: 528 loop : -0.49 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 85 TYR 0.021 0.001 TYR G1138 PHE 0.018 0.001 PHE f 64 TRP 0.017 0.001 TRP b 67 HIS 0.004 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00285 (16239) covalent geometry : angle 0.56195 (22095) SS BOND : bond 0.00170 ( 29) SS BOND : angle 0.53284 ( 58) hydrogen bonds : bond 0.03578 ( 767) hydrogen bonds : angle 4.11233 ( 2229) link_BETA1-4 : bond 0.01648 ( 3) link_BETA1-4 : angle 5.28379 ( 9) link_NAG-ASN : bond 0.00129 ( 18) link_NAG-ASN : angle 1.42575 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.442 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: E 869 MET cc_start: 0.9411 (mtt) cc_final: 0.8962 (mpp) REVERT: F 888 PHE cc_start: 0.9097 (t80) cc_final: 0.8645 (t80) REVERT: d 4 MET cc_start: 0.7545 (mmm) cc_final: 0.7156 (tpt) REVERT: d 93 ASN cc_start: 0.8536 (t0) cc_final: 0.8005 (m110) REVERT: f 46 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8720 (pt0) REVERT: f 70 MET cc_start: 0.8467 (mtt) cc_final: 0.8109 (mtt) REVERT: c 46 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8558 (pt0) REVERT: c 63 LYS cc_start: 0.9473 (ptmm) cc_final: 0.9185 (ptmm) REVERT: c 110 ASP cc_start: 0.8787 (t0) cc_final: 0.8563 (t0) REVERT: e 36 TYR cc_start: 0.8070 (m-80) cc_final: 0.7654 (m-80) REVERT: e 54 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7706 (ttp-110) REVERT: b 23 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8014 (tppp) REVERT: b 110 ASP cc_start: 0.8951 (t0) cc_final: 0.8330 (t0) outliers start: 19 outliers final: 4 residues processed: 109 average time/residue: 0.7015 time to fit residues: 82.6856 Evaluate side-chains 87 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 836 GLN G1088 HIS E1002 GLN E1088 HIS F 836 GLN F1088 HIS d 79 GLN g 79 GLN g 93 ASN f 59 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.053062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.036464 restraints weight = 82137.399| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.30 r_work: 0.2783 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16289 Z= 0.251 Angle : 0.633 10.767 22216 Z= 0.319 Chirality : 0.043 0.171 2544 Planarity : 0.004 0.079 2835 Dihedral : 3.658 29.208 2616 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.51 % Allowed : 10.24 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2007 helix: 2.52 (0.21), residues: 630 sheet: 0.50 (0.22), residues: 519 loop : -0.70 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 18 TYR 0.016 0.002 TYR f 111 PHE 0.016 0.002 PHE E1089 TRP 0.019 0.002 TRP b 67 HIS 0.005 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00563 (16239) covalent geometry : angle 0.61801 (22095) SS BOND : bond 0.00262 ( 29) SS BOND : angle 0.91697 ( 58) hydrogen bonds : bond 0.04373 ( 767) hydrogen bonds : angle 4.33490 ( 2229) link_BETA1-4 : bond 0.01540 ( 3) link_BETA1-4 : angle 5.46528 ( 9) link_NAG-ASN : bond 0.00387 ( 18) link_NAG-ASN : angle 1.65704 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.645 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: G 759 PHE cc_start: 0.8044 (t80) cc_final: 0.7807 (t80) REVERT: G 869 MET cc_start: 0.9233 (mtp) cc_final: 0.9032 (ptm) REVERT: E 759 PHE cc_start: 0.8000 (t80) cc_final: 0.7719 (t80) REVERT: E 869 MET cc_start: 0.9443 (mtt) cc_final: 0.8975 (mpp) REVERT: d 54 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8050 (ttm-80) REVERT: d 93 ASN cc_start: 0.8643 (t0) cc_final: 0.8124 (m110) REVERT: g 78 LEU cc_start: 0.8179 (mp) cc_final: 0.7338 (pp) REVERT: f 70 MET cc_start: 0.8520 (mtt) cc_final: 0.8225 (mtt) REVERT: c 86 LEU cc_start: 0.8986 (tp) cc_final: 0.8642 (tp) REVERT: e 21 LEU cc_start: 0.8732 (mp) cc_final: 0.8252 (tt) REVERT: e 36 TYR cc_start: 0.8235 (m-80) cc_final: 0.7706 (m-80) REVERT: e 54 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8276 (ttm-80) REVERT: b 23 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7978 (tppp) REVERT: b 107 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8494 (t0) REVERT: b 110 ASP cc_start: 0.9046 (t0) cc_final: 0.8479 (t0) outliers start: 26 outliers final: 8 residues processed: 105 average time/residue: 0.6567 time to fit residues: 75.1008 Evaluate side-chains 86 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain f residue 83 LEU Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 87 THR Chi-restraints excluded: chain b residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.054028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.037555 restraints weight = 80731.458| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.27 r_work: 0.2821 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16289 Z= 0.111 Angle : 0.534 8.472 22216 Z= 0.269 Chirality : 0.041 0.138 2544 Planarity : 0.004 0.044 2835 Dihedral : 3.484 29.333 2616 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.87 % Allowed : 12.10 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 2007 helix: 2.57 (0.21), residues: 630 sheet: 0.53 (0.22), residues: 528 loop : -0.68 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 85 TYR 0.014 0.001 TYR E1067 PHE 0.009 0.001 PHE E1121 TRP 0.019 0.001 TRP b 67 HIS 0.002 0.000 HIS b 35 Details of bonding type rmsd covalent geometry : bond 0.00245 (16239) covalent geometry : angle 0.51841 (22095) SS BOND : bond 0.00172 ( 29) SS BOND : angle 0.63396 ( 58) hydrogen bonds : bond 0.03685 ( 767) hydrogen bonds : angle 4.12875 ( 2229) link_BETA1-4 : bond 0.01878 ( 3) link_BETA1-4 : angle 5.59284 ( 9) link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 1.30978 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 759 PHE cc_start: 0.7848 (t80) cc_final: 0.7633 (t80) REVERT: G 869 MET cc_start: 0.9253 (mtp) cc_final: 0.9036 (mtm) REVERT: E 759 PHE cc_start: 0.7883 (t80) cc_final: 0.7603 (t80) REVERT: E 869 MET cc_start: 0.9423 (mtt) cc_final: 0.8937 (mpp) REVERT: d 93 ASN cc_start: 0.8693 (t0) cc_final: 0.8161 (m110) REVERT: f 70 MET cc_start: 0.8432 (mtt) cc_final: 0.8163 (mtt) REVERT: c 110 ASP cc_start: 0.8769 (t0) cc_final: 0.7566 (t70) REVERT: e 54 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8163 (ttm110) REVERT: e 93 ASN cc_start: 0.8647 (t0) cc_final: 0.8380 (m-40) REVERT: b 23 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8031 (tppp) REVERT: b 107 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8491 (t0) REVERT: b 110 ASP cc_start: 0.9012 (t0) cc_final: 0.8479 (t0) outliers start: 15 outliers final: 5 residues processed: 88 average time/residue: 0.6309 time to fit residues: 61.0258 Evaluate side-chains 81 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 87 THR Chi-restraints excluded: chain b residue 107 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 174 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.036717 restraints weight = 81245.562| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.31 r_work: 0.2796 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16289 Z= 0.158 Angle : 0.546 9.998 22216 Z= 0.274 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.043 2835 Dihedral : 3.527 27.586 2616 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.99 % Allowed : 12.74 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2007 helix: 2.56 (0.21), residues: 624 sheet: 0.46 (0.22), residues: 528 loop : -0.72 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 85 TYR 0.015 0.001 TYR E1067 PHE 0.009 0.001 PHE E1089 TRP 0.019 0.001 TRP b 67 HIS 0.005 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00354 (16239) covalent geometry : angle 0.53040 (22095) SS BOND : bond 0.00215 ( 29) SS BOND : angle 0.75556 ( 58) hydrogen bonds : bond 0.03756 ( 767) hydrogen bonds : angle 4.17784 ( 2229) link_BETA1-4 : bond 0.01836 ( 3) link_BETA1-4 : angle 5.48668 ( 9) link_NAG-ASN : bond 0.00154 ( 18) link_NAG-ASN : angle 1.42141 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 759 PHE cc_start: 0.7941 (t80) cc_final: 0.7717 (t80) REVERT: G 869 MET cc_start: 0.9253 (mtp) cc_final: 0.8970 (mtm) REVERT: E 759 PHE cc_start: 0.7980 (t80) cc_final: 0.7728 (t80) REVERT: E 869 MET cc_start: 0.9410 (mtt) cc_final: 0.8943 (mpp) REVERT: d 21 LEU cc_start: 0.8601 (mp) cc_final: 0.8233 (tt) REVERT: d 93 ASN cc_start: 0.8740 (t0) cc_final: 0.8159 (m110) REVERT: f 70 MET cc_start: 0.8520 (mtt) cc_final: 0.8277 (mtt) REVERT: c 86 LEU cc_start: 0.8815 (tp) cc_final: 0.8471 (tp) REVERT: c 110 ASP cc_start: 0.8874 (t0) cc_final: 0.7770 (t70) REVERT: e 4 MET cc_start: 0.7224 (mmm) cc_final: 0.6866 (mmm) REVERT: e 54 