Starting phenix.real_space_refine on Sat Oct 31 02:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.map" model { file = "/net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r91_4765/10_2026/6r91_4765.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 67 5.16 5 C 12664 2.51 5 N 3870 2.21 5 O 4588 1.98 5 H 19079 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40556 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1331 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1762 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1649 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1784 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4581 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 12902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12902 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5760 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 344} Time building chain proxies: 5.96, per 1000 atoms: 0.15 Number of scatterers: 40556 At special positions: 0 Unit cell: (134.16, 184.04, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 288 15.00 O 4588 8.00 N 3870 7.00 C 12664 6.00 H 19079 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 33 sheets defined 34.2% alpha, 25.7% beta 139 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 7.22 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.640A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.546A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.673A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.572A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.285A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.517A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.540A pdb=" N LEU C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.608A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.573A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 78 removed outlier: 3.753A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.578A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.256A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 250 through 256 removed outlier: 3.851A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 384 Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 755 through 759 Processing helix chain 'K' and resid 985 through 990 Processing helix chain 'K' and resid 1044 through 1062 Processing helix chain 'K' and resid 1069 through 1075 Processing helix chain 'K' and resid 1091 through 1096 Processing helix chain 'K' and resid 1097 through 1100 removed outlier: 3.611A pdb=" N ILE K1100 " --> pdb=" O PHE K1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1097 through 1100' Processing helix chain 'K' and resid 1101 through 1109 Processing helix chain 'K' and resid 1125 through 1138 removed outlier: 3.687A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 79 Processing helix chain 'L' and resid 82 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.767A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.219A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.650A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.681A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.950A pdb=" N ILE E 120 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.419A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'K' and resid 1004 through 1009 removed outlier: 3.796A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER K1027 " --> pdb=" O VAL K1040 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL K1040 " --> pdb=" O SER K1027 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU K1029 " --> pdb=" O GLY K1038 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY K1038 " --> pdb=" O LEU K1029 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR K 3 " --> pdb=" O LEU K1043 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 17 through 21 removed outlier: 3.523A pdb=" N GLY K 17 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 61 through 67 removed outlier: 3.740A pdb=" N VAL K 63 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU K 65 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 121 through 124 Processing sheet with id=AB5, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.266A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.266A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 218 through 221 Processing sheet with id=AB8, first strand: chain 'K' and resid 258 through 263 removed outlier: 6.892A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU K 280 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG K 301 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU K 286 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP K 299 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU K 288 " --> pdb=" O LEU K 297 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU K 297 " --> pdb=" O GLU K 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 313 through 316 removed outlier: 6.650A pdb=" N SER K 331 " --> pdb=" O THR K 352 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR K 352 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU K 333 " --> pdb=" O MET K 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 361 through 365 removed outlier: 4.095A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.481A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.481A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER K 762 " --> pdb=" O LEU K 802 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.657A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 870 through 876 removed outlier: 3.716A pdb=" N SER K 872 " --> pdb=" O SER K 883 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL K 888 " --> pdb=" O ASN K 904 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN K 904 " --> pdb=" O VAL K 888 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU K 890 " --> pdb=" O GLU K 902 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 911 through 917 removed outlier: 3.784A pdb=" N LYS K 915 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 922 " --> pdb=" O LYS K 915 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS K 917 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL K 930 " --> pdb=" O ASP K 948 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU K 992 " --> pdb=" O ILE K 945 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG K 947 " --> pdb=" O LEU K 992 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU K 994 " --> pdb=" O ARG K 947 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN K 964 " --> pdb=" O ILE K 959 