Starting phenix.real_space_refine on Wed Sep 17 13:28:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhd_48274/09_2025/9mhd_48274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhd_48274/09_2025/9mhd_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_48274/09_2025/9mhd_48274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhd_48274/09_2025/9mhd_48274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mhd_48274/09_2025/9mhd_48274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhd_48274/09_2025/9mhd_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8923 Number of models: 1 Model: "" Number of chains: 7 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: "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} Restraints were copied for chains: C, D Time building chain proxies: 2.78, per 1000 atoms: 0.31 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: 0.89 Conformation dependent library (CDL) restraints added in 263.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.30 Time building geometry restraints manager: 1.16 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=" CA THR B 124 " pdb=" C THR B 124 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 8.05e-01 bond pdb=" CA THR D 124 " pdb=" C THR D 124 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.32e-01 bond pdb=" CA PHE A 15 " pdb=" C PHE A 15 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.44e-02 4.82e+03 7.03e-01 bond pdb=" CB ASN B 84 " pdb=" CG ASN B 84 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.49e-01 bond pdb=" CA PHE C 15 " pdb=" C PHE C 15 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.44e-02 4.82e+03 6.40e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12144 1.59 - 3.17: 182 3.17 - 4.76: 22 4.76 - 6.34: 5 6.34 - 7.93: 1 Bond angle restraints: 12354 Sorted by residual: angle pdb=" CCF AV0 A 301 " pdb=" OBX AV0 A 301 " pdb=" CCJ AV0 A 301 " ideal model delta sigma weight residual 113.60 121.53 -7.93 3.00e+00 1.11e-01 6.98e+00 angle pdb=" CA TYR C 115 " pdb=" CB TYR C 115 " pdb=" CG TYR C 115 " ideal model delta sigma weight residual 113.90 117.95 -4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" CA TYR A 115 " pdb=" CB TYR A 115 " pdb=" CG TYR A 115 " ideal model delta sigma weight residual 113.90 117.94 -4.04 1.80e+00 3.09e-01 5.03e+00 angle pdb=" C VAL A 153 " pdb=" CA VAL A 153 " pdb=" CB VAL A 153 " ideal model delta sigma weight residual 114.00 111.17 2.83 1.31e+00 5.83e-01 4.67e+00 angle pdb=" C VAL C 153 " pdb=" CA VAL C 153 " pdb=" CB VAL C 153 " ideal model delta sigma weight residual 114.00 111.18 2.82 1.31e+00 5.83e-01 4.64e+00 ... (remaining 12349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 5111 32.37 - 64.74: 414 64.74 - 97.11: 66 97.11 - 129.48: 51 129.48 - 161.85: 2 Dihedral angle restraints: 5644 sinusoidal: 2542 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=" CCC AV0 A 301 " pdb=" CCR AV0 A 301 " pdb=" OBY AV0 A 301 " pdb=" O4 AV0 A 301 " ideal model delta sinusoidal sigma weight residual 298.29 171.39 126.90 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1133 0.049 - 0.099: 209 0.099 - 0.148: 56 0.148 - 0.197: 1 0.197 - 0.247: 1 Chirality restraints: 1400 Sorted by residual: 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 chirality pdb=" C5 AV0 A 301 " pdb=" C4 AV0 A 301 " pdb=" C6 AV0 A 301 " pdb=" O5 AV0 A 301 " both_signs ideal model delta sigma weight residual False -2.50 -2.33 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1397 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.170 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 0.023 9140 Z= 0.123 Angle : 0.499 7.925 12354 Z= 0.268 Chirality : 0.041 0.247 1400 Planarity : 0.004 0.036 1478 Dihedral : 25.775 161.847 3656 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 aren 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 covalent geometry : bond 0.00252 ( 9140) covalent geometry : angle 0.49896 (12354) hydrogen bonds : bond 0.16633 ( 467) hydrogen bonds : angle 5.28700 ( 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 : 0.353 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: 0.6897 time to fit residues: 92.6175 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 : 0.383 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3616 r_free = 0.3616 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111168 restraints weight = 9905.624| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.35 r_work: 0.3120 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9140 Z= 0.159 Angle : 0.636 9.585 12354 Z= 0.299 Chirality : 0.048 0.301 1400 Planarity : 0.004 0.034 1478 Dihedral : 22.557 155.157 1640 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.00 % Allowed : 25.85 % 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 aren not related in a simple way. whole: 1.57 (0.25), residues: 1060 helix: 2.11 (0.21), residues: 592 sheet: 1.36 (0.63), residues: 64 loop : -0.64 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.022 0.001 TYR A 115 PHE 0.008 0.001 PHE B 108 TRP 0.013 0.002 TRP A 73 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9140) covalent geometry : angle 0.63594 (12354) hydrogen bonds : bond 0.06509 ( 467) hydrogen bonds : angle 4.25501 ( 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 147 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.336 Fit side-chains REVERT: A 86 GLN cc_start: 0.6504 (mt0) cc_final: 0.6150 (mm-40) REVERT: A 263 ARG cc_start: 0.7533 (ptp-170) cc_final: 0.7054 (ptp-170) REVERT: C 86 GLN cc_start: 0.6527 (mt0) cc_final: 0.6171 (mm-40) REVERT: C 263 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.7015 (ptp-170) outliers start: 47 outliers final: 22 residues processed: 134 average time/residue: 0.6670 time to fit residues: 94.6594 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 16 ILE Chi-restraints excluded: chain B residue 77 THR 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 16 ILE Chi-restraints excluded: chain D residue 77 THR 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: 2.