Starting phenix.real_space_refine on Tue Jan 21 00:06:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5v_42985/01_2025/8v5v_42985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5v_42985/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v5v_42985/01_2025/8v5v_42985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5v_42985/01_2025/8v5v_42985.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5v_42985/01_2025/8v5v_42985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5v_42985/01_2025/8v5v_42985.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.68, per 1000 atoms: 0.61 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: 3.86 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.17 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: 5.97 Time building geometry restraints manager: 4.45 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: 0.01 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: 1.240 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 37.810 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- 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 16239 Z= 0.153 Angle : 0.446 7.722 22095 Z= 0.229 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (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 TRP 0.005 0.001 TRP b 50 HIS 0.001 0.000 HIS c 35 PHE 0.009 0.001 PHE F 906 TYR 0.008 0.001 TYR E1067 ARG 0.001 0.000 ARG G1014 *********************** 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 : 1.803 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: 0.8062 (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: 0.6796 (m-30) REVERT: f 110 ASP cc_start: 0.8085 (t0) cc_final: 0.7621 (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: 0.8312 (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: 0.8553 (tt) REVERT: b 110 ASP cc_start: 0.8199 (t0) cc_final: 0.7648 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 1.8111 time to fit residues: 417.9033 Evaluate side-chains 85 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1088 HIS E1002 GLN E1088 HIS F1002 GLN F1088 HIS F1142 GLN d 42 GLN e 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.053424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036868 restraints weight = 81730.392| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.27 r_work: 0.2797 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16239 Z= 0.434 Angle : 0.673 8.131 22095 Z= 0.345 Chirality : 0.045 0.150 2544 Planarity : 0.005 0.047 2835 Dihedral : 3.757 30.440 2616 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 9.13 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2007 helix: 2.50 (0.21), residues: 630 sheet: 0.49 (0.22), residues: 519 loop : -0.64 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 67 HIS 0.008 0.002 HIS e 38 PHE 0.021 0.002 PHE E1089 TYR 0.021 0.002 TYR G1138 ARG 0.007 0.001 ARG c 85 *********************** 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 124 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.877 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: G 759 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7769 (t80) REVERT: E 759 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7740 (t80) REVERT: E 869 MET cc_start: 0.9456 (mtt) cc_final: 0.8995 (mpp) REVERT: F 888 PHE cc_start: 0.9116 (t80) cc_final: 0.8604 (t80) REVERT: d 4 MET cc_start: 0.7643 (mmm) cc_final: 0.7318 (tpt) REVERT: d 93 ASN cc_start: 0.8621 (t0) cc_final: 0.8385 (m110) REVERT: f 46 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8747 (pt0) REVERT: f 70 MET cc_start: 0.8652 (mtt) cc_final: 0.8365 (mtt) REVERT: c 110 ASP cc_start: 0.8958 (t0) cc_final: 0.8645 (t0) REVERT: e 36 TYR cc_start: 0.8361 (m-80) cc_final: 0.7810 (m-80) REVERT: e 54 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7735 (ttm110) REVERT: b 23 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8077 (tppp) outliers start: 26 outliers final: 5 residues processed: 110 average time/residue: 1.7527 time to fit residues: 210.0321 Evaluate side-chains 88 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 759 PHE Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain F residue 731 MET 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 69 ILE 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 116 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 