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE K 959 " --> pdb=" O ASN K 964 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 1076 through 1077 Processing sheet with id=AC8, first strand: chain 'K' and resid 1113 through 1114 Processing sheet with id=AC9, first strand: chain 'L' and resid 106 through 109 Processing sheet with id=AD1, first strand: chain 'L' and resid 114 through 119 removed outlier: 6.724A pdb=" N GLY L 130 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU L 117 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA L 128 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP L 119 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR L 126 " --> pdb=" O TRP L 119 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 159 through 161 removed outlier: 6.455A pdb=" N SER L 175 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 204 through 210 removed outlier: 6.279A pdb=" N GLY L 219 " --> pdb=" O CYS L 205 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU L 207 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL L 217 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL L 209 " --> pdb=" O MET L 215 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET L 215 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 245 through 250 removed outlier: 3.610A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 291 through 296 removed outlier: 3.795A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 343 through 344 removed outlier: 6.471A pdb=" N ILE L 372 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN L 385 " --> pdb=" O ILE L 372 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL L 374 " --> pdb=" O MET L 383 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 12.29 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19052 1.03 - 1.22: 132 1.22 - 1.42: 9569 1.42 - 1.62: 12689 1.62 - 1.82: 111 Bond restraints: 41553 Sorted by residual: bond pdb=" C4' 3DR J 98 " pdb=" O4' 3DR J 98 " ideal model delta sigma weight residual 1.423 1.667 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C4' 3DR J 97 " pdb=" O4' 3DR J 97 " ideal model delta sigma weight residual 1.423 1.662 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4' 3DR J 97 " pdb=" C3' 3DR J 97 " ideal model delta sigma weight residual 1.532 1.338 0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C4' 3DR J 98 " pdb=" C3' 3DR J 98 " ideal model delta sigma weight residual 1.532 1.339 0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C1' DC I 87 " pdb=" N1 DC I 87 " ideal model delta sigma weight residual 1.468 1.559 -0.091 1.40e-02 5.10e+03 4.22e+01 ... (remaining 41548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 74969 4.17 - 8.35: 280 8.35 - 12.52: 7 12.52 - 16.69: 2 16.69 - 20.87: 1 Bond angle restraints: 75259 Sorted by residual: angle pdb=" O4' DT I 92 " pdb=" C1' DT I 92 " pdb=" N1 DT I 92 " ideal model delta sigma weight residual 108.00 113.75 -5.75 7.00e-01 2.04e+00 6.74e+01 angle pdb=" C4' DT I 92 " pdb=" O4' DT I 92 " pdb=" C1' DT I 92 " ideal model delta sigma weight residual 110.10 104.12 5.98 1.00e+00 1.00e+00 3.58e+01 angle pdb=" CA LEU C 116 " pdb=" CB LEU C 116 " pdb=" CG LEU C 116 " ideal model delta sigma weight residual 116.30 137.17 -20.87 3.50e+00 8.16e-02 3.55e+01 angle pdb=" N GLY D 105 " pdb=" CA GLY D 105 " pdb=" C GLY D 105 " ideal model delta sigma weight residual 113.18 126.60 -13.42 2.37e+00 1.78e-01 3.21e+01 angle pdb=" N GLY H 105 " pdb=" CA GLY H 105 " pdb=" C GLY H 105 " ideal model delta sigma weight residual 113.18 126.59 -13.41 2.37e+00 1.78e-01 3.20e+01 ... (remaining 75254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 16504 34.94 - 69.88: 1854 69.88 - 104.82: 51 104.82 - 139.76: 7 139.76 - 174.70: 5 Dihedral angle restraints: 18421 sinusoidal: 11933 harmonic: 6488 Sorted by residual: dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -124.02 -55.98 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO L 64 " pdb=" C PRO L 64 " pdb=" N PRO L 65 " pdb=" CA PRO L 65 " ideal model delta harmonic sigma weight residual 180.00 -140.72 -39.28 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA CYS L 66 " pdb=" C CYS L 66 " pdb=" N ARG L 67 " pdb=" CA ARG L 67 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 18418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2659 0.065 - 0.129: 712 0.129 - 0.194: 183 0.194 - 0.258: 14 0.258 - 0.323: 1 Chirality restraints: 3569 Sorted by residual: chirality pdb=" CG LEU L 324 " pdb=" CB LEU L 324 " pdb=" CD1 LEU L 324 " pdb=" CD2 LEU L 324 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' 3DR J 97 " pdb=" C4' 3DR J 97 " pdb=" O3' 3DR J 97 " pdb=" C2' 3DR J 97 " both_signs ideal model delta sigma weight residual False -2.70 -2.44 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ARG A 132 " pdb=" N ARG A 132 " pdb=" C ARG A 132 " pdb=" CB ARG A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3566 not shown) Planarity restraints: 5124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 65 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C ASN F 65 " -0.087 2.00e-02 2.50e+03 pdb=" O ASN F 65 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL F 66 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 65 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C ASN B 65 " 0.078 2.00e-02 2.50e+03 pdb=" O ASN B 65 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL B 66 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 64 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C GLU B 64 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 64 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN B 65 " -0.025 2.00e-02 2.50e+03 ... (remaining 5121 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1767 2.18 - 2.79: 73990 2.79 - 3.39: 108867 3.39 - 4.00: 149111 4.00 - 4.60: 221576 Nonbonded interactions: 555311 Sorted by model distance: nonbonded pdb=" H ASP K 925 " pdb=" O SER K 929 " model vdw 1.578 2.450 nonbonded pdb="HH22 ARG A 41 " pdb=" O3' DT J 85 " model vdw 1.611 2.450 nonbonded pdb="HH12 ARG A 73 " pdb=" OP1 DC I 47 " model vdw 1.647 2.450 nonbonded pdb=" O CYS L 66 " pdb="HE22 GLN L 92 " model vdw 1.649 2.450 nonbonded pdb=" OE1 GLU L 421 " pdb=" H GLU L 421 " model vdw 1.655 2.450 ... (remaining 555306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 136) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 24 through 28 or (resid 29 and (name N or name CA or name C or name O \ or name HA2 or name HA3)) or resid 30 through 103)) } ncs_group { reference = chain 'C' selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 