Starting phenix.real_space_refine on Thu Jul 2 13:44:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhd_48274/07_2026/9mhd_48274.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5863 2.51 5 N 1414 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8923 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2229 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2094 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 257} Chain: "D" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2094 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 257} Chain: "C" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2229 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {' MG': 1, 'AGS': 1, 'AV0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {' MG': 1, 'AGS': 1, 'AV0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.57, per 1000 atoms: 0.18 Number of scatterers: 8923 At special positions: 0 Unit cell: (86.14, 90.86, 110.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 6 15.00 Mg 2 11.99 O 1586 8.00 N 1414 7.00 C 5863 6.00 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: 0.76 Conformation dependent library (CDL) restraints added in 305.2 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 69.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.664A pdb=" N ASN A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 56 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.596A pdb=" N THR A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 5.324A pdb=" N ASN A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.610A pdb=" N TYR A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.596A pdb=" N ILE A 147 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 Proline residue: A 154 - end of helix removed outlier: 3.537A pdb=" N PHE A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.272A pdb=" N MET A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA A 183 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.799A pdb=" N HIS A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.580A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.716A pdb=" N PHE A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.618A pdb=" N ASP A 236 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 263 removed outlier: 3.581A pdb=" N MET A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.551A pdb=" N PHE A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 116 through 132 Proline residue: B 125 - end of helix removed outlier: 3.632A pdb=" N GLU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.070A pdb=" N PHE B 136 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 175 through 192 removed outlier: 4.386A pdb=" N GLN B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 227 through 244 Proline residue: B 232 - end of helix removed outlier: 3.587A pdb=" N LYS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.897A pdb=" N SER B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 116 through 132 Proline residue: D 125 - end of helix removed outlier: 3.632A pdb=" N GLU D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.070A pdb=" N PHE D 136 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 145 through 158 Processing helix chain 'D' and resid 175 through 192 removed outlier: 4.386A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 Processing helix chain 'D' and resid 227 through 244 Proline residue: D 232 - end of helix removed outlier: 3.586A pdb=" N LYS D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 260 removed outlier: 3.896A pdb=" N SER D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 14 through 30 removed outlier: 3.663A pdb=" N ASN C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 56 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.596A pdb=" N THR C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 5.325A pdb=" N ASN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN C 101 " --> pdb=" O GLN C 97 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.610A pdb=" N TYR C 115 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.595A pdb=" N ILE C 147 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 174 Proline residue: C 154 - end of helix removed outlier: 3.536A pdb=" N PHE C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.272A pdb=" N MET C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.799A pdb=" N HIS C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.580A pdb=" N MET C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.717A pdb=" N PHE C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.617A pdb=" N ASP C 236 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 263 removed outlier: 3.580A pdb=" N MET C 241 " --> pdb=" O HIS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.550A pdb=" N PHE C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.603A pdb=" N VAL B 78 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 10 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 80 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 8 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA B 47 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN B 6 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 45 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS B 8 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 43 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 10 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 41 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 12 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS B 35 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.574A pdb=" N SER B 88 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP B 168 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 53 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 52 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA B 214 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 54 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 216 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 56 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE B 213 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR B 224 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TRP B 215 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 83 removed outlier: 6.602A pdb=" N VAL D 78 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL D 10 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 80 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 8 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA D 47 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN D 6 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU D 45 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 8 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 43 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL D 10 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP D 41 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS D 12 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS D 35 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.573A pdb=" N SER D 88 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ASP D 168 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 53 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 52 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA D 214 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY D 54 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE D 216 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 56 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE D 213 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR D 224 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TRP D 215 " --> pdb=" O LYS D 222 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1359 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: 0.99 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 2722 1.37 - 1.52: 3090 1.52 - 1.66: 3236 1.66 - 1.80: 84 1.80 - 1.95: 8 Bond restraints: 9140 Sorted by residual: bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O3B AGS D 301 " pdb=" PB AGS D 301 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3A AGS B 402 " pdb=" PA AGS B 402 " ideal model delta sigma weight residual 1.664 1.588 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " ideal model delta sigma weight residual 1.664 1.588 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" O3B AGS D 301 " pdb=" PG AGS D 301 " ideal model delta sigma weight residual 1.614 1.557 0.057 2.00e-02 2.50e+03 8.15e+00 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12188 2.03 - 4.07: 130 4.07 - 6.10: 22 6.10 - 8.14: 3 8.14 - 10.17: 11 Bond angle restraints: 12354 Sorted by residual: angle pdb=" O3A AGS B 402 " pdb=" PB AGS B 402 " pdb=" O3B AGS B 402 " ideal model delta sigma weight residual 100.38 110.55 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3A AGS D 301 " pdb=" PB AGS D 301 " pdb=" O3B AGS D 301 " ideal model delta sigma weight residual 100.38 110.54 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3A AGS B 402 " pdb=" PA AGS B 402 " pdb=" O5' AGS B 402 " ideal model delta sigma weight residual 97.67 106.32 -8.65 3.00e+00 1.11e-01 8.32e+00 angle pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " pdb=" O5' AGS D 301 " ideal model delta sigma weight residual 97.67 106.29 -8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" PB AGS D 301 " pdb=" O3B AGS D 301 " pdb=" PG AGS D 301 " ideal model delta sigma weight residual 129.21 120.72 8.49 3.00e+00 1.11e-01 8.00e+00 ... (remaining 12349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 5129 32.37 - 64.74: 404 64.74 - 97.11: 90 97.11 - 129.48: 53 129.48 - 161.85: 4 Dihedral angle restraints: 5680 sinusoidal: 2578 harmonic: 3102 Sorted by residual: dihedral pdb=" CBQ AV0 B 401 " pdb=" CBS AV0 B 401 " pdb=" CCM AV0 B 401 " pdb=" O1 AV0 B 401 " ideal model delta sinusoidal sigma weight residual 70.26 -91.59 161.85 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CBQ AV0 D 303 " pdb=" CBS AV0 D 303 " pdb=" CCM AV0 D 303 " pdb=" O1 AV0 D 303 " ideal model delta sinusoidal sigma weight residual 70.26 -91.57 161.83 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O2B AGS D 301 " pdb=" O3B AGS D 301 " pdb=" PB AGS D 301 " pdb=" PG AGS D 301 " ideal model delta sinusoidal sigma weight residual 7.37 161.24 -153.87 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1171 0.054 - 0.107: 187 0.107 - 0.161: 34 0.161 - 0.215: 1 0.215 - 0.268: 3 Chirality restraints: 1396 Sorted by residual: chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS D 301 " pdb=" C2' AGS D 301 " pdb=" C4' AGS D 301 " pdb=" O3' AGS D 301 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CCF AV0 A 301 " pdb=" CBP AV0 A 301 " pdb=" CCQ AV0 A 301 " pdb=" OBX AV0 A 301 " both_signs ideal model delta sigma weight residual False 2.50 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1393 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 161 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 162 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 161 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 162 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 162 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 162 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 231 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO D 232 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 232 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 232 " -0.018 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 66 2.62 - 3.19: 7335 3.19 - 3.76: 12872 3.76 - 4.33: 17982 4.33 - 4.90: 31126 Nonbonded interactions: 69381 Sorted by model distance: nonbonded pdb=" O2G