79 GLN g 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.054181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.037778 restraints weight = 80341.018| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.26 r_work: 0.2832 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16239 Z= 0.174 Angle : 0.520 8.232 22095 Z= 0.267 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.046 2835 Dihedral : 3.444 30.263 2616 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.99 % Allowed : 10.53 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2007 helix: 2.59 (0.21), residues: 630 sheet: 0.54 (0.22), residues: 528 loop : -0.66 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 67 HIS 0.002 0.001 HIS g 38 PHE 0.011 0.001 PHE b 64 TYR 0.014 0.001 TYR G1138 ARG 0.003 0.000 ARG d 18 *********************** 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 109 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 2.064 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: 0.7853 (t80) cc_final: 0.7627 (t80) REVERT: G 869 MET cc_start: 0.9219 (mtp) cc_final: 0.8997 (mtm) REVERT: E 869 MET cc_start: 0.9409 (mtt) cc_final: 0.8939 (mpp) REVERT: F 888 PHE cc_start: 0.9162 (t80) cc_final: 0.8742 (t80) REVERT: d 54 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8241 (ttm-80) REVERT: d 93 ASN cc_start: 0.8691 (t0) cc_final: 0.8163 (m110) REVERT: g 17 GLU cc_start: 0.9214 (pt0) cc_final: 0.8616 (pm20) REVERT: f 70 MET cc_start: 0.8450 (mtt) cc_final: 0.8039 (mtt) REVERT: c 86 LEU cc_start: 0.8959 (tp) cc_final: 0.8732 (tt) REVERT: e 54 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8104 (ttm110) REVERT: b 23 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7945 (tppp) REVERT: b 110 ASP cc_start: 0.9018 (t0) cc_final: 0.8437 (t0) outliers start: 17 outliers final: 4 residues processed: 100 average time/residue: 1.6193 time to fit residues: 177.5062 Evaluate side-chains 82 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 54 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 0.3980 chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 153 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 836 GLN d 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.053800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037322 restraints weight = 80452.167| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.28 r_work: 0.2814 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.003 0.030 16239 Z= 0.196 Angle : 0.527 8.787 22095 Z= 0.268 Chirality : 0.041 0.125 2544 Planarity : 0.004 0.056 2835 Dihedral : 3.473 29.254 2616 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.16 % Allowed : 12.04 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 2007 helix: 2.61 (0.21), residues: 630 sheet: 0.50 (0.22), residues: 528 loop : -0.67 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 67 HIS 0.002 0.001 HIS F1048 PHE 0.015 0.001 PHE b 64 TYR 0.014 0.001 TYR E1067 ARG 0.005 0.000 ARG b 85 *********************** 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 107 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.998 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: 0.7884 (OUTLIER) cc_final: 0.7647 (t80) REVERT: G 869 MET cc_start: 0.9223 (mtp) cc_final: 0.8996 (mtm) REVERT: E 759 PHE cc_start: 0.7394 (t80) cc_final: 0.7172 (t80) REVERT: E 869 MET cc_start: 0.9422 (mtt) cc_final: 0.8941 (mpp) REVERT: F 888 PHE cc_start: 0.9178 (t80) cc_final: 0.8726 (t80) REVERT: d 93 ASN cc_start: 0.8774 (t0) cc_final: 0.8216 (m110) REVERT: g 17 GLU cc_start: 0.9216 (pt0) cc_final: 0.8430 (pm20) REVERT: g 78 LEU cc_start: 0.8235 (mp) cc_final: 0.7182 (pp) REVERT: f 70 MET cc_start: 0.8462 (mtt) cc_final: 0.8204 (mtt) REVERT: c 86 LEU cc_start: 0.8957 (tp) cc_final: 0.8700 (tt) REVERT: c 110 ASP cc_start: 0.8734 (t0) cc_final: 0.7626 (t70) REVERT: e 4 MET cc_start: 0.7341 (mmm) cc_final: 0.6957 (mmm) REVERT: e 54 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8227 (ttm110) REVERT: e 93 ASN cc_start: 0.8699 (t0) cc_final: 0.8394 (m-40) REVERT: b 23 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (tppp) REVERT: b 110 ASP cc_start: 0.9029 (t0) cc_final: 0.8475 (t0) outliers start: 20 outliers final: 6 residues processed: 97 average time/residue: 1.6572 time to fit residues: 176.4747 Evaluate side-chains 84 