12 through 120)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) } 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 group one per residue 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: 0.470 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: 0.060 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 44.870 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 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 : 0.008 0.244 22474 Z= 0.596 Angle : 1.097 20.866 31615 Z= 0.800 Chirality : 0.062 0.323 3569 Planarity : 0.007 0.075 3037 Dihedral : 23.870 174.700 9234 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.57 % Favored : 94.97 % Rotamer: Outliers : 0.65 % Allowed : 3.21 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 1947 helix: 0.61 (0.18), residues: 630 sheet: -0.33 (0.23), residues: 476 loop : -1.55 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG K 388 TYR 0.031 0.004 TYR K 171 PHE 0.045 0.003 PHE K 949 TRP 0.039 0.003 TRP K 207 HIS 0.011 0.002 HIS K 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.60 (22474) covalent geometry : angle 1.09652 / 0.80 (31615) hydrogen bonds : bond 0.13076 / 8.68 ( 1064) hydrogen bonds : angle 5.72916 / 4.19 ( 2762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 458 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9015 (mt0) cc_final: 0.8585 (mt0) REVERT: A 57 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7612 (mmtm) REVERT: A 59 THR cc_start: 0.6750 (p) cc_final: 0.6365 (p) REVERT: A 62 LEU cc_start: 0.8471 (mt) cc_final: 0.8233 (mm) REVERT: B 26 ASN cc_start: 0.7926 (m110) cc_final: 0.7580 (m110) REVERT: C 37 LYS cc_start: 0.5886 (mttm) cc_final: 0.5579 (tmtt) REVERT: C 73 ASP cc_start: 0.8913 (t0) cc_final: 0.8660 (t0) REVERT: C 102 THR cc_start: 0.8035 (m) cc_final: 0.7360 (p) REVERT: D 72 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4912 (tt0) REVERT: D 86 LYS cc_start: 0.8977 (tptt) cc_final: 0.8726 (tppp) REVERT: D 117 LYS cc_start: 0.8450 (tmtt) cc_final: 0.7884 (ttmt) REVERT: E 77 GLN cc_start: 0.8902 (tt0) cc_final: 0.8382 (tp40) REVERT: E 91 MET cc_start: 0.6204 (mmm) cc_final: 0.5584 (mmm) REVERT: E 94 GLN cc_start: 0.7609 (tt0) cc_final: 0.6510 (tp40) REVERT: E 95 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7972 (mm-30) REVERT: E 98 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7796 (tm-30) REVERT: G 31 VAL cc_start: 0.7147 (t) cc_final: 0.6943 (p) REVERT: G 63 ILE cc_start: 0.5900 (mm) cc_final: 0.5545 (tp) REVERT: H 36 GLU cc_start: 0.6574 (pp20) cc_final: 0.5840 (pt0) REVERT: H 87 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7611 (mtt180) REVERT: H 106 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7340 (mp0) REVERT: K 7 VAL cc_start: 0.8352 (p) cc_final: 0.7188 (p) REVERT: K 151 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7935 (mm-30) REVERT: K 166 ASP cc_start: 0.7170 (t0) cc_final: 0.6561 (t0) REVERT: K 202 PHE cc_start: 0.3629 (m-80) cc_final: 0.3324 (m-10) REVERT: K 218 MET cc_start: 0.8006 (mtm) cc_final: 0.6298 (tpp) REVERT: K 258 ILE cc_start: 0.8298 (mt) cc_final: 0.8022 (mt) REVERT: K 713 ARG cc_start: 0.3651 (ttt180) cc_final: 0.3210 (mmt180) REVERT: K 840 GLU cc_start: 0.6311 (tp30) cc_final: 0.5729 (tp30) REVERT: K 873 MET cc_start: 0.4709 (mtm) cc_final: 0.3896 (mpp) REVERT: K 897 LYS cc_start: 0.9234 (mttt) cc_final: 0.8908 (mtpt) REVERT: K 908 ASN cc_start: 0.6647 (m-40) cc_final: 0.6375 (p0) REVERT: K 989 ARG cc_start: 0.4048 (mtm-85) cc_final: 0.3846 (mtm-85) REVERT: K 1092 ASP cc_start: 0.7161 (m-30) cc_final: 0.6851 (p0) REVERT: L 123 HIS cc_start: 0.7004 (t-90) cc_final: 0.6274 (m170) REVERT: L 187 LYS cc_start: 0.9302 (mttm) cc_final: 0.9078 (mmmt) REVERT: L 214 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7521 (mtp-110) REVERT: L 224 ASN cc_start: 0.7281 (p0) cc_final: 0.6573 (t0) REVERT: L 270 TRP cc_start: 0.7125 (m100) cc_final: 0.6444 (m100) REVERT: L 299 ASP cc_start: 0.6924 (t0) cc_final: 0.6600 (t0) REVERT: L 403 MET cc_start: 0.8117 (tpt) cc_final: 0.7515 (tpt) REVERT: L 424 ARG cc_start: 0.6479 (mtm180) cc_final: 0.6136 (ptp-170) outliers start: 11 outliers final: 2 residues processed: 465 average time/residue: 0.3966 time to fit residues: 265.3218 Evaluate side-chains 339 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 336 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN D 68 ASN E 69 GLN F 26 ASN G 25 GLN H 85 ASN K 203 ASN K1034 ASN K1059 ASN K1106 GLN L 91 GLN L 274 GLN ** L 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.183346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142501 restraints weight = 93882.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152057 restraints weight = 35753.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158303 restraints weight = 17882.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.162387 restraints weight = 10820.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.165044 restraints weight = 7561.192| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22474 Z= 0.238 Angle : 0.763 9.164 31615 Z= 0.457 Chirality : 0.047 0.229 3569 Planarity : 0.006 0.072 3037 Dihedral : 27.407 179.589 5424 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 0.06 % Allowed : 2.02 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 1947 helix: 1.21 (0.19), residues: 656 sheet: -0.38 (0.24), residues: 460 loop : -1.41 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 134 TYR 0.021 0.002 TYR K 42 PHE 0.023 0.002 PHE K1030 TRP 0.033 0.003 TRP L 236 HIS 0.012 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.24 (22474) covalent geometry : angle 0.76294 / 0.46 (31615) hydrogen bonds : bond 0.07219 / 4.95 ( 1064) hydrogen bonds : angle 5.20429 / 3.79 ( 2762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9212 (mt0) cc_final: 0.8831 (mt0) REVERT: A 57 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7639 (mmtm) REVERT: A 98 GLU cc_start: 0.8812 (pp20) cc_final: 0.8554 (pp20) REVERT: A 121 MET cc_start: 0.6384 (mtt) cc_final: 0.6119 (mtp) REVERT: B 46 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7446 (mtp-110) REVERT: C 37 LYS cc_start: 0.5949 (mttm) cc_final: 0.5640 (tmtt) REVERT: C 73 ASP cc_start: 0.8910 (t0) cc_final: 0.8648 (t0) REVERT: D 86 LYS cc_start: 0.8926 (tptt) cc_final: 0.8663 (tppp) REVERT: D 117 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8125 (ttmt) REVERT: E 56 GLN cc_start: 0.9080 (mt0) cc_final: 0.8825 (mt0) REVERT: E 77 GLN cc_start: 0.8919 (tt0) cc_final: 0.8428 (tp-100) REVERT: E 91 MET cc_start: 0.6405 (mmm) cc_final: 0.5201 (tpt) REVERT: E 94 GLN cc_start: 