Starting phenix.real_space_refine on Sat May 17 18:42:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5v_42985/05_2025/8v5v_42985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5v_42985/05_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_42985/05_2025/8v5v_42985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5v_42985/05_2025/8v5v_42985.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5v_42985/05_2025/8v5v_42985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5v_42985/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.33, per 1000 atoms: 0.59 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: 4.00 Conformation dependent library (CDL) restraints added in 1.9 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: 2.11 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: 5.36 Time building geometry restraints manager: 4.61 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: 1.170 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.390 Find NCS groups from input model: 0.560 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.900 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 18) link_NAG-ASN : angle 4.05515 ( 54) link_BETA1-4 : bond 0.01826 ( 3) link_BETA1-4 : angle 6.24876 ( 9) hydrogen bonds : bond 0.12059 ( 767) hydrogen bonds : angle 4.61163 ( 2229) SS BOND : bond 0.00147 ( 29) SS BOND : angle 0.35143 ( 58) covalent geometry : bond 0.00232 (16239) covalent geometry : angle 0.44626 (22095) *********************** 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 : 1.821 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: 1.6843 time to fit residues: 389.6918 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 : 1.763 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 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: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.053898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037403 restraints weight = 81542.297| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.28 r_work: 0.2817 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16289 Z= 0.242 Angle : 0.659 8.212 22216 Z= 0.334 Chirality : 0.044 0.158 2544 Planarity : 0.005 0.045 2835 Dihedral : 3.717 30.293 2616 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.51 % Allowed : 8.73 % Favored : 89.76 % 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: 2.51 (0.21), residues: 630 sheet: 0.44 (0.21), residues: 528 loop : -0.62 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 67 HIS 0.008 0.002 HIS e 38 PHE 0.020 0.002 PHE E1089 TYR 0.022 0.001 TYR G1138 ARG 0.010 0.001 ARG c 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 18) link_NAG-ASN : angle 1.46014 ( 54) link_BETA1-4 : bond 0.01589 ( 3) link_BETA1-4 : angle 5.29737 ( 9) hydrogen bonds : bond 0.04202 ( 767) hydrogen bonds : angle 4.35282 ( 2229) SS BOND : bond 0.00233 ( 29) SS BOND : angle 0.87814 ( 58) covalent geometry : bond 0.00546 (16239) covalent geometry : angle 0.64638 (22095) *********************** 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 126 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 2.105 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: 0.7907 (OUTLIER) cc_final: 0.7700 (t80) REVERT: E 759 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7726 (t80) REVERT: E 869 MET cc_start: 0.9448 (mtt) cc_final: 0.8985 (mpp) REVERT: E 900 MET cc_start: 0.9348 (mmm) cc_final: 0.9138 (mtp) REVERT: F 888 PHE cc_start: 0.9105 (t80) cc_final: 0.8584 (t80) REVERT: d 4 MET cc_start: 0.7693 (mmm) cc_final: 0.7439 (tpt) REVERT: d 93 ASN cc_start: 0.8588 (t0) cc_final: 0.8369 (m110) REVERT: g 17 GLU cc_start: 0.9094 (tt0) cc_final: 0.8890 (pt0) REVERT: g 78 LEU cc_start: 0.8394 (mp) cc_final: 0.7469 (pp) REVERT: f 46 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8753 (pt0) REVERT: f 70 MET cc_start: 0.8631 (mtt) cc_final: 0.8332 (mtt) REVERT: c 63 LYS cc_start: 0.9498 (ptmm) cc_final: 0.9270 (ptmm) REVERT: c 110 ASP cc_start: 0.8925 (t0) cc_final: 0.8615 (t0) REVERT: e 36 TYR cc_start: 0.8412 (m-80) cc_final: 0.7942 (m-80) REVERT: e 54 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7869 (ttm110) REVERT: b 23 