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 759 PHE Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain F residue 740 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 836 GLN E 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.052209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035478 restraints weight = 82714.102| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.32 r_work: 0.2750 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16239 Z= 0.360 Angle : 0.592 9.478 22095 Z= 0.303 Chirality : 0.042 0.146 2544 Planarity : 0.004 0.042 2835 Dihedral : 3.756 25.070 2616 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.57 % Allowed : 12.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2007 helix: 2.42 (0.21), residues: 633 sheet: 0.41 (0.21), residues: 531 loop : -0.90 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 67 HIS 0.011 0.001 HIS g 38 PHE 0.014 0.002 PHE E1089 TYR 0.017 0.002 TYR E1067 ARG 0.005 0.001 ARG c 38 *********************** 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 111 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 869 MET cc_start: 0.9251 (mtp) cc_final: 0.9010 (mtm) REVERT: E 759 PHE cc_start: 0.7737 (t80) cc_final: 0.7534 (t80) REVERT: E 869 MET cc_start: 0.9420 (mtt) cc_final: 0.8952 (mpp) REVERT: d 54 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8327 (ttm-80) REVERT: g 17 GLU cc_start: 0.9083 (pt0) cc_final: 0.8672 (pm20) REVERT: f 70 MET cc_start: 0.8621 (mtt) cc_final: 0.8379 (mtt) REVERT: c 110 ASP cc_start: 0.8893 (t0) cc_final: 0.8051 (t70) REVERT: e 4 MET cc_start: 0.7087 (mmm) cc_final: 0.6837 (mmm) REVERT: e 54 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8286 (ttm110) REVERT: e 93 ASN cc_start: 0.8753 (t0) cc_final: 0.8519 (m-40) REVERT: b 23 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8106 (tppp) outliers start: 27 outliers final: 8 residues processed: 102 average time/residue: 1.6590 time to fit residues: 186.0524 Evaluate side-chains 79 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 1096 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 54 ARG 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 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036109 restraints weight = 81551.677| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.28 r_work: 0.2771 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16239 Z= 0.214 Angle : 0.554 12.118 22095 Z= 0.283 Chirality : 0.042 0.162 2544 Planarity : 0.004 0.052 2835 Dihedral : 3.632 24.950 2616 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.11 % Allowed : 13.90 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2007 helix: 2.53 (0.21), residues: 630 sheet: 0.38 (0.21), residues: 534 loop : -0.79 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 67 HIS 0.003 0.001 HIS g 38 PHE 0.014 0.001 PHE c 64 TYR 0.016 0.001 TYR E1067 ARG 0.004 0.000 ARG e 3 *********************** 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 99 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.798 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 869 MET cc_start: 0.9231 (mtp) cc_final: 0.8976 (mtm) REVERT: E 759 PHE cc_start: 0.7880 (t80) cc_final: 0.7668 (t80) REVERT: E 869 MET cc_start: 0.9401 (mtt) cc_final: 0.8934 (mpp) REVERT: d 54 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8396 (ttm-80) REVERT: g 17 GLU cc_start: 0.9080 (pt0) cc_final: 0.8591 (pm20) REVERT: f 81 MET cc_start: 0.8862 (tmm) cc_final: 0.8525 (ttp) REVERT: e 4 MET cc_start: 0.7099 (mmm) cc_final: 0.6816 (mmm) REVERT: e 21 LEU cc_start: 0.8659 (mp) cc_final: 0.8218 (tt) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 1.5759 time to fit residues: 162.6798 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 : 1.793 ------------------------------------------------------------------------------- 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 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 116 ILE Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain b residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 913 GLN E 913 GLN ** E1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.051468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.034709 restraints weight = 82657.447| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.30 r_work: 0.2722 