Starting phenix.real_space_refine on Sat Feb 7 13:49:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qon_53264/02_2026/9qon_53264.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 10436 2.51 5 N 2860 2.21 5 O 3151 1.98 5 H 16396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32930 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 3742 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 3, 'GLN:plan1': 6, 'PHE:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1033 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "C" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1476 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 426 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3776 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "G" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3781 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "O" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3609 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "P" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3928 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "Q" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3765 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain: "R" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3686 Classifications: {'peptide': 241} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "S" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3708 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 9, 'TRANS': 226} Time building chain proxies: 4.91, per 1000 atoms: 0.15 Number of scatterers: 32930 At special positions: 0 Unit cell: (120.12, 130.13, 140.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 3151 8.00 N 2860 7.00 C 10436 6.00 H 16396 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: 2.02 Conformation dependent library (CDL) restraints added in 976.4 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3958 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 50.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.696A pdb=" N CYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 731 removed outlier: 8.075A pdb=" N GLU A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.627A pdb=" N TYR A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.865A pdb=" N ALA A 760 " --> pdb=" O GLU A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 removed outlier: 3.765A pdb=" N LEU A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 781 through 796 removed outlier: 3.932A pdb=" N ILE A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 removed outlier: 3.555A pdb=" N MET A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 805 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 834 through 845 Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 852 through 874 removed outlier: 4.166A pdb=" N ASN A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 929 removed outlier: 4.080A pdb=" N ILE A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 993 through 996 Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1003 through 1010 Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 4.208A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1025 Processing helix chain 'A' and resid 1026 through 1028 No H-bonds generated for 'chain 'A' and resid 1026 through 1028' Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.627A pdb=" N GLN A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 194 removed outlier: 3.783A pdb=" N MET B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 93 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 143 through 188 removed outlier: 4.018A pdb=" N MET C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 77 through 96 Processing helix chain 'F' and resid 20 through 33 removed outlier: 3.561A pdb=" N GLU F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 removed outlier: 3.507A pdb=" N SER F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 122 removed outlier: 3.858A pdb=" N ASP F 113 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 178 through 179 No H-bonds generated for 'chain 'F' and resid 178 through 179' Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.505A pdb=" N MET F 184 " --> pdb=" O MET F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 200 removed outlier: 4.217A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 242 Processing helix chain 'G' and resid 8 through 12 removed outlier: 3.917A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.568A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 36 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.619A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.724A pdb=" N SER G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'O' and resid 19 through 30 Processing helix chain 'O' and resid 79 through 101 removed outlier: 3.556A pdb=" N ARG O 83 " --> pdb=" O GLY O 79 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL O 84 " --> pdb=" O PRO O 80 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU O 85 " --> pdb=" O ASP O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 120 removed outlier: 3.624A pdb=" N TYR O 120 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 177 removed outlier: 3.709A pdb=" N GLY O 169 " --> pdb=" O ASN O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.504A pdb=" N GLU O 196 " --> pdb=" O LEU O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 207 removed outlier: 4.051A pdb=" N ILE O 207 " --> pdb=" O GLU O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 231 removed outlier: 3.817A pdb=" N ASP O 227 " --> pdb=" O THR O 223 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA O 231 " --> pdb=" O ASP O 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 29 Processing helix chain 'P' and resid 79 through 102 removed outlier: 4.151A pdb=" N VAL P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN P 100 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 121 removed outlier: 3.729A pdb=" N TYR P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.586A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 229 through 246 removed outlier: 3.524A pdb=" N LYS P 246 " --> pdb=" O GLU P 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 27 Processing helix chain 'Q' and resid 76 through 98 Processing helix chain 'Q' and resid 103 through 121 removed outlier: 3.563A pdb=" N ILE Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 176 Processing helix chain 'Q' and resid 179 through 182 Processing helix chain 'Q' and resid 183 through 196 Processing helix chain 'Q' and resid 221 through 237 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.978A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.550A pdb=" N ILE R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 removed outlier: 3.631A pdb=" N ALA R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 118 Processing helix chain 'R' and resid 173 through 183 removed outlier: 3.708A pdb=" N SER R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.799A pdb=" N VAL R 237 " --> pdb=" O GLU R 233 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS R 239 " --> pdb=" O GLU R 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 30 removed outlier: 3.520A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS S 30 " --> pdb=" O MET S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 99 Processing helix chain 'S' and resid 104 through 118 removed outlier: 3.685A pdb=" N SER S 110 " --> pdb=" O SER S 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 121 No H-bonds generated for 'chain 'S' and resid 119 through 121' Processing helix chain 'S' and resid 164 through 175 removed outlier: 4.483A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 180 removed outlier: 3.878A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 175 through 180' Processing helix chain 'S' and resid 183 through 197 Processing helix chain 'S' and resid 229 through 234 Processing sheet with id=AA1, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AA2, first strand: chain 'F' and resid 66 through 68 removed outlier: 3.592A pdb=" N GLY F 138 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 76 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN F 147 " --> pdb=" O SER F 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.564A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 79 through 82 removed outlier: 3.507A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 12 through 13 removed outlier: 3.725A pdb=" N LYS O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'O' and resid 65 through 66 removed outlier: 3.601A pdb=" N SER O 76 " --> pdb=" O SER O 132 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER O 132 " --> pdb=" O SER O 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.684A pdb=" N THR P 217 " --> pdb=" O VAL P 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 65 through 67 removed outlier: 3.650A pdb=" N SER P 133 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.626A pdb=" N HIS Q 15 " --> pdb=" O SER Q 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 158 through 161 removed outlier: 3.578A pdb=" N GLY Q 34 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG Q 212 " --> pdb=" O SER Q 216 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER Q 216 " --> pdb=" O ARG Q 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 63 through 64 removed outlier: 3.526A pdb=" N SER Q 130 