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (tppp) outliers start: 26 outliers final: 5 residues processed: 110 average time/residue: 1.6417 time to fit residues: 197.4129 Evaluate side-chains 91 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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: 9.9990 chunk 164 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 836 GLN F 836 GLN d 79 GLN g 79 GLN g 93 ASN e 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.053201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036681 restraints weight = 81042.335| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.27 r_work: 0.2790 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16289 Z= 0.196 Angle : 0.567 8.662 22216 Z= 0.287 Chirality : 0.042 0.130 2544 Planarity : 0.004 0.047 2835 Dihedral : 3.548 28.143 2616 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.45 % Allowed : 10.53 % Favored : 88.02 % 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: 1.00 (0.19), residues: 2007 helix: 2.55 (0.21), residues: 630 sheet: 0.53 (0.22), residues: 519 loop : -0.69 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 67 HIS 0.004 0.001 HIS g 38 PHE 0.012 0.001 PHE E1062 TYR 0.016 0.001 TYR E1067 ARG 0.005 0.001 ARG e 3 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 18) link_NAG-ASN : angle 1.51872 ( 54) link_BETA1-4 : bond 0.01921 ( 3) link_BETA1-4 : angle 5.70231 ( 9) hydrogen bonds : bond 0.04062 ( 767) hydrogen bonds : angle 4.26471 ( 2229) SS BOND : bond 0.00195 ( 29) SS BOND : angle 0.66194 ( 58) covalent geometry : bond 0.00440 (16239) covalent geometry : angle 0.55015 (22095) *********************** 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 116 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.800 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: G 759 PHE cc_start: 0.7969 (t80) cc_final: 0.7735 (t80) REVERT: G 869 MET cc_start: 0.9259 (mtp) cc_final: 0.9024 (mtm) REVERT: E 759 PHE cc_start: 0.8012 (t80) cc_final: 0.7811 (t80) REVERT: E 869 MET cc_start: 0.9426 (mtt) cc_final: 0.8943 (mpp) REVERT: d 54 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8229 (ttm-80) REVERT: d 93 ASN cc_start: 0.8760 (t0) cc_final: 0.8504 (m110) REVERT: c 86 LEU cc_start: 0.8977 (tp) cc_final: 0.8707 (tp) REVERT: e 54 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8147 (ttm110) REVERT: b 23 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7938 (tppp) REVERT: b 107 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8550 (t0) outliers start: 25 outliers final: 4 residues processed: 104 average time/residue: 1.4129 time to fit residues: 162.2256 Evaluate side-chains 85 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 731 MET Chi-restraints excluded: chain G residue 1104 VAL 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 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 192 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.053448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036916 restraints weight = 80387.357| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.27 r_work: 0.2798 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16289 Z= 0.136 Angle : 0.548 9.162 22216 Z= 0.274 Chirality : 0.041 0.136 2544 Planarity : 0.004 0.042 2835 Dihedral : 3.540 27.701 2616 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 12.33 % Favored : 86.56 % 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: 1.01 (0.19), residues: 2007 helix: 2.57 (0.21), residues: 630 sheet: 0.53 (0.22), residues: 519 loop : -0.69 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 67 HIS 0.002 0.001 HIS e 38 PHE 0.011 0.001 PHE f 64 TYR 0.014 0.001 TYR E1067 ARG 0.006 0.000 ARG f 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 18) link_NAG-ASN : angle 1.38223 ( 54) link_BETA1-4 : bond 0.01896 ( 3) link_BETA1-4 : angle 5.60512 ( 9) hydrogen bonds : bond 0.03768 ( 767) hydrogen bonds : angle 4.20008 ( 2229) SS BOND : bond 0.00279 ( 29) SS BOND : angle 0.63965 ( 58) covalent geometry : bond 0.00303 (16239) covalent geometry : angle 0.53207 (22095) *********************** 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 104 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.853 