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16239 Z= 0.437 Angle : 0.636 9.873 22095 Z= 0.326 Chirality : 0.043 0.140 2544 Planarity : 0.004 0.042 2835 Dihedral : 3.932 20.104 2616 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.40 % Allowed : 14.02 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2007 helix: 2.31 (0.21), residues: 630 sheet: 0.27 (0.21), residues: 534 loop : -0.97 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 67 HIS 0.005 0.001 HIS g 38 PHE 0.014 0.002 PHE F 759 TYR 0.018 0.002 TYR E1067 ARG 0.011 0.001 ARG b 85 *********************** 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 103 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.861 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: 0.7547 (t80) cc_final: 0.7325 (t80) REVERT: G 869 MET cc_start: 0.9251 (mtp) cc_final: 0.8983 (mtm) REVERT: E 759 PHE cc_start: 0.7888 (t80) cc_final: 0.7681 (t80) REVERT: E 869 MET cc_start: 0.9413 (mtt) cc_final: 0.8941 (mpp) REVERT: d 54 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8259 (ttm-80) REVERT: g 17 GLU cc_start: 0.9114 (pt0) cc_final: 0.8636 (pm20) REVERT: e 4 MET cc_start: 0.7116 (mmm) cc_final: 0.6834 (mmm) outliers start: 24 outliers final: 9 residues processed: 93 average time/residue: 1.6806 time to fit residues: 171.6348 Evaluate side-chains 78 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 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 116 ILE Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain b residue 116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 913 GLN E 913 GLN E1002 GLN e 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.052514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035985 restraints weight = 80396.127| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.24 r_work: 0.2767 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16239 Z= 0.183 Angle : 0.548 8.502 22095 Z= 0.281 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.039 2835 Dihedral : 3.722 21.631 2616 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.76 % Allowed : 14.95 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 2007 helix: 2.51 (0.21), residues: 630 sheet: 0.29 (0.21), residues: 537 loop : -0.90 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 67 HIS 0.002 0.001 HIS E1064 PHE 0.014 0.001 PHE F 759 TYR 0.016 0.001 TYR E1067 ARG 0.020 0.001 ARG c 85 *********************** 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: 13 poor density : 79 time to evaluate : 1.796 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: G 759 PHE cc_start: 0.7473 (t80) cc_final: 0.7256 (t80) REVERT: G 869 MET cc_start: 0.9212 (mtp) cc_final: 0.8952 (mtm) REVERT: E 759 PHE cc_start: 0.7940 (t80) cc_final: 0.7714 (t80) REVERT: E 869 MET cc_start: 0.9385 (mtt) cc_final: 0.8896 (mpp) REVERT: d 21 LEU cc_start: 0.8387 (mp) cc_final: 0.7994 (tt) REVERT: d 54 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8426 (ttm-80) REVERT: g 17 GLU cc_start: 0.9168 (pt0) cc_final: 0.8661 (pm20) REVERT: g 81 GLU cc_start: 0.8355 (pm20) cc_final: 0.7587 (pm20) REVERT: f 81 MET cc_start: 0.8806 (tmm) cc_final: 0.8553 (ttp) REVERT: c 67 TRP cc_start: 0.8763 (m100) cc_final: 0.8389 (m100) REVERT: e 21 LEU cc_start: 0.8672 (mp) cc_final: 0.8179 (tt) outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 1.7331 time to fit residues: 170.2369 Evaluate side-chains 77 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 f residue 116 ILE 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 16 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 123 optimal weight: 0.0030 chunk 185 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.052880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036286 restraints weight = 80768.110| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.32 r_work: 0.2779 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16239 Z= 0.165 Angle : 0.546 9.091 22095 Z= 0.280 Chirality : 0.041 0.203 2544 Planarity : 0.004 0.037 2835 Dihedral : 3.620 22.489 2616 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.64 % Allowed : 15.47 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2007 helix: 2.73 (0.21), residues: 606 sheet: 0.59 (0.21), residues: 510 loop : -0.89 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP f 67 HIS 0.003 0.001 HIS e 38 PHE 0.042 