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AB5, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.511A pdb=" N ILE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AB7, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.192A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N HIS S 65 " --> pdb=" O ILE S 72 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE S 72 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP S 138 " --> pdb=" O GLY S 141 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN S 152 " --> pdb=" O CYS S 148 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16360 1.03 - 1.23: 62 1.23 - 1.42: 6910 1.42 - 1.62: 9736 1.62 - 1.81: 138 Bond restraints: 33206 Sorted by residual: bond pdb=" N GLY G 4 " pdb=" CA GLY G 4 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N PHE B 142 " pdb=" CA PHE B 142 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N PHE S 2 " pdb=" CA PHE S 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N GLU O 2 " pdb=" CA GLU O 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ILE F 3 " pdb=" CA ILE F 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 33201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 57113 1.18 - 2.36: 2645 2.36 - 3.54: 164 3.54 - 4.72: 49 4.72 - 5.91: 3 Bond angle restraints: 59974 Sorted by residual: angle pdb=" N ILE O 67 " pdb=" CA ILE O 67 " pdb=" C ILE O 67 " ideal model delta sigma weight residual 112.96 108.45 4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N VAL Q 198 " pdb=" CA VAL Q 198 " pdb=" C VAL Q 198 " ideal model delta sigma weight residual 112.12 108.57 3.55 8.40e-01 1.42e+00 1.78e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 111.91 108.95 2.96 8.90e-01 1.26e+00 1.10e+01 angle pdb=" CA ARG A 776 " pdb=" CB ARG A 776 " pdb=" CG ARG A 776 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.72e+00 angle pdb=" CA VAL R 184 " pdb=" C VAL R 184 " pdb=" N TYR R 185 " ideal model delta sigma weight residual 116.60 120.22 -3.62 1.45e+00 4.76e-01 6.22e+00 ... (remaining 59969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13796 17.99 - 35.99: 1199 35.99 - 53.98: 402 53.98 - 71.97: 122 71.97 - 89.97: 36 Dihedral angle restraints: 15555 sinusoidal: 8488 harmonic: 7067 Sorted by residual: dihedral pdb=" CA TYR O 120 " pdb=" C TYR O 120 " pdb=" N THR O 121 " pdb=" CA THR O 121 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE G 210 " pdb=" C PHE G 210 " pdb=" N LYS G 211 " pdb=" CA LYS G 211 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN S 4 " pdb=" C ASN S 4 " pdb=" N GLN S 5 " pdb=" CA GLN S 5 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 15552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1548 0.028 - 0.056: 675 0.056 - 0.084: 183 0.084 - 0.112: 130 0.112 - 0.140: 20 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA ILE F 3 " pdb=" N ILE F 3 " pdb=" C ILE F 3 " pdb=" CB ILE F 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB VAL B 162 " pdb=" CA VAL B 162 " pdb=" CG1 VAL B 162 " pdb=" CG2 VAL B 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE Q 40 " pdb=" N ILE Q 40 " pdb=" C ILE Q 40 " pdb=" CB ILE Q 40 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2553 not shown) Planarity restraints: 4979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 164 " -0.164 9.50e-02 1.11e+02 5.49e-02 3.62e+00 pdb=" NE ARG S 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG S 164 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG S 164 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG S 164 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG S 164 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG S 164 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG S 164 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG S 164 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 705 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C ASP A 705 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 705 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 706 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 829 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 830 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 830 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 830 " 0.020 5.00e-02 4.00e+02 ... (remaining 4976 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 623 2.10 - 2.73: 57186 2.73 - 3.35: 95381 3.35 - 3.98: 118136 3.98 - 4.60: 188467 Nonbonded interactions: 459793 Sorted by model distance: nonbonded pdb=" OE1 GLU Q 179 " pdb=" H GLU Q 179 " model vdw 1.479 2.450 nonbonded pdb=" O GLN C 80 " pdb="HD21 ASN C 84 " model vdw 1.483 2.450 nonbonded pdb=" OE1 GLU Q 99 " pdb=" H GLU Q 99 " model vdw 1.574 2.450 nonbonded pdb="HE21 GLN A 803 " pdb=" OE1 GLU A 855 " model vdw 1.603 2.450 nonbonded pdb=" OD2 ASP C 187 " pdb=" HH TYR O 23 " model vdw 1.614 2.450 ... (remaining 459788 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.200 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.490 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16810 Z= 0.149 Angle : 0.555 5.906 22690 Z= 0.320 Chirality : 0.038 0.140 2556 Planarity : 0.004 0.072 2934 Dihedral : 16.178 89.945 6261 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.77 % Allowed : 17.23 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.18), residues: 2092 helix: 1.15 (0.17), residues: 928 sheet: -0.42 (0.26), residues: 369 loop : -0.10 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 164 TYR 0.013 0.001 TYR O 75 PHE 0.013 0.001 PHE S 154 TRP 0.014 0.001 TRP Q 156 HIS 0.009 0.001 HIS P 53 Details of bonding type rmsd covalent geometry : bond 0.00311 (16810) covalent geometry : angle 0.55529 (22690) hydrogen bonds : bond 0.18768 ( 909) hydrogen bonds : angle 6.99449 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 588 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 557 time to evaluate : 0.889 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: B 149 MET cc_start: 0.5875 (ttp) cc_final: 0.5425 (ttp) REVERT: C 88 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6062 (mm-30) REVERT: F 53 VAL cc_start: 0.7917 (m) cc_final: 0.7679 (p) REVERT: F 122 TYR cc_start: 0.6631 (m-80) cc_final: 0.6380 (m-80) REVERT: F 191 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7878 (mtmm) REVERT: F 234 GLU cc_start: 0.7561 (tt0) cc_final: 0.7320 (tt0) REVERT: G 30 LYS cc_start: 0.7617 (mttp) cc_final: 0.7175 (mmtt) REVERT: G 146 GLU cc_start: 0.7447 (tt0) cc_final: 0.7126 (tt0) REVERT: O 198 PHE cc_start: 0.5126 (t80) cc_final: 0.4562 (t80) REVERT: P 70 GLU cc_start: 0.7317 (tt0) cc_final: 0.6980 (tt0) REVERT: P 239 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5340 (mtpp) REVERT: Q 43 LEU cc_start: 0.7006 (mt) cc_final: 0.6783 (mp) REVERT: Q 191 VAL cc_start: 0.6945 (t) cc_final: 0.6739 (p) REVERT: R 24 VAL cc_start: 0.7684 (t) cc_final: 0.7435 (m) REVERT: R 41 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: R 69 GLU cc_start: 0.7006 (tt0) cc_final: 0.6803 (pp20) REVERT: R 105 GLU cc_start: 0.6666 (pt0) cc_final: 0.6466 (pt0) REVERT: R 111 SER cc_start: 0.7130 (m) cc_final: 0.6786 (m) REVERT: R 154 PHE cc_start: 0.7373 (m-80) cc_final: 0.7006 (m-80) REVERT: S 220 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6097 (mm-30) REVERT: S 222 THR cc_start: 0.7089 (p) cc_final: 0.6882 (p) REVERT: S 224 TYR cc_start: 0.8078 (m-80) cc_final: 0.7707 (m-10) outliers start: 31 outliers final: 8 residues processed: 580 average time/residue: 0.3393 time to fit residues: 278.4976 Evaluate side-chains 444 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 434 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain O residue 160 THR Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 205 ASN Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain S residue 53 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 ASN A 927 ASN B 171 ASN D 84 ASN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN O 51 GLN P 53 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103602 restraints weight = 72150.049| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.17 r_work: 0.3272 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16810 Z= 0.214 Angle : 0.643 6.660 22690 Z= 0.348 Chirality : 0.043 0.169 2556 Planarity : 0.005 0.070 2934 Dihedral : 5.657 59.248 2334 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.32 % Allowed : 18.55 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.18), residues: 2092 helix: 0.94 (0.16), residues: 961 sheet: -0.47 (0.26), residues: 354 loop : -0.36 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 49 TYR 0.014 0.002 TYR B 200 PHE 0.017 0.002 PHE P 12 TRP 0.014 0.002 TRP Q 156 HIS 0.012 0.002 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00485 (16810) covalent geometry : angle 0.64292 (22690) hydrogen bonds : bond 0.05105 ( 909) hydrogen bonds : angle 4.96538 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 586 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 528 time to evaluate : 0.849 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: A 711 GLN cc_start: 0.7846 (mt0) cc_final: 0.7625 (mp10) REVERT: A 840 MET cc_start: 0.6695 (tpp) cc_final: 0.6296 (tpt) REVERT: B 149 MET cc_start: 0.5912 (ttp) cc_final: 0.5470 (ttp) REVERT: F 27 MET cc_start: 0.7037 (mtt) cc_final: 0.6829 (mtm) REVERT: F 31 GLU cc_start: 0.7610 (tt0) cc_final: 0.7405 (mt-10) REVERT: F 42 LYS cc_start: 0.7948 (tttp) cc_final: 0.7554 (tttp) REVERT: F 53 VAL cc_start: 0.8499 (m) cc_final: 