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: 0.7960 (OUTLIER) cc_final: 0.7698 (t80) REVERT: G 869 MET cc_start: 0.9222 (mtp) cc_final: 0.8986 (mtm) REVERT: E 869 MET cc_start: 0.9407 (mtt) cc_final: 0.8931 (mpp) REVERT: d 21 LEU cc_start: 0.8577 (mp) cc_final: 0.8260 (tt) REVERT: d 93 ASN cc_start: 0.8750 (t0) cc_final: 0.8175 (m110) REVERT: f 70 MET cc_start: 0.8635 (mtt) cc_final: 0.8407 (mtt) REVERT: c 86 LEU cc_start: 0.8906 (tp) cc_final: 0.8676 (tt) REVERT: c 110 ASP cc_start: 0.8778 (t0) cc_final: 0.7687 (t70) REVERT: e 54 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8321 (ttp-170) REVERT: e 93 ASN cc_start: 0.8739 (t0) cc_final: 0.8431 (m-40) REVERT: b 23 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8052 (tppp) REVERT: b 110 ASP cc_start: 0.9038 (t0) cc_final: 0.8505 (t0) outliers start: 19 outliers final: 6 residues processed: 95 average time/residue: 1.4762 time to fit residues: 154.5134 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 : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 PHE 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 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: 0.9990 chunk 143 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.052925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.036287 restraints weight = 82379.376| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.31 r_work: 0.2774 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16289 Z= 0.164 Angle : 0.552 10.464 22216 Z= 0.278 Chirality : 0.041 0.136 2544 Planarity : 0.004 0.041 2835 Dihedral : 3.554 26.190 2616 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.34 % Allowed : 13.03 % Favored : 85.63 % 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: 0.93 (0.19), residues: 2007 helix: 2.54 (0.21), residues: 624 sheet: 0.48 (0.22), residues: 519 loop : -0.74 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 67 HIS 0.002 0.001 HIS g 38 PHE 0.010 0.001 PHE F 759 TYR 0.015 0.001 TYR E1067 ARG 0.003 0.000 ARG c 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 18) link_NAG-ASN : angle 1.44071 ( 54) link_BETA1-4 : bond 0.01868 ( 3) link_BETA1-4 : angle 5.59497 ( 9) hydrogen bonds : bond 0.03797 ( 767) hydrogen bonds : angle 4.22485 ( 2229) SS BOND : bond 0.00237 ( 29) SS BOND : angle 0.66667 ( 58) covalent geometry : bond 0.00366 (16239) covalent geometry : angle 0.53657 (22095) *********************** 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 109 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 2.105 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: 0.8010 (OUTLIER) cc_final: 0.7779 (t80) REVERT: G 869 MET cc_start: 0.9230 (mtp) cc_final: 0.8972 (mtm) REVERT: E 869 MET cc_start: 0.9408 (mtt) cc_final: 0.8939 (mpp) REVERT: d 21 LEU cc_start: 0.8621 (mp) cc_final: 0.8262 (tt) REVERT: d 54 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8414 (ttm-80) REVERT: d 93 ASN cc_start: 0.8753 (t0) cc_final: 0.8351 (m110) REVERT: f 70 MET cc_start: 0.8615 (mtt) cc_final: 0.8354 (mtt) REVERT: c 86 LEU cc_start: 0.8964 (tp) cc_final: 0.8743 (tt) REVERT: c 110 ASP cc_start: 0.8865 (t0) cc_final: 0.7857 (t70) REVERT: e 4 MET cc_start: 0.7238 (mmm) cc_final: 0.7005 (mmm) REVERT: e 54 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8357 (ttm110) REVERT: e 93 ASN cc_start: 0.8731 (t0) cc_final: 0.8467 (m-40) REVERT: b 23 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8110 (tppp) REVERT: b 110 ASP cc_start: 0.9019 (t0) cc_final: 0.8297 (t0) outliers start: 23 outliers final: 9 residues processed: 99 average time/residue: 1.5514 time to fit residues: 168.2989 Evaluate side-chains 87 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 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 83 LEU Chi-restraints excluded: chain c residue 116 ILE 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.052934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.036384 restraints weight = 81820.612| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.28 r_work: 0.2777 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16289 Z= 0.139 Angle : 0.556 11.511 22216 Z= 0.279 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.037 