0.7647 (tt0) cc_final: 0.6507 (tp40) REVERT: E 95 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8110 (mm-30) REVERT: G 31 VAL cc_start: 0.7067 (t) cc_final: 0.6853 (m) REVERT: G 63 ILE cc_start: 0.6045 (mm) cc_final: 0.5689 (tp) REVERT: G 65 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6635 (mm-30) REVERT: H 36 GLU cc_start: 0.6850 (pp20) cc_final: 0.6474 (pt0) REVERT: H 106 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7440 (mp0) REVERT: K 127 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7978 (mt-10) REVERT: K 151 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7987 (mm-30) REVERT: K 166 ASP cc_start: 0.7030 (t0) cc_final: 0.6297 (t0) REVERT: K 180 PHE cc_start: 0.3974 (p90) cc_final: 0.3698 (p90) REVERT: K 218 MET cc_start: 0.7988 (mtm) cc_final: 0.6526 (tpp) REVERT: K 713 ARG cc_start: 0.3681 (ttt180) cc_final: 0.3240 (mmt180) REVERT: K 840 GLU cc_start: 0.6530 (tp30) cc_final: 0.6009 (tp30) REVERT: K 844 LYS cc_start: 0.7083 (mmtm) cc_final: 0.6824 (mtmt) REVERT: K 873 MET cc_start: 0.4375 (mtm) cc_final: 0.3215 (mpp) REVERT: K 908 ASN cc_start: 0.6403 (m-40) cc_final: 0.6128 (p0) REVERT: K 1014 MET cc_start: 0.3354 (tpp) cc_final: 0.1873 (mtm) REVERT: L 77 LYS cc_start: 0.6664 (mtpt) cc_final: 0.6283 (mttm) REVERT: L 123 HIS cc_start: 0.7026 (t-90) cc_final: 0.6038 (m170) REVERT: L 125 SER cc_start: 0.7027 (m) cc_final: 0.6628 (m) REVERT: L 214 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7526 (mtp-110) REVERT: L 224 ASN cc_start: 0.7324 (p0) cc_final: 0.6541 (t0) REVERT: L 270 TRP cc_start: 0.7006 (m100) cc_final: 0.6162 (m100) REVERT: L 394 ILE cc_start: 0.8016 (mt) cc_final: 0.7715 (mm) REVERT: L 403 MET cc_start: 0.8275 (tpt) cc_final: 0.7675 (tpt) outliers start: 1 outliers final: 0 residues processed: 382 average time/residue: 0.3489 time to fit residues: 197.6212 Evaluate side-chains 324 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [98, 134, 97, 57, 34, 152, 91, 220, 141, 16, 196] chunk 98 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN H 85 ASN K 93 GLN K 319 ASN K 845 GLN K 877 ASN L 165 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.182948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.146042 restraints weight = 96859.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.154302 restraints weight = 38236.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.159664 restraints weight = 19596.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.163178 restraints weight = 12135.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.165505 restraints weight = 8691.900| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 22474 Z= 0.259 Angle : 0.760 8.181 31615 Z= 0.459 Chirality : 0.047 0.237 3569 Planarity : 0.007 0.156 3037 Dihedral : 27.439 179.068 5424 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 1947 helix: 0.42 (0.19), residues: 656 sheet: -0.45 (0.24), residues: 437 loop : -1.64 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 93 TYR 0.022 0.002 TYR K 42 PHE 0.020 0.002 PHE L 257 TRP 0.017 0.002 TRP K 207 HIS 0.014 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.26 (22474) covalent geometry : angle 0.76013 / 0.46 (31615) hydrogen bonds : bond 0.07382 / 5.11 ( 1064) hydrogen bonds : angle 5.38555 / 3.92 ( 2762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9101 (mt0) cc_final: 0.8829 (mt0) REVERT: A 57 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7803 (mmtt) REVERT: A 98 GLU cc_start: 0.8727 (pp20) cc_final: 0.8400 (pp20) REVERT: A 121 MET cc_start: 0.7044 (mtt) cc_final: 0.6632 (mtp) REVERT: C 62 GLU cc_start: 0.7846 (tt0) cc_final: 0.7544 (mt-10) REVERT: C 73 ASP cc_start: 0.8797 (t0) cc_final: 0.8484 (t0) REVERT: D 86 LYS cc_start: 0.9110 (tptt) cc_final: 0.8818 (tppp) REVERT: D 87 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7298 (mtp180) REVERT: D 117 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8236 (ttmt) REVERT: E 77 GLN cc_start: 0.9053 (tt0) cc_final: 0.8584 (tp-100) REVERT: E 91 MET cc_start: 0.6516 (mmm) cc_final: 0.5992 (tpt) REVERT: E 94 GLN cc_start: 0.7749 (tt0) cc_final: 0.6567 (tp40) REVERT: F 53 GLU cc_start: 0.8179 (pm20) cc_final: 0.7912 (pm20) REVERT: G 31 VAL cc_start: 0.7256 (t) cc_final: 0.7035 (m) REVERT: G 63 ILE cc_start: 0.6228 (mm) cc_final: 0.5821 (tp) REVERT: H 36 GLU cc_start: 0.7071 (pp20) cc_final: 0.6734 (pt0) REVERT: H 103 LEU cc_start: 0.7694 (mp) cc_final: 0.7373 (mp) REVERT: H 106 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7632 (mp0) REVERT: K 151 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8049 (mm-30) REVERT: K 164 VAL cc_start: 0.8313 (t) cc_final: 0.8091 (t) REVERT: K 218 MET cc_start: 0.8270 (mtm) cc_final: 0.6883 (tpp) REVERT: K 287 LYS cc_start: 0.4916 (mttp) cc_final: 0.4692 (mmmt) REVERT: K 713 ARG cc_start: 0.4334 (ttt180) cc_final: 0.3599 (mmt180) REVERT: K 840 GLU cc_start: 0.6458 (tp30) cc_final: 0.6036 (tp30) REVERT: K 844 LYS cc_start: 0.7217 (mmtm) cc_final: 0.6873 (mtmt) REVERT: K 873 MET cc_start: 0.4006 (mtm) cc_final: 0.3103 (mpp) REVERT: K 908 ASN cc_start: 0.6825 (m-40) cc_final: 0.6270 (p0) REVERT: K 910 MET cc_start: 0.6279 (ptp) cc_final: 0.5735 (pmm) REVERT: L 77 LYS cc_start: 0.7061 (mtpt) cc_final: 0.6606 (mttm) REVERT: L 123 HIS cc_start: 0.7717 (t-90) cc_final: 0.6651 (m170) REVERT: L 125 SER cc_start: 0.7568 (m) cc_final: 0.7268 (m) REVERT: L 214 ARG cc_start: 0.8599 (mtt90) cc_final: 0.7826 (mtp-110) REVERT: L 326 LEU cc_start: 0.6276 (pp) cc_final: 0.5992 (pp) REVERT: L 394 ILE cc_start: 0.8516 (mt) cc_final: 0.8214 (mm) REVERT: L 403 MET cc_start: 0.8468 (tpt) cc_final: 0.7814 (tpt) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3473 time to fit residues: 189.2161 Evaluate side-chains 322 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [90, 20, 38, 178, 159, 187, 78, 140, 29, 111, 117] chunk 90 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN K1056 ASN L 92 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.183509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.146434 restraints weight = 97955.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.154830 restraints weight = 39202.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.160264 restraints weight = 20184.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.163833 restraints weight = 12515.