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8313 (ttm110) REVERT: e 93 ASN cc_start: 0.8641 (t0) cc_final: 0.8396 (m-40) REVERT: b 23 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8072 (tppp) REVERT: b 110 ASP cc_start: 0.9020 (t0) cc_final: 0.8498 (t0) outliers start: 17 outliers final: 6 residues processed: 91 average time/residue: 0.6205 time to fit residues: 61.4692 Evaluate side-chains 80 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 50 optimal weight: 0.9980 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.053425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036951 restraints weight = 80630.365| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.26 r_work: 0.2802 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16289 Z= 0.120 Angle : 0.526 8.195 22216 Z= 0.266 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.043 2835 Dihedral : 3.490 27.447 2616 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.93 % Allowed : 13.15 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2007 helix: 2.56 (0.21), residues: 624 sheet: 0.42 (0.21), residues: 543 loop : -0.72 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 85 TYR 0.014 0.001 TYR E1067 PHE 0.009 0.001 PHE E1121 TRP 0.015 0.001 TRP b 67 HIS 0.002 0.000 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00270 (16239) covalent geometry : angle 0.51059 (22095) SS BOND : bond 0.00227 ( 29) SS BOND : angle 0.55700 ( 58) hydrogen bonds : bond 0.03592 ( 767) hydrogen bonds : angle 4.11232 ( 2229) link_BETA1-4 : bond 0.01912 ( 3) link_BETA1-4 : angle 5.54934 ( 9) link_NAG-ASN : bond 0.00088 ( 18) link_NAG-ASN : angle 1.31651 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 759 PHE cc_start: 0.7909 (t80) cc_final: 0.7674 (t80) REVERT: G 869 MET cc_start: 0.9222 (mtp) cc_final: 0.8933 (mtm) REVERT: E 759 PHE cc_start: 0.7969 (t80) cc_final: 0.7708 (t80) REVERT: E 869 MET cc_start: 0.9400 (mtt) cc_final: 0.8933 (mpp) REVERT: d 21 LEU cc_start: 0.8591 (mp) cc_final: 0.8228 (tt) REVERT: d 54 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8226 (ttm-80) REVERT: d 93 ASN cc_start: 0.8716 (t0) cc_final: 0.8161 (m110) REVERT: f 81 MET cc_start: 0.8856 (tmm) cc_final: 0.8496 (ttp) REVERT: c 110 ASP cc_start: 0.8867 (t0) cc_final: 0.7789 (t70) REVERT: e 4 MET cc_start: 0.7196 (mmm) cc_final: 0.6881 (mmm) REVERT: e 54 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8530 (ttm-80) REVERT: e 93 ASN cc_start: 0.8625 (t0) cc_final: 0.8390 (m-40) REVERT: b 110 ASP cc_start: 0.8986 (t0) cc_final: 0.8484 (t0) outliers start: 16 outliers final: 4 residues processed: 91 average time/residue: 0.6463 time to fit residues: 64.7916 Evaluate side-chains 77 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain e residue 54 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.053439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036959 restraints weight = 80622.092| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.26 r_work: 0.2800 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16289 Z= 0.117 Angle : 0.518 8.144 22216 Z= 0.261 Chirality : 0.041 0.145 2544 Planarity : 0.004 0.043 2835 Dihedral : 3.467 26.993 2616 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.81 % Allowed : 13.85 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 2007 helix: 2.57 (0.21), residues: 630 sheet: 0.36 (0.21), residues: 549 loop : -0.65 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG f 85 TYR 0.014 0.001 TYR E1067 PHE 0.010 0.001 PHE F 759 TRP 0.017 0.001 TRP f 67 HIS 0.003 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00261 (16239) covalent geometry : angle 0.50226 (22095) SS BOND : bond 0.00200 ( 29) SS BOND : angle 0.52159 ( 58) hydrogen bonds : bond 0.03502 ( 767) hydrogen bonds : angle 4.08091 ( 2229) link_BETA1-4 : bond 0.01897 ( 3) link_BETA1-4 : angle 5.50474 ( 9) link_NAG-ASN : bond 0.00068 ( 18) link_NAG-ASN : angle 1.31610 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 759 PHE cc_start: 0.7943 (t80) cc_final: 0.7689 (t80) REVERT: G 869 MET cc_start: 0.9213 (mtp) cc_final: 0.8941 (mtm) REVERT: E 759 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7731 (t80) REVERT: E 869 MET cc_start: 0.9407 (mtt) cc_final: 0.8940 (mpp) REVERT: d 21 LEU cc_start: 0.8663 (mp) cc_final: 0.8307 (tt) REVERT: d 54 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8264 (ttm-80) REVERT: d 93 ASN cc_start: 0.8715 (t0) cc_final: 0.8162 (m110) REVERT: f 70 MET cc_start: 0.8726 (mtt) cc_final: 0.8468 (mtt) REVERT: c 110 ASP cc_start: 0.8901 (t0) cc_final: 0.7835 (t70) REVERT: e 4 MET cc_start: 0.7206 (mmm) cc_final: 0.6905 (mmm) REVERT: e 93 ASN cc_start: 0.8626 (t0) cc_final: 0.8391 (m-40) REVERT: b 85 ARG cc_start: 0.7492 (ppt170) cc_final: 0.6263 (ppt170) REVERT: b 110 ASP cc_start: 0.8976 (t0) cc_final: 0.8494 (t0) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.6530 time to fit residues: 62.5043 Evaluate side-chains 79 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain f residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 193 optimal weight: 0.0670 chunk 48 optimal weight: 9.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.035817 restraints weight = 81467.393| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.31 r_work: 0.2763 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16289 Z= 0.207 Angle : 0.581 9.581 22216 Z= 0.294 Chirality : 0.042 0.139 2544 Planarity : 0.004 0.054 2835 Dihedral : 3.637 24.354 2616 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 14.02 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 2007 helix: 2.50 (0.21), residues: 630 sheet: 0.36 (0.21), residues: 537 loop : -0.82 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG c 85 TYR 0.016 0.001 TYR E1067 PHE 0.014 0.001 PHE G 898 TRP 0.055 0.002 TRP b 67 HIS 0.003 0.001 HIS g 38 Details of bonding type rmsd covalent geometry : bond 0.00468 (16239) covalent geometry : angle 0.56611 (22095) SS BOND : bond 0.00219 ( 29) SS BOND : angle 0.67464 ( 58) hydrogen bonds : bond 0.03927 ( 767) hydrogen bonds : angle 4.27505 ( 2229) link_BETA1-4 : bond 0.01758 ( 3) link_BETA1-4 : angle 5.52580 ( 9) link_NAG-ASN : bond 0.00255 ( 18) link_NAG-ASN : angle 1.50315 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.631 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: G 759 PHE cc_start: 0.8020 (t80) cc_final: 0.7749 (t80) REVERT: G 869 MET cc_start: 0.9229 (mtp) cc_final: 0.8950 (mtm) REVERT: E 759 PHE cc_start: 0.8022 (t80) cc_final: 0.7749 (t80) REVERT: E 869 MET cc_start: 0.9411 (mtt) cc_final: 0.8937 (mpp) REVERT: d 21 LEU cc_start: 0.8659 (mp) cc_final: 0.8317 (tt) REVERT: d 54 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (ttm-80) REVERT: e 4 MET cc_start: 0.7103 (mmm) cc_final: 0.6757 (mmm) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.6146 time to fit residues: 56.8382 Evaluate side-chains 80 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 1050 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain g residue 18 ARG Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 42 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.052281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035694 restraints weight = 80623.950| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.28 r_work: 0.2759 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16289 Z= 0.201 Angle : 0.577 10.573 22216 Z= 0.292 Chirality : 0.042 0.145 2544 Planarity : 0.004 0.083 2835 Dihedral : 3.688 22.660 2616 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 14.19 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 2007 helix: 2.45 (0.21), residues: 630 sheet: 0.30 (0.21), residues: 537 loop : -0.80 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG b 85 TYR 0.016 0.001 TYR E1067 PHE 0.013 0.001 PHE F 759 TRP 0.024 0.002 TRP b 67 HIS 0.003 0.001 HIS g 38 Details of bonding type rmsd covalent geometry : bond 0.00453 (16239) covalent geometry : angle 0.56128 (22095) SS BOND : bond 0.00223 ( 29) SS BOND : angle 0.65207 ( 58) hydrogen bonds : bond 0.04012 ( 767) hydrogen bonds : angle 4.29213 ( 2229) link_BETA1-4 : bond 0.01804 ( 3) link_BETA1-4 : angle 5.63217 ( 9) link_NAG-ASN : bond 0.00179 ( 18) link_NAG-ASN : angle 1.46583 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.421 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: G 759 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7767 (t80) REVERT: G 869 MET cc_start: 0.9234 (mtp) cc_final: 0.8953 (mtm) REVERT: E 759 PHE cc_start: 0.8033 (t80) cc_final: 0.7730 (t80) REVERT: E 869 MET cc_start: 