2835 Dihedral : 3.551 25.652 2616 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.05 % Allowed : 13.61 % 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 (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: 2.52 (0.21), residues: 630 sheet: 0.48 (0.21), residues: 519 loop : -0.73 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 67 HIS 0.004 0.001 HIS g 38 PHE 0.009 0.001 PHE E1121 TYR 0.015 0.001 TYR E1067 ARG 0.012 0.000 ARG b 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 18) link_NAG-ASN : angle 1.38790 ( 54) link_BETA1-4 : bond 0.01863 ( 3) link_BETA1-4 : angle 5.61108 ( 9) hydrogen bonds : bond 0.03712 ( 767) hydrogen bonds : angle 4.21785 ( 2229) SS BOND : bond 0.00222 ( 29) SS BOND : angle 0.57051 ( 58) covalent geometry : bond 0.00313 (16239) covalent geometry : angle 0.54077 (22095) *********************** 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 98 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 2.047 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: 0.8013 (OUTLIER) cc_final: 0.7775 (t80) REVERT: G 869 MET cc_start: 0.9224 (mtp) cc_final: 0.8963 (mtm) REVERT: E 869 MET cc_start: 0.9405 (mtt) cc_final: 0.8934 (mpp) REVERT: F 759 PHE cc_start: 0.7579 (t80) cc_final: 0.7366 (t80) REVERT: d 21 LEU cc_start: 0.8661 (mp) cc_final: 0.8316 (tt) REVERT: d 54 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8418 (ttm-80) REVERT: d 93 ASN cc_start: 0.8750 (t0) cc_final: 0.8354 (m110) REVERT: f 81 MET cc_start: 0.8843 (tmm) cc_final: 0.8497 (ttp) REVERT: c 110 ASP cc_start: 0.8893 (t0) cc_final: 0.7922 (t70) REVERT: e 54 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8515 (ttp-170) REVERT: e 93 ASN cc_start: 0.8727 (t0) cc_final: 0.8470 (m-40) REVERT: b 110 ASP cc_start: 0.8997 (t0) cc_final: 0.8287 (t0) outliers start: 18 outliers final: 5 residues processed: 92 average time/residue: 1.4791 time to fit residues: 150.7846 Evaluate side-chains 82 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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 e residue 54 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 49 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 137 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.051818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035108 restraints weight = 82576.574| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.31 r_work: 0.2736 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16289 Z= 0.254 Angle : 0.612 11.691 22216 Z= 0.311 Chirality : 0.043 0.156 2544 Planarity : 0.004 0.039 2835 Dihedral : 3.789 21.662 2616 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.22 % Allowed : 13.67 % Favored : 85.11 % 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: 0.75 (0.19), residues: 2007 helix: 2.37 (0.21), residues: 633 sheet: 0.34 (0.21), residues: 534 loop : -0.87 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP f 67 HIS 0.003 0.001 HIS g 38 PHE 0.015 0.002 PHE E 759 TYR 0.017 0.001 TYR E1067 ARG 0.003 0.001 ARG E1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 18) link_NAG-ASN : angle 1.62685 ( 54) link_BETA1-4 : bond 0.01774 ( 3) link_BETA1-4 : angle 5.67405 ( 9) hydrogen bonds : bond 0.04269 ( 767) hydrogen bonds : angle 4.46025 ( 2229) SS BOND : bond 0.00266 ( 29) SS BOND : angle 0.73808 ( 58) covalent geometry : bond 0.00571 (16239) covalent geometry : angle 0.59681 (22095) *********************** 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 102 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 1.893 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: 0.8030 (OUTLIER) cc_final: 0.7786 (t80) REVERT: G 869 MET cc_start: 0.9236 (mtp) cc_final: 0.8984 (mtm) REVERT: E 869 MET cc_start: 0.9420 (mtt) cc_final: 0.8949 (mpp) REVERT: d 21 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8335 (tt) REVERT: d 54 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8325 (ttm-80) REVERT: g 81 GLU cc_start: 0.8457 (pm20) cc_final: 0.8254 (pm20) REVERT: e 4 MET cc_start: 0.6802 (mmm) cc_final: 0.6543 (mmm) REVERT: e 21 LEU cc_start: 0.8710 (mp) cc_final: 0.8149 (tt) outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 1.4217 time to fit residues: 