0.8117 (p) REVERT: F 59 GLU cc_start: 0.7482 (tp30) cc_final: 0.7105 (tp30) REVERT: F 114 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7531 (mmt-90) REVERT: F 191 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8242 (mtmm) REVERT: F 195 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7837 (tttm) REVERT: F 234 GLU cc_start: 0.8007 (tt0) cc_final: 0.7784 (tt0) REVERT: F 241 GLU cc_start: 0.6712 (pp20) cc_final: 0.6166 (pp20) REVERT: G 138 MET cc_start: 0.8349 (ttp) cc_final: 0.8014 (ttm) REVERT: G 174 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7433 (mp0) REVERT: O 23 TYR cc_start: 0.5966 (m-10) cc_final: 0.5674 (m-10) REVERT: O 75 TYR cc_start: 0.7749 (p90) cc_final: 0.7506 (p90) REVERT: O 133 LEU cc_start: 0.6970 (mp) cc_final: 0.6706 (mp) REVERT: O 180 ASP cc_start: 0.7617 (p0) cc_final: 0.7370 (p0) REVERT: O 198 PHE cc_start: 0.7053 (t80) cc_final: 0.6807 (t80) REVERT: P 28 ILE cc_start: 0.7548 (mt) cc_final: 0.7340 (mm) REVERT: P 178 ASP cc_start: 0.7020 (m-30) cc_final: 0.6669 (t0) REVERT: P 213 ILE cc_start: 0.6772 (mt) cc_final: 0.6571 (mt) REVERT: P 231 LYS cc_start: 0.7958 (tttt) cc_final: 0.7717 (ttpp) REVERT: P 239 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5405 (mtpp) REVERT: Q 45 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.6892 (t) REVERT: Q 62 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6961 (mt) REVERT: Q 99 GLU cc_start: 0.8128 (mp0) cc_final: 0.7784 (mp0) REVERT: Q 122 ASN cc_start: 0.8242 (m-40) cc_final: 0.7595 (t0) REVERT: Q 226 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7078 (tp30) REVERT: R 16 SER cc_start: 0.7117 (p) cc_final: 0.6829 (p) REVERT: R 20 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: R 21 LEU cc_start: 0.8034 (mt) cc_final: 0.7779 (mp) REVERT: R 24 VAL cc_start: 0.8170 (t) cc_final: 0.7863 (m) REVERT: R 29 GLU cc_start: 0.7344 (tp30) cc_final: 0.7050 (tp30) REVERT: R 107 MET cc_start: 0.7229 (ttm) cc_final: 0.6846 (ttm) REVERT: R 118 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7787 (t0) REVERT: R 141 LEU cc_start: 0.7866 (mt) cc_final: 0.7601 (mp) REVERT: R 156 MET cc_start: 0.8160 (tmm) cc_final: 0.7901 (tmm) REVERT: R 164 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8076 (tm-30) REVERT: R 192 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7980 (mtpp) REVERT: R 197 SER cc_start: 0.8359 (t) cc_final: 0.8147 (m) REVERT: S 35 THR cc_start: 0.7970 (p) cc_final: 0.7751 (p) REVERT: S 153 TYR cc_start: 0.8296 (p90) cc_final: 0.7916 (p90) REVERT: S 155 ASP cc_start: 0.6795 (t0) cc_final: 0.6415 (t0) REVERT: S 224 TYR cc_start: 0.8311 (m-80) cc_final: 0.8063 (m-80) outliers start: 58 outliers final: 36 residues processed: 565 average time/residue: 0.3311 time to fit residues: 266.6129 Evaluate side-chains 526 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 486 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 HIS Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 160 SER Chi-restraints excluded: chain S residue 177 SER Chi-restraints excluded: chain S residue 229 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS A 923 ASN A 927 ASN B 171 ASN C 97 HIS D 84 ASN G 75 ASN O 165 ASN P 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106115 restraints weight = 71553.648| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.00 r_work: 0.3265 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16810 Z= 0.250 Angle : 0.655 8.358 22690 Z= 0.356 Chirality : 0.043 0.193 2556 Planarity : 0.005 0.065 2934 Dihedral : 5.393 46.178 2323 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.32 % Allowed : 21.81 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.18), residues: 2092 helix: 0.95 (0.17), residues: 948 sheet: -0.70 (0.26), residues: 364 loop : -0.66 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 49 TYR 0.022 0.002 TYR O 144 PHE 0.019 0.002 PHE S 154 TRP 0.012 0.002 TRP A 741 HIS 0.010 0.002 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00578 (16810) covalent geometry : angle 0.65497 (22690) hydrogen bonds : bond 0.05595 ( 909) hydrogen bonds : angle 4.76094 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 615 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 557 time to evaluate : 0.702 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: A 721 VAL cc_start: 0.7685 (t) cc_final: 0.7426 (p) REVERT: A 744 MET cc_start: 0.7943 (mmt) cc_final: 0.7674 (mmm) REVERT: A 777 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 837 GLU cc_start: 0.6896 (tt0) cc_final: 0.6607 (tt0) REVERT: B 149 MET cc_start: 0.5900 (ttp) cc_final: 0.5438 (ttp) REVERT: B 188 GLN cc_start: 0.7697 (tp40) cc_final: 0.7195 (tp40) REVERT: B 190 MET cc_start: 0.7496 (ttm) cc_final: 0.7219 (ttm) REVERT: F 37 ILE cc_start: 0.8385 (pt) cc_final: 0.8135 (pt) REVERT: F 42 LYS cc_start: 0.8522 (tttp) cc_final: 0.8218 (tttp) REVERT: F 51 LYS cc_start: 0.7496 (ttmm) cc_final: 0.7204 (mtpp) REVERT: F 59 GLU cc_start: 0.7775 (tp30) cc_final: 0.7463 (tp30) REVERT: F 93 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6874 (mm-30) REVERT: F 101 ASN cc_start: 0.8691 (t0) cc_final: 0.8419 (m-40) REVERT: F 105 ASN cc_start: 0.8526 (m-40) cc_final: 0.8272 (m-40) REVERT: F 183 GLU cc_start: 0.7853 (tp30) cc_final: 0.7472 (tp30) REVERT: F 187 ARG cc_start: 0.7387 (tpp80) cc_final: 0.7048 (tpp80) REVERT: F 191 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8564 (mtmm) REVERT: F 195 LYS cc_start: 0.8249 (tmtt) cc_final: 0.8021 (tttm) REVERT: F 204 VAL cc_start: 0.8627 (p) cc_final: 0.8312 (m) REVERT: F 234 GLU cc_start: 0.7750 (tt0) cc_final: 0.7544 (tt0) REVERT: F 236 GLU cc_start: 0.7697 (tt0) cc_final: 0.7490 (mt-10) REVERT: F 237 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7759 (ttpp) REVERT: F 241 GLU cc_start: 0.6699 (pp20) cc_final: 0.5885 (pp20) REVERT: G 34 GLN cc_start: 0.8693 (mm110) cc_final: 0.8359 (mm-40) REVERT: G 104 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8323 (ttpp) REVERT: G 147 GLN cc_start: 0.8823 (mp10) cc_final: 0.8580 (mt0) REVERT: G 173 THR cc_start: 0.8539 (t) cc_final: 0.8229 (t) REVERT: G 174 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7789 (mp0) REVERT: G 234 GLU cc_start: 0.8161 (tp30) cc_final: 0.7658 (tp30) REVERT: O 70 HIS cc_start: 0.8238 (p-80) cc_final: 0.7774 (p-80) REVERT: O 101 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8208 (mm110) REVERT: O 104 ILE cc_start: 0.8137 (tt) cc_final: 0.7912 (tt) REVERT: O 119 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7113 (mt-10) REVERT: O 135 ILE cc_start: 0.8572 (mp) cc_final: 0.8321 (mt) REVERT: P 6 ASP cc_start: 0.8434 (t0) cc_final: 0.8201 (t0) REVERT: P 15 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7540 (mt-10) REVERT: P 124 PHE cc_start: 0.7926 (p90) cc_final: 0.7551 (p90) REVERT: P 143 TYR cc_start: 0.8455 (m-80) cc_final: 0.8037 (m-80) REVERT: P 177 GLN cc_start: 0.8382 (tt0) cc_final: 0.8052 (tp40) REVERT: P 178 ASP cc_start: 0.7890 (m-30) cc_final: 0.7583 (t0) REVERT: P 201 MET cc_start: 0.7497 (ttm) cc_final: 0.7295 (ttm) REVERT: P 222 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8039 (mmmt) REVERT: P 231 LYS cc_start: 0.8183 (tttt) cc_final: 0.7869 (mtpp) REVERT: P 234 GLU cc_start: 0.7600 (tp30) cc_final: 0.7246 (tp30) REVERT: Q 20 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: Q 24 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7660 (tp30) REVERT: Q 26 VAL cc_start: 0.8833 (t) cc_final: 0.8617 (p) REVERT: Q 27 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8710 (ttmt) REVERT: Q 62 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7855 (mt) REVERT: Q 90 GLU cc_start: 0.8121 (tp30) cc_final: 0.7816 (tp30) REVERT: Q 124 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8089 (mtt90) REVERT: Q 153 TYR cc_start: 0.8713 (p90) cc_final: 0.8455 (p90) REVERT: Q 175 ASN cc_start: 0.8326 (m110) cc_final: 0.7978 (m110) REVERT: Q 197 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7742 (mm-30) REVERT: Q 226 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7435 (tp30) REVERT: R 16 SER cc_start: 0.8249 (p) cc_final: 0.7929 (p) REVERT: R 62 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (t) REVERT: R 65 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7634 (mm-30) REVERT: R 70 ILE cc_start: 0.8179 (mm) cc_final: 0.7598 (mt) REVERT: R 90 ASP cc_start: 0.8004 (t0) cc_final: 0.7589 (t70) REVERT: R 114 GLN cc_start: 0.8525 (tt0) cc_final: 0.8325 (tt0) REVERT: R 117 SER cc_start: 0.8301 (t) cc_final: 0.7916 (t) REVERT: R 119 LEU cc_start: 0.8427 (tp) cc_final: 0.8224 (tt) REVERT: R 152 GLN cc_start: 0.8348 (mt0) cc_final: 0.7988 (mt0) REVERT: R 159 SER cc_start: 0.8666 (m) cc_final: 0.8335 (p) REVERT: R 170 ILE cc_start: 0.8038 (tp) cc_final: 0.7738 (pt) REVERT: R 192 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8110 (mtpp) REVERT: R 196 LYS cc_start: 0.8272 (tttp) cc_final: 0.8039 (ttmm) REVERT: R 197 SER cc_start: 0.9014 (t) cc_final: 0.8773 (m) REVERT: R 216 GLU cc_start: 0.7261 (tp30) cc_final: 0.7061 (tp30) REVERT: S 27 GLU cc_start: 0.8273 (tp30) cc_final: 0.7977 (tp30) REVERT: S 29 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8093 (p) REVERT: S 65 HIS cc_start: 0.8225 (m90) cc_final: 0.7992 (m90) REVERT: S 74 ILE cc_start: 0.7920 (mt) cc_final: 0.7610 (mm) REVERT: S 118 ILE cc_start: 0.8295 (mm) cc_final: 0.8079 (mt) REVERT: S 122 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8026 (mtp-110) REVERT: S 128 TYR cc_start: 0.8037 (m-10) cc_final: 