0.001 PHE F 759 TYR 0.015 0.001 TYR E1067 ARG 0.006 0.000 ARG c 85 *********************** 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 88 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.908 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: 0.7639 (t80) cc_final: 0.7409 (t80) REVERT: G 869 MET cc_start: 0.9182 (mtp) cc_final: 0.8911 (mtm) REVERT: E 759 PHE cc_start: 0.7876 (t80) cc_final: 0.7630 (t80) REVERT: E 869 MET cc_start: 0.9383 (mtt) cc_final: 0.8891 (mpp) REVERT: F 759 PHE cc_start: 0.7327 (t80) cc_final: 0.7106 (t80) REVERT: d 21 LEU cc_start: 0.8399 (mp) cc_final: 0.7983 (tt) REVERT: d 54 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8303 (ttm-80) REVERT: g 17 GLU cc_start: 0.9234 (pt0) cc_final: 0.8760 (pm20) REVERT: g 81 GLU cc_start: 0.8428 (pm20) cc_final: 0.7808 (pm20) REVERT: c 67 TRP cc_start: 0.8759 (m100) cc_final: 0.8407 (m100) REVERT: e 4 MET cc_start: 0.6744 (mmm) cc_final: 0.6503 (mmm) REVERT: e 21 LEU cc_start: 0.8660 (mp) cc_final: 0.8176 (tt) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 1.6446 time to fit residues: 157.7356 Evaluate side-chains 78 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 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 f residue 116 ILE 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 35 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 156 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.052301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035657 restraints weight = 82263.656| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.33 r_work: 0.2757 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16239 Z= 0.253 Angle : 0.564 9.940 22095 Z= 0.290 Chirality : 0.042 0.245 2544 Planarity : 0.004 0.044 2835 Dihedral : 3.668 21.128 2616 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.52 % Allowed : 15.65 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2007 helix: 2.65 (0.21), residues: 609 sheet: 0.55 (0.21), residues: 510 loop : -0.96 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP f 67 HIS 0.004 0.001 HIS f 35 PHE 0.060 0.001 PHE F 759 TYR 0.015 0.001 TYR E1067 ARG 0.008 0.000 ARG c 85 ********************** 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 82 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.964 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: 0.7500 (t80) cc_final: 0.7282 (t80) REVERT: G 869 MET cc_start: 0.9205 (mtp) cc_final: 0.8943 (mtm) REVERT: E 759 PHE cc_start: 0.7933 (t80) cc_final: 0.7691 (t80) REVERT: E 869 MET cc_start: 0.9396 (mtt) cc_final: 0.8921 (mpp) REVERT: d 21 LEU cc_start: 0.8473 (mp) cc_final: 0.8026 (tt) REVERT: d 54 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8412 (ttm-80) REVERT: d 93 ASN cc_start: 0.8523 (t0) cc_final: 0.8129 (m-40) REVERT: g 17 GLU cc_start: 0.9252 (pt0) cc_final: 0.8777 (pm20) REVERT: g 81 GLU cc_start: 0.8440 (pm20) cc_final: 0.7845 (pm20) REVERT: f 81 MET cc_start: 0.8708 (ttp) cc_final: 0.8264 (ttm) REVERT: c 67 TRP cc_start: 0.8753 (m100) cc_final: 0.8404 (m100) REVERT: e 4 MET cc_start: 0.6878 (mmm) cc_final: 0.6601 (mmm) REVERT: e 21 LEU cc_start: 0.8665 (mp) cc_final: 0.8183 (tt) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 1.6330 time to fit residues: 148.9794 Evaluate side-chains 77 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 f residue 116 ILE 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 187 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.052284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035638 restraints weight = 81275.101| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.32 r_work: 0.2757 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16239 Z= 0.249 Angle : 0.565 9.769 22095 Z= 0.290 Chirality : 0.042 0.131 2544 Planarity : 0.004 0.068 2835 Dihedral : 3.711 20.794 2616 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.58 % Allowed : 15.59 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2007 helix: 2.59 (0.21), residues: 609 sheet: 0.54 (0.21), residues: 510 loop : -0.99 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP b 67 HIS 0.002 0.001 HIS g 38 PHE 0.039 0.001 PHE F 759 TYR 0.016 0.001 TYR E1067 ARG 0.020 0.001 ARG d 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10121.85 seconds wall clock time: 183 minutes 15.28 seconds (10995.28 seconds total)