143.3802 Evaluate side-chains 83 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 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 21 LEU 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: 7.9990 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.052473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035891 restraints weight = 80600.565| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.27 r_work: 0.2765 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16289 Z= 0.138 Angle : 0.554 8.756 22216 Z= 0.282 Chirality : 0.042 0.153 2544 Planarity : 0.005 0.165 2835 Dihedral : 3.705 23.969 2616 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.81 % Allowed : 14.37 % Favored : 84.82 % 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: 0.81 (0.19), residues: 2007 helix: 2.44 (0.21), residues: 633 sheet: 0.35 (0.21), residues: 534 loop : -0.83 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP c 67 HIS 0.002 0.001 HIS g 38 PHE 0.012 0.001 PHE E 759 TYR 0.016 0.001 TYR E1067 ARG 0.020 0.001 ARG c 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 18) link_NAG-ASN : angle 1.42185 ( 54) link_BETA1-4 : bond 0.01873 ( 3) link_BETA1-4 : angle 5.76234 ( 9) hydrogen bonds : bond 0.03897 ( 767) hydrogen bonds : angle 4.30138 ( 2229) SS BOND : bond 0.00230 ( 29) SS BOND : angle 0.56489 ( 58) covalent geometry : bond 0.00308 (16239) covalent geometry : angle 0.53746 (22095) *********************** 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 95 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.960 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: 0.8096 (OUTLIER) cc_final: 0.7815 (t80) REVERT: G 869 MET cc_start: 0.9218 (mtp) cc_final: 0.8945 (mtm) REVERT: E 869 MET cc_start: 0.9402 (mtt) cc_final: 0.8924 (mpp) REVERT: d 21 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8316 (tt) REVERT: g 93 ASN cc_start: 0.8735 (m-40) cc_final: 0.8274 (m-40) REVERT: f 81 MET cc_start: 0.8920 (tmm) cc_final: 0.8510 (ttp) REVERT: e 21 LEU cc_start: 0.8748 (mp) cc_final: 0.8229 (tt) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 1.4087 time to fit residues: 138.9253 Evaluate side-chains 80 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 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 f residue 116 ILE Chi-restraints excluded: chain c residue 110 ASP 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: 2.9990 chunk 162 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 185 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.052841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.036253 restraints weight = 80825.569| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.31 r_work: 0.2778 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16289 Z= 0.109 Angle : 0.548 8.710 22216 Z= 0.278 Chirality : 0.041 0.133 2544 Planarity : 0.004 0.101 2835 Dihedral : 3.611 22.757 2616 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.58 % Allowed : 15.07 % Favored : 84.35 % 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: 0.86 (0.19), residues: 2007 helix: 2.49 (0.21), residues: 630 sheet: 0.32 (0.21), residues: 537 loop : -0.75 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP b 67 HIS 0.001 0.000 HIS G1088 PHE 0.014 0.001 PHE E 759 TYR 0.015 0.001 TYR E1067 ARG 0.007 0.000 ARG f 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 18) link_NAG-ASN : angle 1.38632 ( 54) link_BETA1-4 : bond 0.01919 ( 3) link_BETA1-4 : angle 5.70373 ( 9) hydrogen bonds : bond 0.03672 ( 767) hydrogen bonds : angle 4.21944 ( 2229) SS BOND : bond 0.00221 ( 29) SS BOND : angle 0.52880 ( 58) covalent geometry : bond 0.00237 (16239) covalent geometry : angle 0.53174 (22095) *********************** 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 86 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.854 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: 0.8122 (OUTLIER) cc_final: 0.7845 (t80) REVERT: G 869 MET cc_start: 0.9197 (mtp) cc_final: 0.8930 (mtm) REVERT: E 869 MET cc_start: 0.9399 (mtt) cc_final: 0.8922 (mpp) REVERT: E 888 PHE cc_start: 0.9204 (t80) cc_final: 0.8888 (t80) REVERT: d 21 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8310 (tt) REVERT: d 