0.9403 (mtt) cc_final: 0.8922 (mpp) REVERT: d 21 LEU cc_start: 0.8652 (mp) cc_final: 0.8317 (tt) REVERT: d 54 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8366 (ttm-80) REVERT: e 4 MET cc_start: 0.7080 (mmm) cc_final: 0.6854 (mmm) REVERT: e 21 LEU cc_start: 0.8680 (mp) cc_final: 0.8199 (tt) outliers start: 16 outliers final: 8 residues processed: 84 average time/residue: 0.6631 time to fit residues: 61.1192 Evaluate side-chains 79 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 PHE Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 1050 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain g residue 18 ARG Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 28 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1005 GLN b 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036688 restraints weight = 80255.509| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.30 r_work: 0.2796 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16289 Z= 0.108 Angle : 0.552 8.132 22216 Z= 0.279 Chirality : 0.041 0.155 2544 Planarity : 0.004 0.053 2835 Dihedral : 3.548 23.810 2616 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.41 % Allowed : 14.95 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.19), residues: 2007 helix: 2.49 (0.21), residues: 630 sheet: 0.34 (0.21), residues: 537 loop : -0.76 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 18 TYR 0.015 0.001 TYR E1067 PHE 0.029 0.001 PHE F 759 TRP 0.016 0.001 TRP f 67 HIS 0.002 0.000 HIS b 35 Details of bonding type rmsd covalent geometry : bond 0.00238 (16239) covalent geometry : angle 0.53717 (22095) SS BOND : bond 0.00228 ( 29) SS BOND : angle 0.53333 ( 58) hydrogen bonds : bond 0.03564 ( 767) hydrogen bonds : angle 4.11324 ( 2229) link_BETA1-4 : bond 0.01924 ( 3) link_BETA1-4 : angle 5.62412 ( 9) link_NAG-ASN : bond 0.00157 ( 18) link_NAG-ASN : angle 1.31703 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.635 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: G 759 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7681 (t80) REVERT: G 869 MET cc_start: 0.9190 (mtp) cc_final: 0.8917 (mtm) REVERT: E 759 PHE cc_start: 0.8095 (t80) cc_final: 0.7825 (t80) REVERT: E 869 MET cc_start: 0.9383 (mtt) cc_final: 0.8903 (mpp) REVERT: d 21 LEU cc_start: 0.8643 (mp) cc_final: 0.8298 (tt) REVERT: d 54 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8284 (ttm-80) REVERT: g 81 GLU cc_start: 0.8522 (pm20) cc_final: 0.7791 (pm20) REVERT: e 4 MET cc_start: 0.7097 (mmm) cc_final: 0.6750 (mmm) REVERT: e 21 LEU cc_start: 0.8653 (mp) cc_final: 0.8189 (tt) outliers start: 7 outliers final: 7 residues processed: 82 average time/residue: 0.6778 time to fit residues: 61.2154 Evaluate side-chains 79 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 PHE Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 54 ARG Chi-restraints excluded: chain g residue 18 ARG Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain b residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 191 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035702 restraints weight = 80858.681| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.30 r_work: 0.2762 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16289 Z= 0.202 Angle : 0.585 9.685 22216 Z= 0.296 Chirality : 0.042 0.171 2544 Planarity : 0.004 0.072 2835 Dihedral : 3.626 22.036 2616 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.87 % Allowed : 14.43 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), residues: 2007 helix: 2.48 (0.21), residues: 630 sheet: 0.28 (0.21), residues: 537 loop : -0.79 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 18 TYR 0.021 0.001 TYR b 111 PHE 0.033 0.001 PHE F 759 TRP 0.034 0.001 TRP c 67 HIS 0.003 0.001 HIS g 38 Details of bonding type rmsd covalent geometry : bond 0.00458 (16239) covalent geometry : angle 0.57042 (22095) SS BOND : bond 0.00232 ( 29) SS BOND : angle 0.64450 ( 58) hydrogen bonds : bond 0.03824 ( 767) hydrogen bonds : angle 4.22892 ( 2229) link_BETA1-4 : bond 0.01773 ( 3) link_BETA1-4 : angle 5.58924 ( 9) link_NAG-ASN : bond 0.00211 ( 18) link_NAG-ASN : angle 1.47419 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4583.32 seconds wall clock time: 78 minutes 58.57 seconds (4738.57 seconds total)