0.7740 (m-10) REVERT: S 138 ASP cc_start: 0.7756 (p0) cc_final: 0.7477 (p0) REVERT: S 153 TYR cc_start: 0.8283 (p90) cc_final: 0.7413 (p90) REVERT: S 182 CYS cc_start: 0.7996 (m) cc_final: 0.7763 (m) outliers start: 58 outliers final: 41 residues processed: 586 average time/residue: 0.3602 time to fit residues: 297.0186 Evaluate side-chains 568 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 523 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 206 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain P residue 239 LYS Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 207 GLU Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN D 84 ASN P 167 ASN R 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103980 restraints weight = 70943.370| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.97 r_work: 0.3221 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16810 Z= 0.213 Angle : 0.569 6.645 22690 Z= 0.310 Chirality : 0.040 0.151 2556 Planarity : 0.005 0.072 2934 Dihedral : 5.181 44.449 2323 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.09 % Allowed : 24.33 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.18), residues: 2092 helix: 1.08 (0.17), residues: 950 sheet: -0.64 (0.25), residues: 371 loop : -0.62 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 3 TYR 0.020 0.002 TYR O 75 PHE 0.021 0.002 PHE R 226 TRP 0.009 0.002 TRP P 139 HIS 0.009 0.001 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00484 (16810) covalent geometry : angle 0.56947 (22690) hydrogen bonds : bond 0.04571 ( 909) hydrogen bonds : angle 4.53781 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 599 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 545 time to evaluate : 0.924 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: A 721 VAL cc_start: 0.7803 (t) cc_final: 0.7593 (p) REVERT: A 753 PRO cc_start: 0.6903 (Cg_exo) cc_final: 0.6616 (Cg_endo) REVERT: A 777 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 784 GLN cc_start: 0.7325 (tp40) cc_final: 0.7120 (tp40) REVERT: A 837 GLU cc_start: 0.7130 (tt0) cc_final: 0.6826 (tt0) REVERT: A 910 ASN cc_start: 0.5643 (OUTLIER) cc_final: 0.5336 (p0) REVERT: A 920 LEU cc_start: 0.7976 (mm) cc_final: 0.7718 (mp) REVERT: B 149 MET cc_start: 0.6153 (ttp) cc_final: 0.5664 (ttp) REVERT: B 187 ASP cc_start: 0.7931 (t0) cc_final: 0.7701 (t0) REVERT: B 188 GLN cc_start: 0.7833 (tp40) cc_final: 0.7476 (tp40) REVERT: C 161 LYS cc_start: 0.6418 (mtmt) cc_final: 0.6202 (mmmt) REVERT: C 163 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7164 (ttp-170) REVERT: C 168 GLU cc_start: 0.7774 (tp30) cc_final: 0.7491 (tp30) REVERT: F 51 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7324 (mtpp) REVERT: F 59 GLU cc_start: 0.7884 (tp30) cc_final: 0.7554 (tp30) REVERT: F 93 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7110 (mm-30) REVERT: F 101 ASN cc_start: 0.8680 (t0) cc_final: 0.8409 (m-40) REVERT: F 187 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7099 (tpp80) REVERT: F 191 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8513 (mtmm) REVERT: F 203 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6830 (mt-10) REVERT: F 236 GLU cc_start: 0.7789 (tt0) cc_final: 0.7581 (mt-10) REVERT: F 237 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7786 (ttpp) REVERT: F 241 GLU cc_start: 0.6634 (pp20) cc_final: 0.5856 (pp20) REVERT: G 26 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7351 (mt-10) REVERT: G 97 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8017 (mm-30) REVERT: G 113 MET cc_start: 0.7984 (mmp) cc_final: 0.7509 (mmp) REVERT: G 147 GLN cc_start: 0.8785 (mp10) cc_final: 0.8534 (mt0) REVERT: G 173 THR cc_start: 0.8735 (t) cc_final: 0.8336 (p) REVERT: G 174 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8073 (mp0) REVERT: O 101 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8270 (mm110) REVERT: O 118 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7131 (tp40) REVERT: O 135 ILE cc_start: 0.8646 (mp) cc_final: 0.8390 (mt) REVERT: O 149 ASP cc_start: 0.7909 (m-30) cc_final: 0.7592 (p0) REVERT: O 154 TYR cc_start: 0.8555 (p90) cc_final: 0.8348 (p90) REVERT: O 175 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8464 (mtpp) REVERT: P 15 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7847 (mt-10) REVERT: P 67 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7223 (pptt) REVERT: P 124 PHE cc_start: 0.7917 (p90) cc_final: 0.7531 (p90) REVERT: P 166 ASN cc_start: 0.8130 (t0) cc_final: 0.7748 (m-40) REVERT: P 177 GLN cc_start: 0.8556 (tt0) cc_final: 0.8161 (tp40) REVERT: P 178 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7644 (t0) REVERT: P 211 VAL cc_start: 0.8733 (m) cc_final: 0.8456 (p) REVERT: P 222 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7954 (mmmt) REVERT: P 234 GLU cc_start: 0.7350 (tp30) cc_final: 0.6938 (tp30) REVERT: Q 5 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7507 (tpp80) REVERT: Q 47 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8124 (ttpp) REVERT: Q 62 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7985 (mt) REVERT: Q 67 ASP cc_start: 0.8412 (m-30) cc_final: 0.8203 (m-30) REVERT: Q 124 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.8032 (mtt90) REVERT: Q 175 ASN cc_start: 0.8394 (m110) cc_final: 0.8112 (m110) REVERT: Q 197 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8017 (mt-10) REVERT: Q 215 GLN cc_start: 0.7946 (tt0) cc_final: 0.7737 (tt0) REVERT: Q 227 LYS cc_start: 0.7875 (tmmt) cc_final: 0.7430 (ttmt) REVERT: R 51 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6646 (mt-10) REVERT: R 62 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (t) REVERT: R 114 GLN cc_start: 0.8510 (tt0) cc_final: 0.8274 (tt0) REVERT: R 117 SER cc_start: 0.8553 (t) cc_final: 0.8086 (p) REVERT: R 156 MET cc_start: 0.7951 (tmm) cc_final: 0.7697 (tmm) REVERT: R 159 SER cc_start: 0.8580 (m) cc_final: 0.8086 (p) REVERT: R 164 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7534 (tm-30) REVERT: R 170 ILE cc_start: 0.7994 (tp) cc_final: 0.7782 (pt) REVERT: S 27 GLU cc_start: 0.8347 (tp30) cc_final: 0.7996 (tp30) REVERT: S 29 VAL cc_start: 0.8338 (m) cc_final: 0.8107 (p) REVERT: S 36 VAL cc_start: 0.8700 (m) cc_final: 0.8352 (p) REVERT: S 47 VAL cc_start: 0.8607 (p) cc_final: 0.8396 (m) REVERT: S 118 ILE cc_start: 0.8251 (mm) cc_final: 0.8030 (mt) REVERT: S 122 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7790 (mtp-110) REVERT: S 153 TYR cc_start: 0.8289 (p90) cc_final: 0.7624 (p90) REVERT: S 229 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (t) outliers start: 54 outliers final: 38 residues processed: 570 average time/residue: 0.3571 time to fit residues: 285.8508 Evaluate side-chains 565 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 521 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 910 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain O residue 227 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 207 GLU Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 227 ASP Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN R 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104973 restraints weight = 70809.200| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.95 r_work: 0.3220 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.8632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16810 Z= 0.190 Angle : 0.542 5.932 22690 Z= 0.294 Chirality : 0.039 0.156 2556 Planarity : 0.004 0.043 2934 Dihedral : 4.993 46.185 2319 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.26 % Allowed : 24.90 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.18), residues: 2092 helix: 1.21 (0.17), residues: 951 sheet: -0.54 (0.25), residues: 370 loop : -0.53 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 90 TYR 0.012 0.001 TYR A 854 PHE 0.018 0.001 PHE R 226 TRP 0.007 0.001 TRP A 843 HIS 0.007 0.001 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00427 (16810) covalent geometry : angle 0.54152 (22690) hydrogen bonds : bond 0.04378 ( 909) hydrogen bonds : angle 4.44568 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 593 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 536 time to evaluate : 0.898 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: A 721 VAL cc_start: 0.7915 (t) cc_final: 0.7689 (p) REVERT: A 753 PRO cc_start: 0.6886 (Cg_exo) cc_final: 0.6602 (Cg_endo) REVERT: A 757 GLU cc_start: 0.7624 (pm20) cc_final: 0.7187 (pm20) REVERT: A 777 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 784 GLN cc_start: 0.7451 (tp40) cc_final: 0.7116 (tp40) REVERT: A 797 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6293 (mm-30) REVERT: A 837 GLU cc_start: 0.7225 (tt0) cc_final: 0.6886 (tt0) REVERT: A 910 ASN cc_start: 0.5062 (OUTLIER) cc_final: 0.4702 (p0) REVERT: B 149 MET cc_start: 0.6165 (ttp) cc_final: 0.5668 (ttp) REVERT: B 188 GLN cc_start: 0.7945 (tp40) cc_final: 0.7552 (tp40) REVERT: C 88 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 161 LYS cc_start: 0.6549 (mtmt) cc_final: 0.6314 (mmmt) REVERT: C 163 ARG cc_start: 0.7993 (ptt90) cc_final: 0.7764 (ptt180) REVERT: C 167 GLU cc_start: 0.8161 (tp30) cc_final: 0.7767 (mm-30) REVERT: C 168 GLU cc_start: 0.7907 (tp30) cc_final: 0.7515 (tp30) REVERT: F 42 LYS cc_start: 0.8266 (tttp) cc_final: 0.7876 (tttp) REVERT: F 51 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7413 (mtpp) REVERT: F 59 GLU cc_start: 0.7922 (tp30) cc_final: 0.7603 (tp30) REVERT: F 64 