54 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8433 (ttm-80) REVERT: f 81 MET cc_start: 0.8888 (tmm) cc_final: 0.8561 (ttp) REVERT: e 21 LEU cc_start: 0.8747 (mp) cc_final: 0.8277 (tt) outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 1.4556 time to fit residues: 135.6853 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 : 1.869 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.052514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.035900 restraints weight = 82061.212| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.32 r_work: 0.2767 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16289 Z= 0.142 Angle : 0.568 9.821 22216 Z= 0.289 Chirality : 0.041 0.134 2544 Planarity : 0.004 0.080 2835 Dihedral : 3.622 22.057 2616 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.70 % Allowed : 15.24 % Favored : 84.06 % 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 (0.18), residues: 2007 helix: 2.48 (0.21), residues: 630 sheet: 0.54 (0.21), residues: 510 loop : -0.83 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP f 67 HIS 0.002 0.001 HIS g 38 PHE 0.027 0.001 PHE F 759 TYR 0.015 0.001 TYR E1067 ARG 0.013 0.000 ARG e 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 18) link_NAG-ASN : angle 1.43124 ( 54) link_BETA1-4 : bond 0.01816 ( 3) link_BETA1-4 : angle 5.65600 ( 9) hydrogen bonds : bond 0.03722 ( 767) hydrogen bonds : angle 4.24881 ( 2229) SS BOND : bond 0.00212 ( 29) SS BOND : angle 0.57814 ( 58) covalent geometry : bond 0.00321 (16239) covalent geometry : angle 0.55219 (22095) ********************** 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: 12 poor density : 72 time to evaluate : 1.848 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: 0.8127 (OUTLIER) cc_final: 0.7856 (t80) REVERT: G 869 MET cc_start: 0.9201 (mtp) cc_final: 0.8930 (mtm) REVERT: E 869 MET cc_start: 0.9412 (mtt) cc_final: 0.8935 (mpp) REVERT: E 888 PHE cc_start: 0.9207 (t80) cc_final: 0.8855 (t80) REVERT: d 21 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8322 (tt) REVERT: d 54 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8450 (ttm-80) REVERT: f 81 MET cc_start: 0.8913 (tmm) cc_final: 0.8556 (ttp) REVERT: e 21 LEU cc_start: 0.8746 (mp) cc_final: 0.8225 (tt) REVERT: b 67 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (m-90) REVERT: b 81 MET cc_start: 0.7904 (tpt) cc_final: 0.7541 (tpt) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 1.3907 time to fit residues: 126.5115 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 : 1.896 ------------------------------------------------------------------------------- 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 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 c residue 116 ILE Chi-restraints excluded: chain b residue 67 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 187 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.051907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.035225 restraints weight = 81606.916| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.31 r_work: 0.2739 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16289 Z= 0.217 Angle : 0.605 13.626 22216 Z= 0.307 Chirality : 0.043 0.160 2544 Planarity : 0.004 0.060 2835 Dihedral : 3.774 19.977 2616 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.70 % Allowed : 15.30 % Favored : 84.00 % 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: 0.68 (0.19), residues: 2007 helix: 2.38 (0.21), residues: 630 sheet: 0.21 (0.21), residues: 537 loop : -0.89 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 67 HIS 0.003 0.001 HIS d 38 PHE 0.050 0.001 PHE E 759 TYR 0.016 0.001 TYR E1067 ARG 0.008 0.001 ARG e 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 18) link_NAG-ASN : angle 1.55962 ( 54) link_BETA1-4 : bond 0.01718 ( 3) link_BETA1-4 : angle 5.71002 ( 9) hydrogen bonds : bond 0.04082 ( 767) hydrogen bonds : angle 4.42779 ( 2229) SS BOND : bond 0.00286 ( 29) SS BOND : angle 0.70631 ( 58) covalent geometry : bond 0.00490 (16239) covalent geometry : angle 0.58911 (22095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10062.87 seconds wall clock time: 174 minutes 28.65 seconds (10468.65 seconds total)