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.166156 restraints weight = 8921.864| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22474 Z= 0.223 Angle : 0.716 8.160 31615 Z= 0.433 Chirality : 0.046 0.270 3569 Planarity : 0.006 0.093 3037 Dihedral : 27.463 176.813 5424 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 1947 helix: 0.37 (0.19), residues: 655 sheet: -0.57 (0.24), residues: 445 loop : -1.71 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 84 TYR 0.020 0.002 TYR K 42 PHE 0.019 0.002 PHE L 257 TRP 0.016 0.002 TRP K 207 HIS 0.012 0.002 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 (22474) covalent geometry : angle 0.71639 / 0.43 (31615) hydrogen bonds : bond 0.06509 / 4.49 ( 1064) hydrogen bonds : angle 5.21220 / 3.80 ( 2762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7764 (mmtm) REVERT: A 98 GLU cc_start: 0.8760 (pp20) cc_final: 0.8395 (pp20) REVERT: B 94 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7115 (tp40) REVERT: C 62 GLU cc_start: 0.7849 (tt0) cc_final: 0.7527 (mt-10) REVERT: C 73 ASP cc_start: 0.8777 (t0) cc_final: 0.8473 (t0) REVERT: D 86 LYS cc_start: 0.9117 (tptt) cc_final: 0.8821 (tppp) REVERT: D 87 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7406 (mtp180) REVERT: D 117 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8238 (ttmt) REVERT: E 77 GLN cc_start: 0.9013 (tt0) cc_final: 0.8619 (tp-100) REVERT: E 91 MET cc_start: 0.6543 (mmm) cc_final: 0.6084 (tpt) REVERT: E 100 TYR cc_start: 0.7576 (t80) cc_final: 0.7192 (t80) REVERT: F 51 ILE cc_start: 0.8740 (mm) cc_final: 0.8503 (mm) REVERT: F 53 GLU cc_start: 0.8285 (pm20) cc_final: 0.7772 (pm20) REVERT: G 63 ILE cc_start: 0.6260 (mm) cc_final: 0.5847 (tp) REVERT: H 36 GLU cc_start: 0.7109 (pp20) cc_final: 0.6819 (pt0) REVERT: H 106 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7623 (mp0) REVERT: K 1 MET cc_start: 0.3063 (mpp) cc_final: 0.2786 (mpp) REVERT: K 7 VAL cc_start: 0.8734 (p) cc_final: 0.8328 (p) REVERT: K 151 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8101 (mm-30) REVERT: K 287 LYS cc_start: 0.5242 (mttp) cc_final: 0.5010 (mmmt) REVERT: K 288 GLU cc_start: 0.6049 (tp30) cc_final: 0.3936 (pt0) REVERT: K 312 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7421 (tm-30) REVERT: K 713 ARG cc_start: 0.4293 (ttt180) cc_final: 0.3591 (mmt180) REVERT: K 840 GLU cc_start: 0.6281 (tp30) cc_final: 0.5953 (tp30) REVERT: K 844 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6868 (mtmt) REVERT: K 873 MET cc_start: 0.4104 (mtm) cc_final: 0.3192 (mpp) REVERT: K 910 MET cc_start: 0.5943 (ptp) cc_final: 0.5202 (pmm) REVERT: K 989 ARG cc_start: 0.4375 (mtm-85) cc_final: 0.4160 (mtm-85) REVERT: L 77 LYS cc_start: 0.7217 (mtpt) cc_final: 0.6803 (mttm) REVERT: L 123 HIS cc_start: 0.7576 (t-90) cc_final: 0.6664 (m170) REVERT: L 125 SER cc_start: 0.7530 (m) cc_final: 0.7229 (m) REVERT: L 214 ARG cc_start: 0.8640 (mtt90) cc_final: 0.7819 (mtp-110) REVERT: L 240 MET cc_start: 0.7181 (mmm) cc_final: 0.6405 (mmm) REVERT: L 326 LEU cc_start: 0.6270 (pp) cc_final: 0.5917 (pp) REVERT: L 394 ILE cc_start: 0.8778 (mt) cc_final: 0.8529 (mp) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.3532 time to fit residues: 187.5201 Evaluate side-chains 314 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [92, 198, 110, 38, 18, 172, 21, 205, 104, 194, 94] chunk 92 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 826 ASN K 993 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.174026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.137905 restraints weight = 100632.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145668 restraints weight = 39880.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.150694 restraints weight = 20630.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.153953 restraints weight = 12929.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.156128 restraints weight = 9371.392| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 22474 Z= 0.330 Angle : 0.845 10.346 31615 Z= 0.504 Chirality : 0.048 0.240 3569 Planarity : 0.007 0.093 3037 Dihedral : 27.565 174.599 5424 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.06 % Favored : 91.83 % Rotamer: Outliers : 0.12 % Allowed : 2.73 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 1947 helix: -0.77 (0.18), residues: 656 sheet: -0.92 (0.24), residues: 433 loop : -2.22 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 84 TYR 0.024 0.003 TYR K 42 PHE 0.043 0.003 PHE B 101 TRP 0.020 0.002 TRP K 207 HIS 0.014 0.003 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.33 (22474) covalent geometry : angle 0.84517 / 0.50 (31615) hydrogen bonds : bond 0.08483 / 5.86 ( 1064) hydrogen bonds : angle 5.95991 / 4.33 ( 2762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7919 (mmtm) REVERT: A 93 LEU cc_start: 0.9006 (tt) cc_final: 0.8621 (tt) REVERT: A 97 CYS cc_start: 0.9552 (m) cc_final: 0.9218 (m) REVERT: A 98 GLU cc_start: 0.8790 (pp20) cc_final: 0.8376 (pp20) REVERT: A 107 ASP cc_start: 0.8804 (t0) cc_final: 0.8403 (t0) REVERT: C 62 GLU cc_start: 0.7837 (tt0) cc_final: 0.7311 (mt-10) REVERT: D 86 LYS cc_start: 0.9165 (tptt) cc_final: 0.8830 (tppp) REVERT: D 117 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8510 (ttmt) REVERT: E 77 GLN cc_start: 0.9106 (tt0) cc_final: 0.8794 (tp40) REVERT: E 104 LEU cc_start: 0.9200 (tp) cc_final: 0.8855 (mt) REVERT: F 53 GLU cc_start: 0.8503 (pm20) cc_final: 0.7969 (pm20) REVERT: H 106 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7760 (mp0) REVERT: K 7 VAL cc_start: 0.8885 (p) cc_final: 0.8606 (p) REVERT: K 151 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8125 (mm-30) REVERT: K 180 PHE cc_start: 0.5295 (p90) cc_final: 0.4989 (p90) REVERT: K 287 LYS cc_start: 0.5411 (mttp) cc_final: 0.5190 (mmmt) REVERT: K 840 GLU cc_start: 0.5979 (tp30) cc_final: 0.5765 (tp30) REVERT: K 844 LYS cc_start: 0.7421 (mmtm) cc_final: 0.6972 (mtmt) REVERT: K 873 MET cc_start: 0.4271 (mtm) cc_final: 0.3378 (mpp) REVERT: K 897 LYS cc_start: 0.9337 (mttt) cc_final: 0.9019 (mtpt) REVERT: K 910 MET cc_start: 0.6291 (ptp) cc_final: 0.5628 (pmm) REVERT: K 989 ARG cc_start: 0.4651 (mtm-85) cc_final: 0.4421 (mtm-85) REVERT: K 1014 MET cc_start: 0.2616 (tpp) cc_final: 0.0782 (mtm) REVERT: K 1072 PHE cc_start: 0.7006 (t80) cc_final: 0.4925 (m-10) REVERT: L 77 LYS cc_start: 0.7338 (mtpt) cc_final: 0.6851 (mttm) REVERT: L 214 ARG cc_start: 0.8726 (mtt90) cc_final: 0.7868 (mtp-110) REVERT: L 326 LEU cc_start: 0.6463 (pp) cc_final: 0.6081 (pp) REVERT: L 394 ILE cc_start: 0.8904 (mt) cc_final: 0.8222 (mp) outliers start: 2 outliers final: 0 residues processed: 360 average time/residue: 0.3519 time to fit residues: 189.4547 Evaluate side-chains 313 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [67, 167, 28, 99, 65, 168, 214, 26, 64, 57, 176] chunk 67 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.0470 chunk 168 optimal weight: 0.9980 chunk 214 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 952 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.185467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.147775 restraints weight = 107555.