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7966 (mmmm) REVERT: F 93 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7195 (mm-30) REVERT: F 187 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7145 (tpp80) REVERT: F 237 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7801 (ttpp) REVERT: F 241 GLU cc_start: 0.6572 (pp20) cc_final: 0.5818 (pp20) REVERT: G 26 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7550 (mt-10) REVERT: G 112 ASP cc_start: 0.7578 (t0) cc_final: 0.7305 (p0) REVERT: G 113 MET cc_start: 0.8108 (mmp) cc_final: 0.7261 (mmp) REVERT: G 147 GLN cc_start: 0.8856 (mp10) cc_final: 0.8602 (mt0) REVERT: G 173 THR cc_start: 0.8716 (t) cc_final: 0.8353 (p) REVERT: G 174 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8095 (mp0) REVERT: O 101 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8315 (mm-40) REVERT: O 118 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7342 (tp40) REVERT: O 135 ILE cc_start: 0.8675 (mp) cc_final: 0.8423 (mt) REVERT: O 149 ASP cc_start: 0.7917 (m-30) cc_final: 0.7670 (p0) REVERT: O 198 PHE cc_start: 0.8489 (t80) cc_final: 0.8257 (t80) REVERT: P 15 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7874 (mt-10) REVERT: P 17 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7966 (ptm160) REVERT: P 50 ARG cc_start: 0.7712 (ptm160) cc_final: 0.7414 (ptm160) REVERT: P 67 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7273 (pptt) REVERT: P 124 PHE cc_start: 0.7978 (p90) cc_final: 0.7590 (p90) REVERT: P 166 ASN cc_start: 0.8098 (t0) cc_final: 0.7745 (m-40) REVERT: P 167 ASN cc_start: 0.8784 (m-40) cc_final: 0.8566 (m-40) REVERT: P 177 GLN cc_start: 0.8390 (tt0) cc_final: 0.7966 (tp40) REVERT: P 178 ASP cc_start: 0.8032 (m-30) cc_final: 0.7599 (t0) REVERT: P 211 VAL cc_start: 0.8725 (m) cc_final: 0.8473 (p) REVERT: P 222 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7985 (mmmt) REVERT: P 234 GLU cc_start: 0.7395 (tp30) cc_final: 0.7006 (tp30) REVERT: Q 5 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7566 (tpp80) REVERT: Q 47 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8107 (ttpp) REVERT: Q 62 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8025 (mt) REVERT: Q 124 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.8027 (mtt90) REVERT: Q 143 ARG cc_start: 0.8351 (mmt90) cc_final: 0.7485 (mtt-85) REVERT: Q 175 ASN cc_start: 0.8452 (m110) cc_final: 0.8227 (m-40) REVERT: Q 197 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7842 (mt-10) REVERT: Q 224 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7811 (mm-30) REVERT: R 90 ASP cc_start: 0.8122 (t0) cc_final: 0.7540 (t0) REVERT: R 114 GLN cc_start: 0.8544 (tt0) cc_final: 0.8329 (tt0) REVERT: R 117 SER cc_start: 0.8624 (t) cc_final: 0.8258 (p) REVERT: R 159 SER cc_start: 0.8589 (m) cc_final: 0.8116 (p) REVERT: R 164 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7585 (tm-30) REVERT: R 216 GLU cc_start: 0.7307 (tp30) cc_final: 0.7041 (tp30) REVERT: S 27 GLU cc_start: 0.8313 (tp30) cc_final: 0.7962 (tp30) REVERT: S 36 VAL cc_start: 0.8665 (m) cc_final: 0.8406 (p) REVERT: S 118 ILE cc_start: 0.8304 (mm) cc_final: 0.8085 (mt) REVERT: S 122 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7821 (mtp-110) REVERT: S 138 ASP cc_start: 0.7694 (p0) cc_final: 0.7322 (p0) REVERT: S 153 TYR cc_start: 0.8277 (p90) cc_final: 0.7650 (p90) REVERT: S 178 GLU cc_start: 0.7514 (mp0) cc_final: 0.6767 (mp0) outliers start: 57 outliers final: 45 residues processed: 559 average time/residue: 0.3932 time to fit residues: 302.2354 Evaluate side-chains 566 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 517 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 910 ASN Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 206 LEU Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 207 GLU Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 183 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 227 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN D 84 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN R 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102773 restraints weight = 70828.440| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.95 r_work: 0.3207 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.9136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16810 Z= 0.223 Angle : 0.561 6.242 22690 Z= 0.306 Chirality : 0.040 0.158 2556 Planarity : 0.004 0.048 2934 Dihedral : 5.053 51.007 2319 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.09 % Allowed : 24.79 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.18), residues: 2092 helix: 1.19 (0.17), residues: 951 sheet: -0.49 (0.26), residues: 369 loop : -0.61 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 223 TYR 0.018 0.002 TYR O 75 PHE 0.023 0.002 PHE R 226 TRP 0.008 0.001 TRP A 843 HIS 0.008 0.001 HIS S 190 Details of bonding type rmsd covalent geometry : bond 0.00500 (16810) covalent geometry : angle 0.56130 (22690) hydrogen bonds : bond 0.04507 ( 909) hydrogen bonds : angle 4.43966 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 594 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 540 time to evaluate : 0.581 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: A 705 ASP cc_start: 0.8182 (t0) cc_final: 0.7869 (t0) REVERT: A 711 GLN cc_start: 0.7666 (mt0) cc_final: 0.7444 (mt0) REVERT: A 721 VAL cc_start: 0.8015 (t) cc_final: 0.7794 (p) REVERT: A 753 PRO cc_start: 0.7005 (Cg_exo) cc_final: 0.6761 (Cg_endo) REVERT: A 757 GLU cc_start: 0.7726 (pm20) cc_final: 0.7279 (pm20) REVERT: A 777 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 797 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6407 (mm-30) REVERT: A 837 GLU cc_start: 0.7242 (tt0) cc_final: 0.6894 (tt0) REVERT: B 149 MET cc_start: 0.6155 (ttp) cc_final: 0.5657 (ttp) REVERT: B 169 ILE cc_start: 0.7945 (tt) cc_final: 0.7677 (pt) REVERT: B 188 GLN cc_start: 0.8042 (tp40) cc_final: 0.7595 (tp40) REVERT: C 88 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7215 (mm-30) REVERT: C 161 LYS cc_start: 0.6743 (mtmt) cc_final: 0.6510 (mmmt) REVERT: C 163 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7746 (ptt180) REVERT: C 167 GLU cc_start: 0.8333 (tp30) cc_final: 0.7956 (mm-30) REVERT: C 196 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8106 (mm-40) REVERT: F 30 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8361 (t) REVERT: F 42 LYS cc_start: 0.8241 (tttp) cc_final: 0.7826 (tttp) REVERT: F 51 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7798 (mtpp) REVERT: F 109 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8684 (ttpt) REVERT: F 189 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7796 (tp) REVERT: F 192 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: F 237 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7830 (ttpp) REVERT: F 241 GLU cc_start: 0.6789 (pp20) cc_final: 0.6066 (pp20) REVERT: G 112 ASP cc_start: 0.7625 (t0) cc_final: 0.7371 (p0) REVERT: G 113 MET cc_start: 0.8230 (mmp) cc_final: 0.7893 (mmp) REVERT: G 116 LYS cc_start: 0.8532 (tttt) cc_final: 0.8309 (tttm) REVERT: G 147 GLN cc_start: 0.8869 (mp10) cc_final: 0.8635 (mt0) REVERT: G 173 THR cc_start: 0.8716 (t) cc_final: 0.8404 (p) REVERT: G 174 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8130 (mp0) REVERT: G 202 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7319 (mp) REVERT: G 234 GLU cc_start: 0.7854 (tp30) cc_final: 0.7470 (tp30) REVERT: O 48 GLU cc_start: 0.7753 (tp30) cc_final: 0.7462 (tp30) REVERT: O 101 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8150 (mm110) REVERT: O 118 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: O 135 ILE cc_start: 0.8674 (mp) cc_final: 0.8433 (mt) REVERT: O 149 ASP cc_start: 0.8019 (m-30) cc_final: 0.7786 (p0) REVERT: O 175 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8465 (mtpp) REVERT: O 198 PHE cc_start: 0.8476 (t80) cc_final: 0.7971 (t80) REVERT: P 15 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7896 (mt-10) REVERT: P 17 ARG cc_start: 0.8268 (ptm160) cc_final: 0.7956 (ptm160) REVERT: P 50 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7656 (ptm160) REVERT: P 124 PHE cc_start: 0.7963 (p90) cc_final: 0.7573 (p90) REVERT: P 166 ASN cc_start: 0.8404 (t0) cc_final: 0.8143 (m-40) REVERT: P 177 GLN cc_start: 0.8448 (tt0) cc_final: 0.8035 (tp40) REVERT: P 178 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: P 181 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7716 (tm-30) REVERT: P 222 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8052 (mmmt) REVERT: P 231 LYS cc_start: 0.8370 (tttt) cc_final: 0.7883 (ttmm) REVERT: P 234 GLU cc_start: 0.7453 (tp30) cc_final: 0.7169 (tp30) REVERT: P 242 GLU cc_start: 0.7291 (tp30) cc_final: 0.6912 (tp30) REVERT: P 246 LYS cc_start: 0.6613 (mmtt) cc_final: 0.6395 (mmtt) REVERT: Q 5 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7721 (tpp80) REVERT: Q 47 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8073 (ttpp) REVERT: Q 62 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8147 (mt) REVERT: Q 90 GLU cc_start: 0.8327 (tp30) cc_final: 0.8127 (tp30) REVERT: Q 143 ARG cc_start: 0.8431 (mmt90) cc_final: 0.7734 (mtt-85) REVERT: Q 175 ASN cc_start: 0.8452 (m110) cc_final: 0.8251 (m-40) REVERT: Q 197 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8210 (mt-10) REVERT: Q 224 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7639 (mm-30) REVERT: Q 231 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7549 (mm-30) REVERT: R 10 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7820 (mtt180) REVERT: R 90 ASP cc_start: 0.8192 (t0) cc_final: 0.7598 (t0) REVERT: R 114 GLN cc_start: 0.8577 (tt0) cc_final: 0.8372 (tt0) REVERT: R 117 SER cc_start: 0.8668 (t) cc_final: 0.8286 (p) REVERT: R 156 MET cc_start: 0.7973 (tmm) cc_final: 0.7599 (tmm) REVERT: R 159 SER cc_start: 0.8555 (m) cc_final: 0.8111 (p) REVERT: R 164 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7594 (tm-30) REVERT: R 207 GLU cc_start: 0.7882 (pt0) cc_final: 0.7343 (pp20) REVERT: R 216 GLU cc_start: 0.7255 (tp30) cc_final: 0.6943 (tp30) REVERT: R 235 GLU cc_start: 0.8037 (tp30) cc_final: 0.7812 (mm-30) REVERT: S 27 GLU cc_start: 0.8179 (tp30) cc_final: 0.7893 (tp30) REVERT: S 118 ILE cc_start: 0.8344 (mm) cc_final: 0.8144 (mt) REVERT: S 138 ASP cc_start: 0.7842 (p0) cc_final: 0.7489 (p0) REVERT: S 153 TYR cc_start: 0.8311 (p90) cc_final: 0.7675 (p90) REVERT: S 171 TYR cc_start: 0.8311 (t80) cc_final: 0.7789 (t80) REVERT: S 178 GLU cc_start: 0.7545 (mp0) cc_final: 0.7344 (mp0) REVERT: S 182 CYS cc_start: 0.7940 (m) cc_final: 0.7614 (m) outliers start: 54 outliers final: 37 residues processed: 563 average time/residue: 0.3815 time to fit residues: 296.2485 Evaluate side-chains 577 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 533 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 206 LEU Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 215 GLN Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 227 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 152 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN R 182 GLN S 16 GLN S 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103672 restraints weight = 70943.869| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.96 r_work: 0.3226 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.9284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16810 Z= 0.153 Angle : 0.523 6.715 22690 Z= 0.281 Chirality : 0.039 0.144 2556 Planarity : 0.004 0.059 2934 Dihedral : 4.891 50.725 2319 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.80 % Allowed : 25.64 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.18), residues: 2092 helix: 1.44 (0.17), residues: 952 sheet: -0.37 (0.26), residues: 368 loop : -0.48 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 122 TYR 0.013 0.001 TYR O 75 PHE 0.015 0.001 PHE R 226 TRP 0.008 0.001 TRP A 843 HIS 0.006 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00345 (16810) covalent geometry : angle 0.52250 (22690) hydrogen bonds : bond 0.04003 ( 909) hydrogen bonds : angle 4.28773 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 591 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 542 time to evaluate : 0.748 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: A 705 ASP cc_start: 0.8249 (t0) cc_final: 0.7944 (t0) REVERT: A 721 VAL cc_start: 0.8022 (t) cc_final: 0.7804 (p) REVERT: A 753 PRO cc_start: 0.7022 (Cg_exo) cc_final: 0.6797 (Cg_endo) REVERT: A 757 GLU cc_start: 0.7740 (pm20) cc_final: 0.7326 (pm20) REVERT: A 777 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 797 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6406 (mm-30) REVERT: A 837 GLU cc_start: 0.7262 (tt0) cc_final: 0.6882 (tt0) REVERT: A 858 VAL cc_start: 0.6875 (t) cc_final: 0.6594 (p) REVERT: B 149 MET cc_start: 0.6092 (ttp) cc_final: 0.5582 (ttp) REVERT: B 169 ILE cc_start: 0.7965 (tt) cc_final: 0.7722 (pt) REVERT: B 188 GLN cc_start: 0.8034 (tp40) cc_final: 0.7609 (tp40) REVERT: C 88 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7240 (mm-30) REVERT: C 161 LYS cc_start: 0.6781 (mtmt) cc_final: 0.6553 (mmmt) REVERT: C 167 GLU cc_start: 0.8348 (tp30) cc_final: 0.8092 (mm-30) REVERT: C 196 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8106 (mm-40) REVERT: F 42 LYS cc_start: 0.8244 (tttp) cc_final: 0.7834 (tttp) REVERT: F 51 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7748 (mtpp) REVERT: F 59 GLU cc_start: 0.8032 (tp30) cc_final: 0.7780 (tp30) REVERT: F 109 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8699 (ttpt) REVERT: F 170 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7741 (mm-40) REVERT: F 237 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7860 (ttpp) REVERT: F 241 GLU cc_start: 0.6692 (pp20) cc_final: 0.5994 (pp20) REVERT: G 55 LYS cc_start: 0.8822 (mttt) cc_final: 0.8585 (mtpt) REVERT: G 113 MET cc_start: 0.8218 (mmp) cc_final: 0.7911 (mmp) REVERT: G 116 LYS cc_start: 0.8537 (tttt) cc_final: 0.8324 (tttm) REVERT: G 147 GLN cc_start: 0.8832 (mp10) cc_final: 0.8590 (mt0) REVERT: G 173 THR cc_start: 0.8722 (t) cc_final: 0.8403 (p) REVERT: G 174 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8079 (mp0) REVERT: G 234 GLU cc_start: 0.7839 (tp30) cc_final: 0.7468 (tp30) REVERT: O 48 GLU cc_start: 0.7745 (tp30) cc_final: 0.7488 (tp30) REVERT: O 101 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8162 (mm110) REVERT: O 118 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7571 (tp40) REVERT: O 135 ILE cc_start: 0.8673 (mp) cc_final: 0.8438 (mt) REVERT: O 175 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8477 (mtpp) REVERT: O 198 PHE cc_start: 0.8541 (t80) cc_final: 0.7999 (t80) REVERT: P 15 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7901 (mt-10) REVERT: P 17 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7922 (ptm160) REVERT: P 124 PHE cc_start: 0.7961 (p90) cc_final: 0.7572 (p90) REVERT: P 166 ASN cc_start: 0.8411 (t0) cc_final: 0.8151 (m-40) REVERT: P 177 GLN cc_start: 0.8436 (tt0) cc_final: 0.8008 (tp40) REVERT: P 178 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7678 (t70) REVERT: P 181 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7686 (tm-30) REVERT: P 184 MET cc_start: 0.8618 (mmp) cc_final: 0.8259 (mmm) REVERT: P 222 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8037 (mmmt) REVERT: P 231 LYS cc_start: 0.8342 (tttt) cc_final: 0.7968 (ttpp) REVERT: P 234 GLU cc_start: 0.7589 (tp30) cc_final: 0.7278 (tp30) REVERT: P 242 GLU cc_start: 0.7378 (tp30) cc_final: 0.6897 (tp30) REVERT: P 246 LYS cc_start: 0.6691 (mmtt) cc_final: 0.6409 (mmtt) REVERT: Q 5 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7785 (tpp80) REVERT: Q 47 LYS cc_start: 0.8230 (ttmt) cc_final: 0.8022 (ttpp) REVERT: Q 90 GLU cc_start: 0.8355 (tp30) cc_final: 0.8136 (tp30) REVERT: Q 224 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7469 (mm-30) REVERT: Q 231 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7484 (mm-30) REVERT: R 90 ASP cc_start: 0.8180 (t0) cc_final: 0.7596 (t0) REVERT: R 117 SER cc_start: 0.8616 (t) cc_final: 0.8330 (p) REVERT: R 159 SER cc_start: 0.8606 (m) cc_final: 0.8186 (p) REVERT: R 164 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7661 (tm-30) REVERT: R 207 GLU cc_start: 0.7838 (pt0) cc_final: 0.7363 (pp20) REVERT: R 216 GLU cc_start: 0.7295 (tp30) cc_final: 0.7007 (tp30) REVERT: R 231 LYS cc_start: 0.8281 (tttt) cc_final: 0.8074 (tttp) REVERT: R 235 GLU cc_start: 0.8118 (tp30) cc_final: 0.7881 (mm-30) REVERT: S 27 GLU cc_start: 0.8142 (tp30) cc_final: 0.7935 (tp30) REVERT: S 118 ILE cc_start: 0.8288 (mm) cc_final: 0.8081 (mt) REVERT: S 138 ASP cc_start: 0.7826 (p0) cc_final: 0.7484 (p0) REVERT: S 153 TYR cc_start: 0.8257 (p90) cc_final: 0.7698 (p90) REVERT: S 171 TYR cc_start: 0.8264 (t80) cc_final: 0.7792 (t80) REVERT: S 178 GLU cc_start: 0.7642 (mp0) cc_final: 0.7304 (mp0) REVERT: S 182 CYS cc_start: 0.7895 (m) cc_final: 0.7545 (m) outliers start: 49 outliers final: 39 residues processed: 564 average time/residue: 0.3653 time to fit residues: 286.3633 Evaluate side-chains 558 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 517 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 207 SER Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 207 GLU Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 203 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 184 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN S 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104396 restraints weight = 70529.251| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.96 r_work: 0.3233 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.9351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16810 Z= 0.124 Angle : 0.508 8.152 22690 Z= 0.273 Chirality : 0.039 0.144 2556 Planarity : 0.004 0.048 2934 Dihedral : 4.774 48.982 2319 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.58 % Allowed : 25.87 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.19), residues: 2092 helix: 1.60 (0.17), residues: 955 sheet: -0.27 (0.26), residues: 366 loop : -0.38 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 122 TYR 0.009 0.001 TYR O 75 PHE 0.014 0.001 PHE R 226 TRP 0.008 0.001 TRP A 843 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00279 (16810) covalent geometry : angle 0.50841 (22690) hydrogen bonds : bond 0.03820 ( 909) hydrogen bonds : angle 4.21108 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 566 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 521 time to evaluate : 0.789 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: A 705 ASP cc_start: 0.8260 (t0) cc_final: 0.7936 (t0) REVERT: A 721 VAL cc_start: 0.8026 (t) cc_final: 0.7822 (p) REVERT: A 757 GLU cc_start: 0.7759 (pm20) cc_final: 0.7352 (pm20) REVERT: A 777 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 797 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6421 (mm-30) REVERT: A 837 GLU cc_start: 