AGS B 402 " pdb="MG MG B 403 " model vdw 2.045 2.170 nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 2.045 2.170 nonbonded pdb="MG MG D 302 " pdb=" O HOH D 402 " model vdw 2.066 2.170 nonbonded pdb="MG MG B 403 " pdb=" O HOH B 502 " model vdw 2.067 2.170 nonbonded pdb=" OG SER D 64 " pdb="MG MG D 302 " model vdw 2.159 2.170 ... (remaining 69376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 270) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 1 through 264) selection = (chain 'D' and resid 1 through 264) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.004 0.090 9140 Z= 0.176 Angle : 0.598 10.170 12354 Z= 0.289 Chirality : 0.042 0.268 1396 Planarity : 0.004 0.036 1478 Dihedral : 26.628 161.847 3692 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.36 % Allowed : 26.49 % Favored : 69.15 % 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: 1.67 (0.26), residues: 1060 helix: 2.09 (0.21), residues: 586 sheet: 1.52 (0.66), residues: 64 loop : -0.41 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.015 0.001 TYR C 115 PHE 0.008 0.001 PHE C 158 TRP 0.012 0.001 TRP A 73 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 ( 9140) covalent geometry : angle 0.59795 / 0.29 (12354) hydrogen bonds : bond 0.16633 / 11.68 ( 467) hydrogen bonds : angle 5.28700 / 3.82 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.202 Fit side-chains REVERT: C 9 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6883 (mttm) outliers start: 41 outliers final: 34 residues processed: 127 average time/residue: 0.5328 time to fit residues: 71.8223 Evaluate side-chains 125 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 208 HIS B 59 ASN D 59 ASN C 25 GLN C 208 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111305 restraints weight = 9939.203| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.38 r_work: 0.3117 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9140 Z= 0.159 Angle : 0.666 10.508 12354 Z= 0.305 Chirality : 0.049 0.315 1396 Planarity : 0.004 0.035 1478 Dihedral : 22.467 154.394 1676 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.21 % Allowed : 25.85 % Favored : 68.94 % 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: 1.49 (0.25), residues: 1060 helix: 2.03 (0.21), residues: 592 sheet: 1.34 (0.62), residues: 64 loop : -0.66 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.022 0.001 TYR C 115 PHE 0.010 0.001 PHE D 108 TRP 0.011 0.002 TRP C 73 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9140) covalent geometry : angle 0.66596 / 0.30 (12354) hydrogen bonds : bond 0.06499 / 4.48 ( 467) hydrogen bonds : angle 4.21347 / 3.06 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.302 Fit side-chains REVERT: A 86 GLN cc_start: 0.6550 (mt0) cc_final: 0.6267 (mm-40) REVERT: A 263 ARG cc_start: 0.7463 (ptp-170) cc_final: 0.6922 (ptp-170) REVERT: B 121 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7686 (ttpt) REVERT: B 188 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 121 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7644 (ttpt) REVERT: D 188 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 86 GLN cc_start: 0.6546 (mt0) cc_final: 0.6263 (mm-40) REVERT: C 210 MET cc_start: 0.4701 (tpt) cc_final: 0.4437 (mmt) REVERT: C 263 ARG cc_start: 0.7481 (ptp-170) cc_final: 0.6945 (ptp-170) outliers start: 49 outliers final: 22 residues processed: 138 average time/residue: 0.5163 time to fit residues: 75.8762 Evaluate side-chains 122 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 259 HIS C 25 GLN C 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109731 restraints weight = 9947.196| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.33 r_work: 0.3100 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9140 Z= 0.177 Angle : 0.620 7.935 12354 Z= 0.296 Chirality : 0.049 0.435 1396 Planarity : 0.004 0.038 1478 Dihedral : 17.753 154.482 1624 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.94 % Allowed : 27.13 % Favored : 68.94 % 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: 1.50 (0.25), residues: 1060 helix: 2.08 (0.21), residues: 588 sheet: 1.35 (0.61), residues: 64 loop : -0.71 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.024 0.001 TYR A 115 PHE 0.012 0.001 PHE B 108 TRP 0.012 0.002 TRP A 39 HIS 0.005 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9140) covalent geometry : angle 0.62017 / 0.30 (12354) hydrogen bonds : bond 0.07114 / 4.89 ( 467) hydrogen bonds : angle 4.22795 / 3.08 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.269 Fit side-chains REVERT: A 86 GLN cc_start: 0.6537 (mt0) cc_final: 0.6169 (mm-40) REVERT: B 35 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7221 (ttmm) REVERT: B 139 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8211 (mm-40) REVERT: D 35 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7232 (ttmm) REVERT: D 139 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8226 (mm-40) REVERT: C 86 GLN cc_start: 0.6529 (mt0) cc_final: 0.6163 (mm-40) outliers start: 37 outliers final: 19 residues processed: 127 average time/residue: 0.5994 time to fit residues: 80.5117 Evaluate side-chains 115 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 139 GLN B 157 ASN B 192 GLN D 157 ASN D 192 GLN C 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113916 restraints weight = 9965.607| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.96 r_work: 0.3095 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9140 Z= 0.150 Angle : 0.553 7.602 12354 Z= 0.270 Chirality : 0.046 0.405 1396 Planarity : 0.004 0.039 1478 Dihedral : 15.729 170.516 1620 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.47 % Allowed : 26.28 % Favored : 69.26 % 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: 1.57 (0.25), residues: 1060 helix: 2.16 (0.21), residues: 590 sheet: 1.28 (0.61), residues: 64 loop : -0.71 