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.156104 restraints weight = 44564.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.161530 restraints weight = 23634.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.165086 restraints weight = 15035.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.167431 restraints weight = 10969.219| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22474 Z= 0.155 Angle : 0.663 7.633 31615 Z= 0.403 Chirality : 0.045 0.243 3569 Planarity : 0.005 0.054 3037 Dihedral : 27.612 175.604 5424 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.55 % Favored : 94.35 % Rotamer: Outliers : 0.12 % Allowed : 1.31 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 1947 helix: 0.49 (0.19), residues: 654 sheet: -0.85 (0.24), residues: 456 loop : -1.91 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 93 TYR 0.015 0.001 TYR K 42 PHE 0.020 0.002 PHE L 257 TRP 0.013 0.002 TRP K 207 HIS 0.013 0.001 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (22474) covalent geometry : angle 0.66316 / 0.40 (31615) hydrogen bonds : bond 0.05778 / 3.97 ( 1064) hydrogen bonds : angle 4.90311 / 3.59 ( 2762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7683 (mmtm) REVERT: A 98 GLU cc_start: 0.8725 (pp20) cc_final: 0.8272 (pp20) REVERT: C 62 GLU cc_start: 0.7596 (tt0) cc_final: 0.7185 (mt-10) REVERT: D 86 LYS cc_start: 0.9141 (tptt) cc_final: 0.8811 (tppp) REVERT: D 87 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7110 (mtm180) REVERT: D 117 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8485 (ttmt) REVERT: E 77 GLN cc_start: 0.8980 (tt0) cc_final: 0.8645 (tp40) REVERT: E 104 LEU cc_start: 0.9129 (tp) cc_final: 0.8752 (mt) REVERT: F 53 GLU cc_start: 0.8377 (pm20) cc_final: 0.7743 (pm20) REVERT: F 60 LYS cc_start: 0.7191 (tttp) cc_final: 0.6965 (ttmm) REVERT: G 63 ILE cc_start: 0.6272 (mm) cc_final: 0.5886 (tp) REVERT: H 106 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8116 (mp0) REVERT: K 151 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8003 (mm-30) REVERT: K 218 MET cc_start: 0.8192 (mtm) cc_final: 0.7255 (tpt) REVERT: K 287 LYS cc_start: 0.5455 (mttp) cc_final: 0.5035 (mmmt) REVERT: K 288 GLU cc_start: 0.6146 (tp30) cc_final: 0.3884 (pt0) REVERT: K 312 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6476 (tm-30) REVERT: K 326 SER cc_start: 0.6888 (t) cc_final: 0.6636 (p) REVERT: K 713 ARG cc_start: 0.4135 (ttt180) cc_final: 0.3396 (mmt180) REVERT: K 840 GLU cc_start: 0.5950 (tp30) cc_final: 0.5658 (tp30) REVERT: K 844 LYS cc_start: 0.7330 (mmtm) cc_final: 0.6879 (mtmt) REVERT: K 873 MET cc_start: 0.4244 (mtm) cc_final: 0.3277 (mpp) REVERT: K 875 GLU cc_start: 0.4882 (pp20) cc_final: 0.4599 (tm-30) REVERT: K 897 LYS cc_start: 0.9306 (mttt) cc_final: 0.8987 (mtpt) REVERT: K 910 MET cc_start: 0.6599 (ptp) cc_final: 0.5912 (pmm) REVERT: K 989 ARG cc_start: 0.4336 (mtm-85) cc_final: 0.4135 (mtm-85) REVERT: K 1014 MET cc_start: 0.3144 (tpp) cc_final: 0.1506 (mtm) REVERT: K 1036 MET cc_start: -0.0305 (ttt) cc_final: -0.0596 (ttt) REVERT: K 1072 PHE cc_start: 0.6967 (t80) cc_final: 0.5130 (m-10) REVERT: L 77 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6756 (mttm) REVERT: L 214 ARG cc_start: 0.8554 (mtt90) cc_final: 0.7618 (mtp-110) REVERT: L 270 TRP cc_start: 0.6427 (m100) cc_final: 0.5003 (m100) REVERT: L 326 LEU cc_start: 0.6537 (pp) cc_final: 0.6186 (pp) REVERT: L 394 ILE cc_start: 0.8824 (mt) cc_final: 0.8331 (mp) outliers start: 2 outliers final: 0 residues processed: 356 average time/residue: 0.3455 time to fit residues: 183.3700 Evaluate side-chains 308 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [162, 183, 11, 118, 37, 193, 133, 60, 134, 3, 130] chunk 162 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 809 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.181454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.144067 restraints weight = 107294.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.152175 restraints weight = 44587.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.157445 restraints weight = 23662.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.160910 restraints weight = 15058.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.163210 restraints weight = 10977.138| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22474 Z= 0.208 Angle : 0.687 8.200 31615 Z= 0.417 Chirality : 0.045 0.232 3569 Planarity : 0.006 0.105 3037 Dihedral : 27.579 174.834 5424 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 1947 helix: 0.32 (0.19), residues: 656 sheet: -0.82 (0.24), residues: 447 loop : -1.98 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 46 TYR 0.017 0.002 TYR K 42 PHE 0.059 0.002 PHE G 26 TRP 0.014 0.001 TRP K 207 HIS 0.015 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 (22474) covalent geometry : angle 0.68723 / 0.42 (31615) hydrogen bonds : bond 0.06153 / 4.24 ( 1064) hydrogen bonds : angle 5.11204 / 3.74 ( 2762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7655 (mmtt) REVERT: A 98 GLU cc_start: 0.8767 (pp20) cc_final: 0.8328 (pp20) REVERT: C 62 GLU cc_start: 0.7706 (tt0) cc_final: 0.7286 (mt-10) REVERT: D 86 LYS cc_start: 0.9139 (tptt) cc_final: 0.8806 (tppp) REVERT: D 117 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8381 (ttmt) REVERT: D 121 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8601 (tmtt) REVERT: E 77 GLN cc_start: 0.9012 (tt0) cc_final: 0.8715 (tp40) REVERT: E 104 LEU cc_start: 0.9163 (tp) cc_final: 0.8798 (mt) REVERT: F 53 GLU cc_start: 0.8311 (pm20) cc_final: 0.7678 (pm20) REVERT: F 60 LYS cc_start: 0.7248 (tttp) cc_final: 0.7007 (ttmm) REVERT: G 63 ILE cc_start: 0.6367 (mm) cc_final: 0.5972 (tp) REVERT: H 106 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8175 (mp0) REVERT: K 151 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8079 (mm-30) REVERT: K 218 MET cc_start: 0.8202 (mtm) cc_final: 0.7287 (tpt) REVERT: K 287 LYS cc_start: 0.5530 (mttp) cc_final: 0.5129 (mmmt) REVERT: K 288 GLU cc_start: 0.5999 (tp30) cc_final: 0.3818 (pt0) REVERT: K 312 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6870 (tm-30) REVERT: K 713 ARG cc_start: 0.4529 (ttt180) cc_final: 0.3652 (mmt180) REVERT: K 840 GLU cc_start: 0.5817 (tp30) cc_final: 0.5588 (tp30) REVERT: K 844 LYS cc_start: 0.7369 (mmtm) cc_final: 0.6903 (mtmt) REVERT: K 873 MET cc_start: 0.4352 (mtm) cc_final: 0.3372 (mpp) REVERT: K 875 GLU cc_start: 0.4413 (pp20) cc_final: 0.4032 (tm-30) REVERT: K 910 MET cc_start: 0.6635 (ptp) cc_final: 0.5921 (pmm) REVERT: K 1014 MET cc_start: 0.3256 (tpp) cc_final: 0.1787 (mtm) REVERT: K 1072 PHE cc_start: 0.7068 (t80) cc_final: 0.5071 (m-10) REVERT: L 77 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6809 (mttm) REVERT: L 214 ARG cc_start: 0.8594 (mtt90) cc_final: 0.7705 (mtp-110) REVERT: L 270 TRP cc_start: 0.6492 (m100) cc_final: 0.4928 (m100) REVERT: L 326 LEU cc_start: 0.6623 (pp) cc_final: 0.6266 (pp) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.3339 time to fit residues: 172.4688 Evaluate side-chains 303 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [37, 3, 118, 113, 47, 162, 88, 72, 73, 171, 60] chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 809 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.182424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.145359 restraints weight = 95778.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.153734 restraints weight = 37761.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.159202 restraints weight = 19314.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.162800 restraints weight = 11928.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.165195 restraints weight = 8472.650| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22474 Z= 0.154 Angle : 0.645 7.959 31615 Z= 0.392 Chirality : 0.044 0.222 3569 Planarity : 0.005 0.065 3037 Dihedral : 27.593 175.901 5424 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 1947 helix: 0.75 (0.19), residues: 656 sheet: -0.79 (0.24), residues: 454 loop : -1.85 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 426 TYR 0.045 0.002 TYR D 84 PHE 0.020 0.002 PHE G 26 TRP 0.014 0.001 TRP L 236 HIS 0.007 0.001 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (22474) covalent geometry : angle 0.64475 / 0.39 (31615) hydrogen bonds : bond 0.05420 / 3.72 ( 1064) hydrogen bonds : angle 4.73882 / 3.47 ( 2762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7563 (mmtm) REVERT: A 98 GLU cc_start: 0.8767 (pp20) cc_final: 0.8368 (pp20) REVERT: D 84 TYR cc_start: 0.5445 (m-80) cc_final: 0.5186 (m-10) REVERT: D 86 LYS cc_start: 0.9082 (tptt) cc_final: 0.8771 (tppp) REVERT: D 117 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8435 (ttpt) REVERT: D 121 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8644 (tmtt) REVERT: E 63 ILE cc_start: 0.7911 (mm) cc_final: 0.7339 (tt) REVERT: E 77 GLN cc_start: 0.8743 (tt0) cc_final: 0.8286 (tp40) REVERT: E 104 LEU cc_start: 0.9169 (tp) cc_final: 0.8783 (mt) REVERT: F 53 GLU cc_start: 0.8285 (pm20) cc_final: 0.7702 (pm20) REVERT: F 60 LYS cc_start: 0.7116 (tttp) cc_final: 0.6877 (ttmm) REVERT: G 63 ILE cc_start: 0.6356 (mm) cc_final: 0.5980 (tp) REVERT: H 106 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8106 (mp0) REVERT: K 151 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8101 (mm-30) REVERT: K 218 MET cc_start: 0.8141 (mtm) cc_final: 0.7247 (tpt) REVERT: K 288 GLU cc_start: 0.5990 (tp30) cc_final: 0.3809 (pt0) REVERT: K 840 GLU cc_start: 0.5653 (tp30) cc_final: 0.5409 (tp30) REVERT: K 844 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6832 (mtmt) REVERT: K 873 MET cc_start: 0.4312 (mtm) cc_final: 0.3338 (mpp) REVERT: K 875 GLU cc_start: 0.4370 (pp20) cc_final: 0.3995 (tm-30) REVERT: K 910 MET cc_start: 0.6643 (ptp) cc_final: 0.5938 (pmm) REVERT: K 1014 MET cc_start: 0.3225 (tpp) cc_final: 0.1815 (mtm) REVERT: K 1072 PHE cc_start: 0.6965 (t80) cc_final: 0.5211 (m-10) REVERT: L 77 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6800 (mttm) REVERT: L 214 ARG cc_start: 0.8555 (mtt90) cc_final: 0.7633 (mtp-110) REVERT: L 270 TRP cc_start: 0.6390 (m100) cc_final: 0.4846 (m100) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.3280 time to fit residues: 166.2022 Evaluate side-chains 298 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [111, 77, 3, 18, 103, 68, 199, 182, 117, 203, 156] chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 199 optimal weight: 0.0770 chunk 182 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 809 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.182296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.145091 restraints weight = 108277.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.153160 restraints weight = 45003.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.158450 restraints weight = 23940.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.161919 restraints weight = 15267.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.164293 restraints weight = 11145.196| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22474 Z= 0.185 Angle : 0.664 6.914 31615 Z= 0.402 Chirality : 0.044 0.228 3569 Planarity : 0.005 0.057 3037 Dihedral : 27.579 175.277 5424 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.45 % Favored : 92.50 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1947 helix: 0.67 (0.19), residues: 650 sheet: -0.74 (0.25), residues: 432 loop : -1.95 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.031 0.002 TYR D 84 PHE 0.024 0.002 PHE B 101 TRP 0.014 0.002 TRP K 207 HIS 0.011 0.002 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (22474) covalent geometry : angle 0.66390 / 0.40 (31615) hydrogen bonds : bond 0.05822 / 4.02 ( 1064) hydrogen bonds : angle 4.85109 / 3.55 ( 2762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7631 (mmtm) REVERT: A 98 GLU cc_start: 0.8769 (pp20) cc_final: 0.8343 (pp20) REVERT: D 84 TYR cc_start: 0.5500 (m-80) cc_final: 0.5212 (m-10) REVERT: D 86 LYS cc_start: 0.9112 (tptt) cc_final: 0.8831 (tppp) REVERT: D 117 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8483 (ttpt) REVERT: D 121 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8653 (tmtt) REVERT: E 63 ILE cc_start: 0.8144 (mm) cc_final: 0.7559 (tt) REVERT: E 77 GLN cc_start: 0.8766 (tt0) cc_final: 0.8305 (tp40) REVERT: E 104 LEU cc_start: 0.9172 (tp) cc_final: 0.8778 (mt) REVERT: F 28 GLN cc_start: 0.6997 (mp10) cc_final: 0.6750 (mp10) REVERT: F 53 GLU cc_start: 0.8305 (pm20) cc_final: 0.7790 (pm20) REVERT: F 60 LYS cc_start: 0.7226 (tttp) cc_final: 0.6806 (ttpt) REVERT: G 63 ILE cc_start: 0.6405 (mm) cc_final: 0.6043 (tp) REVERT: H 106 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8155 (mp0) REVERT: K 1 MET cc_start: 0.2576 (mpp) cc_final: 0.2246 (mpp) REVERT: K 151 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8139 (mm-30) REVERT: K 218 MET cc_start: 0.8168 (mtm) cc_final: 0.7263 (tpt) REVERT: K 288 GLU cc_start: 0.6060 (tp30) cc_final: 0.3873 (pm20) REVERT: K 298 LYS cc_start: 0.7185 (tttt) cc_final: 0.6942 (ttmt) REVERT: K 312 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7466 (tm-30) REVERT: K 840 GLU cc_start: 0.5733 (tp30) cc_final: 0.5510 (tp30) REVERT: K 844 LYS cc_start: 0.7369 (mmtm) cc_final: 0.6881 (mtmt) REVERT: K 873 MET cc_start: 0.4471 (mtm) cc_final: 0.3435 (mpp) REVERT: K 875 GLU cc_start: 0.4368 (pp20) cc_final: 0.3967 (tm-30) REVERT: K 910 MET cc_start: 0.6675 (ptp) cc_final: 0.5939 (pmm) REVERT: K 989 ARG cc_start: 0.4130 (mtm-85) cc_final: 0.3843 (ttm-80) REVERT: K 1014 MET cc_start: 0.3323 (tpp) cc_final: 0.1884 (mtm) REVERT: K 1072 PHE cc_start: 0.6807 (t80) cc_final: 0.4777 (m-10) REVERT: L 77 LYS cc_start: 0.7295 (mtpt) cc_final: 0.6840 (mttm) REVERT: L 214 ARG cc_start: 0.8591 (mtt90) cc_final: 0.7670 (mtp-110) REVERT: L 240 MET cc_start: 0.6971 (mmm) cc_final: 0.6412 (mmm) REVERT: L 356 TYR cc_start: 0.7823 (t80) cc_final: 0.7620 (t80) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.3336 time to fit residues: 169.9541 Evaluate side-chains 301 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [143, 136, 12, 36, 117, 93, 174, 191, 219, 101, 8] chunk 143 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 chunk 93 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 191 optimal weight: 0.0770 chunk 219 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN F 94 GLN H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.184815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.147669 restraints weight = 95420.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.156136 restraints weight = 37803.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.161695 restraints weight = 19397.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.165375 restraints weight = 11975.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.167807 restraints weight = 8482.779| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22474 Z= 0.137 Angle : 0.615 6.703 31615 Z= 0.375 Chirality : 0.043 0.206 3569 Planarity : 0.005 0.057 3037 Dihedral : 27.602 176.829 5424 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 1947 helix: 1.19 (0.19), residues: 651 sheet: -0.70 (0.25), residues: 445 loop : -1.75 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 426 TYR 0.035 0.002 TYR D 84 PHE 0.015 0.001 PHE L 257 TRP 0.011 0.001 TRP L 236 HIS 0.010 0.001 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (22474) covalent geometry : angle 0.61542 / 0.38 (31615) hydrogen bonds : bond 0.04928 / 3.38 ( 1064) hydrogen bonds : angle 4.43274 / 3.25 ( 2762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7521 (mmtm) REVERT: A 98 GLU cc_start: 0.8725 (pp20) cc_final: 0.8303 (pp20) REVERT: A 121 MET cc_start: 0.5642 (mtp) cc_final: 0.5069 (mtp) REVERT: D 86 LYS cc_start: 0.9094 (tptt) cc_final: 0.8863 (tppp) REVERT: D 117 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8452 (ttpt) REVERT: D 121 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8623 (tmtt) REVERT: E 63 ILE cc_start: 0.8058 (mm) cc_final: 0.7543 (tt) REVERT: E 77 GLN cc_start: 0.8629 (tt0) cc_final: 0.8164 (tp40) REVERT: E 104 LEU cc_start: 0.9140 (tp) cc_final: 0.8750 (mt) REVERT: F 28 GLN cc_start: 0.7218 (mp10) cc_final: 0.6960 (mp10) REVERT: F 53 GLU cc_start: 0.8219 (pm20) cc_final: 0.7614 (pm20) REVERT: F 60 LYS cc_start: 0.7136 (tttp) cc_final: 0.6739 (ttpt) REVERT: G 37 LYS cc_start: 0.6252 (mttm) cc_final: 0.5967 (ttmm) REVERT: H 106 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8061 (mp0) REVERT: K 1 MET cc_start: 0.2537 (mpp) cc_final: 0.2193 (mpp) REVERT: K 151 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8114 (mm-30) REVERT: K 254 LYS cc_start: 0.6038 (tttt) cc_final: 0.5215 (tmmt) REVERT: K 272 LEU cc_start: 0.6043 (mt) cc_final: 0.5760 (mt) REVERT: K 288 GLU cc_start: 0.6102 (tp30) cc_final: 0.3891 (pt0) REVERT: K 312 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7434 (tm-30) REVERT: K 713 ARG cc_start: 0.4018 (ttt180) cc_final: 0.3345 (mmt180) REVERT: K 840 GLU cc_start: 0.5512 (tp30) cc_final: 0.5269 (tp30) REVERT: K 844 LYS cc_start: 0.7298 (mmtm) cc_final: 0.6851 (mtmt) REVERT: K 873 MET cc_start: 0.4147 (mtm) cc_final: 0.3233 (mpp) REVERT: K 875 GLU cc_start: 0.4362 (pp20) cc_final: 0.3978 (tm-30) REVERT: K 908 ASN cc_start: 0.7525 (m-40) cc_final: 0.6389 (p0) REVERT: K 910 MET cc_start: 0.6675 (ptp) cc_final: 0.6228 (pmm) REVERT: K 989 ARG cc_start: 0.4156 (mtm-85) cc_final: 0.3860 (ttm-80) REVERT: K 1014 MET cc_start: 0.3352 (tpp) cc_final: 0.1930 (mtm) REVERT: K 1072 PHE cc_start: 0.6896 (t80) cc_final: 0.5149 (m-10) REVERT: L 77 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6734 (mttm) REVERT: L 177 MET cc_start: 0.8246 (tpp) cc_final: 0.7928 (tpp) REVERT: L 214 ARG cc_start: 0.8550 (mtt90) cc_final: 0.7649 (mtp-110) REVERT: L 240 MET cc_start: 0.6940 (mmm) cc_final: 0.6374 (mmm) REVERT: L 315 TYR cc_start: 0.5227 (m-80) cc_final: 0.4897 (m-80) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.3523 time to fit residues: 182.8328 Evaluate side-chains 304 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [204, 219, 43, 163, 36, 34, 211, 7, 147, 47, 92] chunk 204 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 90 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.182814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145833 restraints weight = 96516.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.154177 restraints weight = 38252.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.159674 restraints weight = 19629.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.163292 restraints weight = 12125.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.165710 restraints weight = 8621.937| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22474 Z= 0.152 Angle : 0.619 6.604 31615 Z= 0.377 Chirality : 0.043 0.204 3569 Planarity : 0.005 0.072 3037 Dihedral : 27.581 175.898 5424 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 1947 helix: 1.23 (0.19), residues: 649 sheet: -0.68 (0.25), residues: 442 loop : -1.78 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.030 0.002 TYR D 84 PHE 0.015 0.001 PHE L 257 TRP 0.012 0.001 TRP K 207 HIS 0.013 0.001 HIS K 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (22474) covalent geometry : angle 0.61901 / 0.38 (31615) hydrogen bonds : bond 0.05043 / 3.47 ( 1064) hydrogen bonds : angle 4.47757 / 3.28 ( 2762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7111.33 seconds wall clock time: 121 minutes 42.39 seconds (7302.39 seconds total)