0.7240 (tt0) cc_final: 0.6880 (tt0) REVERT: A 858 VAL cc_start: 0.6860 (t) cc_final: 0.6581 (p) REVERT: B 149 MET cc_start: 0.6324 (ttp) cc_final: 0.5850 (ttp) REVERT: B 169 ILE cc_start: 0.7988 (tt) cc_final: 0.7743 (pt) REVERT: B 188 GLN cc_start: 0.8031 (tp40) cc_final: 0.7608 (tp40) REVERT: C 88 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 161 LYS cc_start: 0.6783 (mtmt) cc_final: 0.6565 (mmmt) REVERT: C 167 GLU cc_start: 0.8331 (tp30) cc_final: 0.8073 (mm-30) REVERT: C 196 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8097 (mm-40) REVERT: F 42 LYS cc_start: 0.8301 (tttp) cc_final: 0.7881 (tttp) REVERT: F 51 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7507 (mtpp) REVERT: F 59 GLU cc_start: 0.8030 (tp30) cc_final: 0.7770 (tp30) REVERT: F 187 ARG cc_start: 0.7658 (tpp80) cc_final: 0.7441 (mmm160) REVERT: F 192 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: F 237 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7876 (ttpp) REVERT: F 241 GLU cc_start: 0.6640 (pp20) cc_final: 0.5947 (pp20) REVERT: G 55 LYS cc_start: 0.8830 (mttt) cc_final: 0.8587 (mtpt) REVERT: G 147 GLN cc_start: 0.8833 (mp10) cc_final: 0.8574 (mt0) REVERT: G 173 THR cc_start: 0.8720 (t) cc_final: 0.8397 (p) REVERT: G 174 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8103 (mp0) REVERT: G 202 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7279 (mp) REVERT: G 234 GLU cc_start: 0.7695 (tp30) cc_final: 0.7347 (tp30) REVERT: O 48 GLU cc_start: 0.7753 (tp30) cc_final: 0.7489 (tp30) REVERT: O 101 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8162 (mm110) REVERT: O 118 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: O 135 ILE cc_start: 0.8660 (mp) cc_final: 0.8429 (mt) REVERT: O 175 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8495 (mtpp) REVERT: O 198 PHE cc_start: 0.8487 (t80) cc_final: 0.7974 (t80) REVERT: O 224 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7988 (mt-10) REVERT: P 15 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7884 (mp0) REVERT: P 17 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7902 (ptm160) REVERT: P 124 PHE cc_start: 0.7930 (p90) cc_final: 0.7515 (p90) REVERT: P 166 ASN cc_start: 0.8392 (t0) cc_final: 0.8136 (m-40) REVERT: P 177 GLN cc_start: 0.8433 (tt0) cc_final: 0.8027 (tp40) REVERT: P 178 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7657 (t0) REVERT: P 181 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7672 (tm-30) REVERT: P 184 MET cc_start: 0.8601 (mmp) cc_final: 0.8271 (mmm) REVERT: P 199 LYS cc_start: 0.8768 (tppt) cc_final: 0.8439 (tppt) REVERT: P 222 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8038 (mmmt) REVERT: P 231 LYS cc_start: 0.8328 (tttt) cc_final: 0.7939 (ttpp) REVERT: P 234 GLU cc_start: 0.7574 (tp30) cc_final: 0.7264 (tp30) REVERT: P 242 GLU cc_start: 0.7387 (tp30) cc_final: 0.6884 (tp30) REVERT: P 246 LYS cc_start: 0.6781 (mmtt) cc_final: 0.6578 (mmtt) REVERT: Q 5 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7766 (tpp80) REVERT: Q 67 ASP cc_start: 0.8149 (m-30) cc_final: 0.7896 (m-30) REVERT: Q 224 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7476 (mm-30) REVERT: Q 231 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7473 (mm-30) REVERT: R 90 ASP cc_start: 0.8193 (t0) cc_final: 0.7609 (t0) REVERT: R 117 SER cc_start: 0.8610 (t) cc_final: 0.8287 (p) REVERT: R 156 MET cc_start: 0.7913 (tmm) cc_final: 0.7424 (tmm) REVERT: R 159 SER cc_start: 0.8616 (m) cc_final: 0.8238 (p) REVERT: R 164 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7635 (tm-30) REVERT: R 207 GLU cc_start: 0.7787 (pt0) cc_final: 0.7337 (pp20) REVERT: R 216 GLU cc_start: 0.7254 (tp30) cc_final: 0.6973 (tp30) REVERT: R 231 LYS cc_start: 0.8279 (tttt) cc_final: 0.8070 (tttp) REVERT: R 235 GLU cc_start: 0.8145 (tp30) cc_final: 0.7887 (mm-30) REVERT: S 8 ASN cc_start: 0.8402 (m-40) cc_final: 0.8153 (m-40) REVERT: S 27 GLU cc_start: 0.8128 (tp30) cc_final: 0.7838 (tp30) REVERT: S 138 ASP cc_start: 0.7793 (p0) cc_final: 0.7450 (p0) REVERT: S 153 TYR cc_start: 0.8250 (p90) cc_final: 0.7694 (p90) REVERT: S 171 TYR cc_start: 0.8232 (t80) cc_final: 0.7697 (t80) REVERT: S 178 GLU cc_start: 0.7619 (mp0) cc_final: 0.7296 (mp0) REVERT: S 182 CYS cc_start: 0.7916 (m) cc_final: 0.7562 (m) outliers start: 45 outliers final: 38 residues processed: 543 average time/residue: 0.3633 time to fit residues: 274.6824 Evaluate side-chains 557 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 515 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 207 SER Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 185 ASP Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 183 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 192 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 89 optimal weight: 0.1980 chunk 198 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 122 ASN R 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105389 restraints weight = 69895.625| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.9428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16810 Z= 0.108 Angle : 0.498 8.440 22690 Z= 0.266 Chirality : 0.038 0.142 2556 Planarity : 0.004 0.052 2934 Dihedral : 4.626 45.128 2319 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 26.90 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.19), residues: 2092 helix: 1.77 (0.17), residues: 956 sheet: -0.12 (0.26), residues: 361 loop : -0.29 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 122 TYR 0.019 0.001 TYR B 178 PHE 0.012 0.001 PHE R 226 TRP 0.007 0.001 TRP A 843 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00244 (16810) covalent geometry : angle 0.49798 (22690) hydrogen bonds : bond 0.03555 ( 909) hydrogen bonds : angle 4.10487 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 571 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 534 time to evaluate : 0.930 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: A 705 ASP cc_start: 0.8285 (t0) cc_final: 0.7957 (t0) REVERT: A 721 VAL cc_start: 0.8023 (t) cc_final: 0.7796 (p) REVERT: A 757 GLU cc_start: 0.7793 (pm20) cc_final: 0.7465 (pm20) REVERT: A 797 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6405 (mm-30) REVERT: A 837 GLU cc_start: 0.7225 (tt0) cc_final: 0.6865 (tt0) REVERT: A 858 VAL cc_start: 0.6871 (t) cc_final: 0.6580 (p) REVERT: A 920 LEU cc_start: 0.8089 (mm) cc_final: 0.7852 (mp) REVERT: B 169 ILE cc_start: 0.7986 (tt) cc_final: 0.7762 (pt) REVERT: B 188 GLN cc_start: 0.7995 (tp40) cc_final: 0.7556 (tp40) REVERT: C 88 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7102 (mm-30) REVERT: C 161 LYS cc_start: 0.6766 (mtmt) cc_final: 0.6555 (mmmt) REVERT: C 167 GLU cc_start: 0.8246 (tp30) cc_final: 0.7702 (mm-30) REVERT: C 196 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8046 (mm-40) REVERT: F 42 LYS cc_start: 0.8228 (tttp) cc_final: 0.7807 (tttp) REVERT: F 59 GLU cc_start: 0.8003 (tp30) cc_final: 0.7773 (tp30) REVERT: F 150 MET cc_start: 0.8241 (ttp) cc_final: 0.7842 (ttp) REVERT: F 187 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7421 (mmm160) REVERT: F 192 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: F 218 GLU cc_start: 0.7223 (tp30) cc_final: 0.6842 (tp30) REVERT: F 237 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7853 (ttpp) REVERT: F 241 GLU cc_start: 0.6579 (pp20) cc_final: 0.5892 (pp20) REVERT: G 55 LYS cc_start: 0.8797 (mttt) cc_final: 0.8593 (mtpt) REVERT: G 147 GLN cc_start: 0.8810 (mp10) cc_final: 0.8573 (mt0) REVERT: G 173 THR cc_start: 0.8726 (t) cc_final: 0.8385 (p) REVERT: G 174 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8091 (mp0) REVERT: G 205 VAL cc_start: 0.8675 (t) cc_final: 0.8350 (p) REVERT: G 223 GLU cc_start: 0.7623 (tp30) cc_final: 0.7358 (tp30) REVERT: G 234 GLU cc_start: 0.7657 (tp30) cc_final: 0.7295 (tp30) REVERT: O 48 GLU cc_start: 0.7779 (tp30) cc_final: 0.7524 (tp30) REVERT: O 101 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8370 (mm110) REVERT: O 118 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7562 (tp40) REVERT: O 135 ILE cc_start: 0.8659 (mp) cc_final: 0.8413 (mt) REVERT: O 175 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8488 (mtpp) REVERT: O 198 PHE cc_start: 0.8498 (t80) cc_final: 0.7982 (t80) REVERT: O 224 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8007 (mt-10) REVERT: P 15 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7874 (mt-10) REVERT: P 17 ARG cc_start: 0.8221 (ptm160) cc_final: 0.7887 (ptm160) REVERT: P 124 PHE cc_start: 0.7950 (p90) cc_final: 0.7578 (p90) REVERT: P 166 ASN cc_start: 0.8408 (t0) cc_final: 0.8159 (m-40) REVERT: P 177 GLN cc_start: 0.8424 (tt0) cc_final: 0.8019 (tp40) REVERT: P 178 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7646 (t0) REVERT: P 181 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7522 (tm-30) REVERT: P 184 MET cc_start: 0.8507 (mmp) cc_final: 0.8249 (mmm) REVERT: P 199 LYS cc_start: 0.8757 (tppt) cc_final: 0.8444 (tppt) REVERT: P 222 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8013 (mmmt) REVERT: P 231 LYS cc_start: 0.8321 (tttt) cc_final: 0.7874 (ttpp) REVERT: P 234 GLU cc_start: 0.7575 (tp30) cc_final: 0.7266 (tp30) REVERT: P 242 GLU cc_start: 0.7386 (tp30) cc_final: 0.6883 (tp30) REVERT: P 246 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6584 (mmtt) REVERT: Q 5 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7774 (tpp80) REVERT: Q 67 ASP cc_start: 0.8141 (m-30) cc_final: 0.7907 (m-30) REVERT: Q 227 LYS