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.020 0.001 TYR C 115 PHE 0.010 0.001 PHE B 108 TRP 0.011 0.002 TRP A 73 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9140) covalent geometry : angle 0.55343 / 0.27 (12354) hydrogen bonds : bond 0.06193 / 4.27 ( 467) hydrogen bonds : angle 4.06724 / 2.95 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.273 Fit side-chains REVERT: A 86 GLN cc_start: 0.6174 (mt0) cc_final: 0.5846 (mm-40) REVERT: B 23 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6400 (ttm170) REVERT: B 139 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (mm-40) REVERT: D 23 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6386 (ttm170) REVERT: D 121 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7358 (ttpt) REVERT: D 139 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: C 86 GLN cc_start: 0.6162 (mt0) cc_final: 0.5837 (mm-40) REVERT: C 210 MET cc_start: 0.4267 (tpt) cc_final: 0.4054 (mmt) outliers start: 42 outliers final: 23 residues processed: 129 average time/residue: 0.5859 time to fit residues: 79.9744 Evaluate side-chains 126 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 259 HIS B 157 ASN B 192 GLN D 157 ASN D 192 GLN C 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113131 restraints weight = 10000.639| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.97 r_work: 0.3102 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9140 Z= 0.142 Angle : 0.531 6.733 12354 Z= 0.262 Chirality : 0.045 0.391 1396 Planarity : 0.004 0.039 1478 Dihedral : 14.880 176.071 1620 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.36 % Allowed : 26.28 % Favored : 69.36 % 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: 1.61 (0.25), residues: 1060 helix: 2.21 (0.21), residues: 590 sheet: 1.28 (0.61), residues: 64 loop : -0.73 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.021 0.001 TYR A 115 PHE 0.010 0.001 PHE D 108 TRP 0.011 0.002 TRP C 39 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9140) covalent geometry : angle 0.53143 / 0.26 (12354) hydrogen bonds : bond 0.06046 / 4.17 ( 467) hydrogen bonds : angle 4.01892 / 2.92 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.300 Fit side-chains REVERT: A 86 GLN cc_start: 0.6267 (mt0) cc_final: 0.5996 (mm-40) REVERT: B 23 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6402 (ttm-80) REVERT: B 139 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8075 (mm-40) REVERT: D 23 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6400 (ttm-80) REVERT: C 86 GLN cc_start: 0.6257 (mt0) cc_final: 0.5989 (mm-40) REVERT: C 260 MET cc_start: 0.8003 (mmp) cc_final: 0.7763 (mmp) outliers start: 41 outliers final: 20 residues processed: 133 average time/residue: 0.5751 time to fit residues: 80.7422 Evaluate side-chains 126 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 203 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 97 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 139 GLN B 157 ASN D 157 ASN C 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121653 restraints weight = 9809.573| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.92 r_work: 0.3268 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9140 Z= 0.103 Angle : 0.455 4.939 12354 Z= 0.229 Chirality : 0.042 0.263 1396 Planarity : 0.003 0.037 1478 Dihedral : 13.557 179.709 1614 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.19 % Allowed : 27.66 % Favored : 69.15 % 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: 1.87 (0.26), residues: 1060 helix: 2.41 (0.21), residues: 590 sheet: 1.39 (0.62), residues: 64 loop : -0.58 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 263 TYR 0.012 0.001 TYR A 115 PHE 0.006 0.001 PHE B 108 TRP 0.012 0.001 TRP C 81 HIS 0.002 0.000 HIS C 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 9140) covalent geometry : angle 0.45455 / 0.23 (12354) hydrogen bonds : bond 0.04288 / 3.00 ( 467) hydrogen bonds : angle 3.77077 / 2.73 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.218 Fit side-chains REVERT: A 1 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5674 (mpp) REVERT: A 130 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6995 (mp) REVERT: A 208 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.5554 (t70) REVERT: B 139 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7793 (mm-40) REVERT: C 130 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6995 (mp) outliers start: 30 outliers final: 9 residues processed: 116 average time/residue: 0.5177 time to fit residues: 63.6284 Evaluate side-chains 111 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 157 ASN D 157 ASN C 25 GLN C 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119928 restraints weight = 9876.193| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.93 r_work: 0.3125 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9140 Z= 0.110 Angle : 0.455 4.917 12354 Z= 0.232 Chirality : 0.041 0.222 1396 Planarity : 0.004 0.038 1478 Dihedral : 13.283 178.959 1610 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.83 % Allowed : 27.13 % Favored : 69.04 % 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: 1.86 (0.26), residues: 1060 helix: 2.43 (0.21), residues: 592 sheet: 1.33 (0.62), residues: 64 loop : -0.64 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.017 0.001 TYR C 115 PHE 0.007 0.001 PHE D 108 TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9140) covalent geometry : angle 0.45527 / 0.23 (12354) hydrogen bonds : bond 0.04766 / 3.31 ( 467) hydrogen bonds : angle 3.76254 / 2.72 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.305 Fit side-chains REVERT: A 74 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7812 (tp) REVERT: A 130 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7097 (mp) REVERT: B 139 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8137 (mm-40) REVERT: D 18 ARG cc_start: 0.7520 (tpp80) cc_final: 0.7232 (mmm-85) REVERT: C 74 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7808 (tp) REVERT: C 130 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7089 (mp) outliers start: 36 outliers final: 13 residues processed: 125 average time/residue: 0.4942 time to fit residues: 65.7349 Evaluate side-chains 116 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 208 HIS B 157 ASN D 157 ASN C 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114415 restraints weight = 9949.027| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.93 r_work: 0.3099 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9140 Z= 0.142 Angle : 0.491 4.982 12354 Z= 0.253 Chirality : 0.042 0.165 1396 Planarity : 0.004 0.038 1478 Dihedral : 13.270 178.040 1610 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.83 % Allowed : 27.13 % Favored : 69.04 % 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: 1.71 (0.25), residues: 1060 helix: 2.27 (0.21), residues: 588 sheet: 1.26 (0.62), residues: 64 loop : -0.60 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 263 TYR 0.023 0.001 TYR A 115 PHE 0.010 0.001 PHE D 108 TRP 0.011 0.002 TRP A 39 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9140) covalent geometry : angle 0.49132 / 0.25 (12354) hydrogen bonds : bond 0.05976 / 4.13 ( 467) hydrogen bonds : angle 3.90313 / 2.83 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.442 Fit side-chains REVERT: B 139 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8064 (mm-40) outliers start: 36 outliers final: 17 residues processed: 128 average time/residue: 0.5209 time to fit residues: 70.8559 Evaluate side-chains 118 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 157 ASN D 157 ASN C 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118133 restraints weight = 9826.015| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.89 r_work: 0.3095 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9140 Z= 0.123 Angle : 0.466 4.924 12354 Z= 0.241 Chirality : 0.041 0.142 1396 Planarity : 0.004 0.041 1478 Dihedral : 13.079 176.343 1610 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.98 % Allowed : 27.55 % Favored : 69.47 % 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: 1.74 (0.25), residues: 1060 helix: 2.29 (0.21), residues: 590 sheet: 1.25 (0.62), residues: 64 loop : -0.60 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 263 TYR 0.018 0.001 TYR C 115 PHE 0.008 0.001 PHE D 108 TRP 0.010 0.001 TRP A 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9140) covalent geometry : angle 0.46604 / 0.24 (12354) hydrogen bonds : bond 0.05384 / 3.73 ( 467) hydrogen bonds : angle 3.83712 / 2.78 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.303 Fit side-chains REVERT: A 130 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 123 MET cc_start: 0.7049 (mtp) cc_final: 0.6637 (ptp) REVERT: B 139 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: D 123 MET cc_start: 0.7028 (mtp) cc_final: 0.6625 (ptp) REVERT: C 130 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7144 (mp) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.5099 time to fit residues: 65.3822 Evaluate side-chains 117 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 259 HIS B 157 ASN D 157 ASN C 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119922 restraints weight = 9818.847| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.90 r_work: 0.3151 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9140 Z= 0.107 Angle : 0.449 5.135 12354 Z= 0.231 Chirality : 0.040 0.141 1396 Planarity : 0.003 0.037 1478 Dihedral : 12.840 173.741 1610 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.77 % Allowed : 27.77 % Favored : 69.47 % 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: 1.83 (0.25), residues: 1060 helix: 2.37 (0.21), residues: 590 sheet: 1.31 (0.62), residues: 64 loop : -0.58 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.016 0.001 TYR A 115 PHE 0.007 0.001 PHE B 108 TRP 0.011 0.001 TRP C 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9140) covalent geometry : angle 0.44904 / 0.23 (12354) hydrogen bonds : bond 0.04819 / 3.36 ( 467) hydrogen bonds : angle 3.74819 / 2.71 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.319 Fit side-chains REVERT: A 74 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 123 MET cc_start: 0.7056 (mtp) cc_final: 0.6696 (ptp) REVERT: B 139 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: D 123 MET cc_start: 0.7009 (mtp) cc_final: 0.6657 (ptp) REVERT: C 74 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7769 (tp) outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 0.5385 time to fit residues: 66.4590 Evaluate side-chains 116 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 157 ASN D 157 ASN C 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118482 restraints weight = 10018.462| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.75 r_work: 0.3287 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9140 Z= 0.121 Angle : 0.467 5.112 12354 Z= 0.242 Chirality : 0.041 0.141 1396 Planarity : 0.004 0.037 1478 Dihedral : 12.813 171.935 1610 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.77 % Allowed : 27.66 % Favored : 69.57 % 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: 1.78 (0.25), residues: 1060 helix: 2.33 (0.21), residues: 590 sheet: 1.26 (0.62), residues: 64 loop : -0.59 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.019 0.001 TYR C 115 PHE 0.008 0.001 PHE D 108 TRP 0.010 0.001 TRP C 73 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9140) covalent geometry : angle 0.46660 / 0.24 (12354) hydrogen bonds : bond 0.05324 / 3.69 ( 467) hydrogen bonds : angle 3.78866 / 2.74 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.56 seconds wall clock time: 44 minutes 40.69 seconds (2680.69 seconds total)