cc_start: 0.8100 (tmmt) cc_final: 0.7779 (ttmt) REVERT: Q 231 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7436 (mm-30) REVERT: R 90 ASP cc_start: 0.8160 (t0) cc_final: 0.7589 (t0) REVERT: R 117 SER cc_start: 0.8576 (t) cc_final: 0.8352 (p) REVERT: R 119 LEU cc_start: 0.8260 (mt) cc_final: 0.7978 (mt) REVERT: R 159 SER cc_start: 0.8523 (m) cc_final: 0.8205 (p) REVERT: R 164 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7675 (tm-30) REVERT: R 207 GLU cc_start: 0.7794 (pt0) cc_final: 0.7345 (pp20) REVERT: R 216 GLU cc_start: 0.7248 (tp30) cc_final: 0.6941 (tp30) REVERT: R 231 LYS cc_start: 0.8262 (tttt) cc_final: 0.8019 (tttp) REVERT: R 235 GLU cc_start: 0.8123 (tp30) cc_final: 0.7829 (mm-30) REVERT: S 8 ASN cc_start: 0.8315 (m-40) cc_final: 0.8046 (m-40) REVERT: S 27 GLU cc_start: 0.8120 (tp30) cc_final: 0.7827 (tp30) REVERT: S 138 ASP cc_start: 0.7751 (p0) cc_final: 0.7423 (p0) REVERT: S 153 TYR cc_start: 0.8258 (p90) cc_final: 0.7239 (p90) REVERT: S 171 TYR cc_start: 0.8194 (t80) cc_final: 0.7655 (t80) REVERT: S 178 GLU cc_start: 0.7651 (mp0) cc_final: 0.7322 (mp0) outliers start: 37 outliers final: 27 residues processed: 549 average time/residue: 0.3571 time to fit residues: 272.3212 Evaluate side-chains 557 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 527 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 155 ASN Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 207 SER Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 HIS R 182 GLN S 21 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101638 restraints weight = 71855.201| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.99 r_work: 0.3186 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.9731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16810 Z= 0.292 Angle : 0.611 8.494 22690 Z= 0.333 Chirality : 0.042 0.154 2556 Planarity : 0.005 0.053 2934 Dihedral : 5.075 53.883 2319 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.77 % Allowed : 27.07 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.18), residues: 2092 helix: 1.24 (0.17), residues: 951 sheet: -0.42 (0.26), residues: 361 loop : -0.62 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 57 TYR 0.020 0.002 TYR O 120 PHE 0.021 0.002 PHE R 226 TRP 0.012 0.002 TRP P 139 HIS 0.011 0.002 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00660 (16810) covalent geometry : angle 0.61080 (22690) hydrogen bonds : bond 0.04904 ( 909) hydrogen bonds : angle 4.48593 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 995 is missing expected H atoms. Skipping. Residue LYS 996 is missing expected H atoms. Skipping. Residue LEU 999 is missing expected H atoms. Skipping. Residue TYR 1000 is missing expected H atoms. Skipping. Residue ILE 1002 is missing expected H atoms. Skipping. Residue LEU 1004 is missing expected H atoms. Skipping. Residue TYR 1007 is missing expected H atoms. Skipping. Residue LEU 1008 is missing expected H atoms. Skipping. Residue THR 1009 is missing expected H atoms. Skipping. Residue LEU 1012 is missing expected H atoms. Skipping. Residue TYR 1021 is missing expected H atoms. Skipping. Residue ILE 1022 is missing expected H atoms. Skipping. Residue MET 1023 is missing expected H atoms. Skipping. Residue SER 1025 is missing expected H atoms. Skipping. Residue LEU 1028 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue LEU 1036 is missing expected H atoms. Skipping. Residue THR 1038 is missing expected H atoms. Skipping. Residue ILE 1039 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Evaluate side-chains 572 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 541 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 ASP cc_start: 0.8304 (t0) cc_final: 0.8083 (t0) REVERT: A 721 VAL cc_start: 0.8176 (t) cc_final: 0.7959 (p) REVERT: A 733 ASP cc_start: 0.7377 (t0) cc_final: 0.7046 (t0) REVERT: A 757 GLU cc_start: 0.7844 (pm20) cc_final: 0.7525 (pm20) REVERT: A 797 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 837 GLU cc_start: 0.7406 (tt0) cc_final: 0.7134 (tt0) REVERT: A 858 VAL cc_start: 0.6910 (t) cc_final: 0.6630 (p) REVERT: A 869 HIS cc_start: 0.7804 (t-90) cc_final: 0.7572 (t-90) REVERT: B 188 GLN cc_start: 0.8120 (tp40) cc_final: 0.7897 (tp40) REVERT: C 167 GLU cc_start: 0.8423 (tp30) cc_final: 0.8174 (mm-30) REVERT: C 196 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8067 (mm-40) REVERT: F 42 LYS cc_start: 0.8277 (tttp) cc_final: 0.7886 (tttp) REVERT: F 59 GLU cc_start: 0.8078 (tp30) cc_final: 0.7865 (tp30) REVERT: F 109 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8653 (ttpt) REVERT: F 189 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7824 (tp) REVERT: F 192 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: F 237 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7851 (ttpp) REVERT: F 241 GLU cc_start: 0.6820 (pp20) cc_final: 0.6170 (pp20) REVERT: G 55 LYS cc_start: 0.8822 (mttt) cc_final: 0.8603 (mtpt) REVERT: G 147 GLN cc_start: 0.8800 (mp10) cc_final: 0.8575 (mt0) REVERT: G 173 THR cc_start: 0.8765 (t) cc_final: 0.8453 (p) REVERT: G 174 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8127 (mp0) REVERT: G 223 GLU cc_start: 0.7684 (tp30) cc_final: 0.7423 (tp30) REVERT: G 234 GLU cc_start: 0.7742 (tp30) cc_final: 0.7431 (tp30) REVERT: O 10 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7935 (p) REVERT: O 48 GLU cc_start: 0.7728 (tp30) cc_final: 0.7500 (tp30) REVERT: O 101 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8375 (mm110) REVERT: O 118 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: O 135 ILE cc_start: 0.8674 (mp) cc_final: 0.8456 (mt) REVERT: O 175 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8469 (mtpp) REVERT: O 198 PHE cc_start: 0.8470 (t80) cc_final: 0.7993 (t80) REVERT: P 15 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7920 (mt-10) REVERT: P 124 PHE cc_start: 0.8013 (p90) cc_final: 0.7627 (p90) REVERT: P 177 GLN cc_start: 0.8409 (tt0) cc_final: 0.8089 (tp40) REVERT: P 181 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7707 (tm-30) REVERT: P 184 MET cc_start: 0.8716 (mmp) cc_final: 0.8449 (mmm) REVERT: P 199 LYS cc_start: 0.8796 (tppt) cc_final: 0.8494 (tppt) REVERT: P 222 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8040 (mmmt) REVERT: P 231 LYS cc_start: 0.8373 (tttt) cc_final: 0.7945 (ttpp) REVERT: P 235 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7688 (tp-100) REVERT: P 242 GLU cc_start: 0.7522 (tp30) cc_final: 0.6975 (tp30) REVERT: P 246 LYS cc_start: 0.6991 (mmtt) cc_final: 0.6785 (mmtt) REVERT: Q 5 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7889 (tpp80) REVERT: Q 55 ASP cc_start: 0.7255 (t0) cc_final: 0.6985 (t0) REVERT: Q 67 ASP cc_start: 0.8215 (m-30) cc_final: 0.7945 (m-30) REVERT: Q 143 ARG cc_start: 0.8501 (mmt90) cc_final: 0.7866 (mtt-85) REVERT: Q 227 LYS cc_start: 0.8314 (tmmt) cc_final: 0.8000 (ttmt) REVERT: Q 231 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7444 (mm-30) REVERT: R 74 ILE cc_start: 0.8148 (tt) cc_final: 0.7910 (mt) REVERT: R 90 ASP cc_start: 0.8266 (t0) cc_final: 0.7685 (t0) REVERT: R 117 SER cc_start: 0.8681 (t) cc_final: 0.8478 (p) REVERT: R 156 MET cc_start: 0.7824 (tmm) cc_final: 0.7167 (tmm) REVERT: R 159 SER cc_start: 0.8584 (m) cc_final: 0.8344 (p) REVERT: R 164 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7717 (tm-30) REVERT: R 166 ASP cc_start: 0.7855 (m-30) cc_final: 0.7568 (m-30) REVERT: R 207 GLU cc_start: 0.7698 (pt0) cc_final: 0.7236 (pp20) REVERT: R 216 GLU cc_start: 0.7376 (tp30) cc_final: 0.7080 (tp30) REVERT: R 231 LYS cc_start: 0.8363 (tttt) cc_final: 0.8158 (tttp) REVERT: R 235 GLU cc_start: 0.8138 (tp30) cc_final: 0.7742 (mm-30) REVERT: S 27 GLU cc_start: 0.8173 (tp30) cc_final: 0.7861 (tp30) REVERT: S 138 ASP cc_start: 0.7990 (p0) cc_final: 0.7683 (p0) REVERT: S 153 TYR cc_start: 0.8303 (p90) cc_final: 0.7725 (p90) REVERT: S 171 TYR cc_start: 0.8413 (t80) cc_final: 0.7942 (t80) REVERT: S 208 LYS cc_start: 0.8590 (tttt) cc_final: 0.8365 (tttt) outliers start: 31 outliers final: 23 residues processed: 557 average time/residue: 0.3540 time to fit residues: 276.2057 Evaluate side-chains 559 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 532 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 207 SER Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 129 ILE Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 0.0870 chunk 134 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103942 restraints weight = 70617.214| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.98 r_work: 0.3218 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.9806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16810 Z= 0.144 Angle : 0.544 8.072 22690 Z= 0.291 Chirality : 0.039 0.144 2556 Planarity : 0.004 0.046 2934 Dihedral : 4.879 53.788 2319 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 27.70 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.18), residues: 2092 helix: 1.53 (0.17), residues: 956 sheet: -0.29 (0.26), residues: 356 loop : -0.50 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 57 TYR 0.010 0.001 TYR G 125 PHE 0.023 0.001 PHE A 762 TRP 0.008 0.001 TRP A 843 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00326 (16810) covalent geometry : angle 0.54362 (22690) hydrogen bonds : bond 0.04032 ( 909) hydrogen bonds : angle 4.27876 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8965.26 seconds wall clock time: 152 minutes 24.77 seconds (9144.77 seconds total)