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3616 r_free = 0.3616 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111139 restraints weight = 9917.484| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.36 r_work: 0.3110 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9140 Z= 0.148 Angle : 0.602 8.199 12354 Z= 0.281 Chirality : 0.046 0.331 1400 Planarity : 0.004 0.038 1478 Dihedral : 16.770 156.227 1588 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.47 % Allowed : 27.13 % Favored : 68.40 % 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 aren not related in a simple way. whole: 1.67 (0.25), residues: 1060 helix: 2.19 (0.21), residues: 590 sheet: 1.36 (0.62), residues: 64 loop : -0.58 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.021 0.001 TYR A 115 PHE 0.011 0.001 PHE B 108 TRP 0.012 0.002 TRP C 73 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9140) covalent geometry : angle 0.60183 (12354) hydrogen bonds : bond 0.06181 ( 467) hydrogen bonds : angle 4.11072 ( 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 143 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.382 Fit side-chains REVERT: A 86 GLN cc_start: 0.6549 (mt0) cc_final: 0.6248 (mm-40) REVERT: A 210 MET cc_start: 0.4642 (tpt) cc_final: 0.4370 (mmt) REVERT: B 35 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7210 (ttmm) REVERT: D 35 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7213 (ttmm) REVERT: C 86 GLN cc_start: 0.6541 (mt0) cc_final: 0.6245 (mm-40) REVERT: C 210 MET cc_start: 0.4721 (tpt) cc_final: 0.4493 (mmt) outliers start: 42 outliers final: 22 residues processed: 131 average time/residue: 0.6996 time to fit residues: 96.8086 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 203 ILE 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 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 67 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 203 ILE 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: 3.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3592 r_free = 0.3592 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108407 restraints weight = 10039.185| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.38 r_work: 0.3079 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9140 Z= 0.197 Angle : 0.608 8.262 12354 Z= 0.299 Chirality : 0.048 0.438 1400 Planarity : 0.004 0.038 1478 Dihedral : 15.034 152.179 1584 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.43 % Allowed : 26.06 % Favored : 68.51 % 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 aren not related in a simple way. whole: 1.43 (0.25), residues: 1060 helix: 2.02 (0.21), residues: 592 sheet: 1.24 (0.60), residues: 64 loop : -0.75 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 23 TYR 0.027 0.002 TYR C 115 PHE 0.013 0.001 PHE D 108 TRP 0.013 0.002 TRP A 39 HIS 0.005 0.001 HIS C 11 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9140) covalent geometry : angle 0.60829 (12354) hydrogen bonds : bond 0.07453 ( 467) hydrogen bonds : angle 4.19958 ( 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 143 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 0.363 Fit side-chains REVERT: A 86 GLN cc_start: 0.6485 (mt0) cc_final: 0.6111 (mm-40) REVERT: A 242 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7747 (mm) REVERT: B 23 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6582 (ttm-80) REVERT: B 35 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7157 (ttmm) REVERT: B 149 ARG cc_start: 0.7443 (ttm110) cc_final: 0.6670 (mtp180) REVERT: D 23 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6574 (ttm-80) REVERT: D 35 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7142 (ttmm) REVERT: D 149 ARG cc_start: 0.7453 (ttm110) cc_final: 0.6678 (mtp180) REVERT: C 86 GLN cc_start: 0.6470 (mt0) cc_final: 0.6098 (mm-40) REVERT: C 242 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7740 (mm) outliers start: 51 outliers final: 28 residues processed: 132 average time/residue: 0.7016 time to fit residues: 97.9236 Evaluate side-chains 124 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET 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 195 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 23 ARG 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 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 35 LYS 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 53 MET 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 195 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 157 ASN B 192 GLN D 157 ASN D 192 GLN C 25 GLN C 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113698 restraints weight = 9983.905| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.98 r_work: 0.3084 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9140 Z= 0.129 Angle : 0.516 7.536 12354 Z= 0.256 Chirality : 0.045 0.403 1400 Planarity : 0.004 0.037 1478 Dihedral : 13.852 149.321 1584 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.62 % Allowed : 27.87 % Favored : 68.51 % 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 aren not related in a simple way. whole: 1.68 (0.25), residues: 1060 helix: 2.25 (0.21), residues: 592 sheet: 1.30 (0.61), residues: 64 loop : -0.67 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.017 0.001 TYR A 115 PHE 0.009 0.001 PHE D 108 TRP 0.011 0.001 TRP C 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9140) covalent geometry : angle 0.51599 (12354) hydrogen bonds : bond 0.05690 ( 467) hydrogen bonds : angle 3.99885 ( 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 127 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.644 Fit side-chains REVERT: A 86 GLN cc_start: 0.6224 (mt0) cc_final: 0.5966 (mm-40) REVERT: A 130 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7081 (mp) REVERT: C 86 GLN cc_start: 0.6225 (mt0) cc_final: 0.5965 (mm-40) outliers start: 34 outliers final: 20 residues processed: 118 average time/residue: 0.6984 time to fit residues: 87.5132 Evaluate side-chains 114 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 80 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 53 ILE 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 53 ILE 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 80 MET Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 208 HIS B 157 ASN B 192 GLN D 157 ASN D 192 GLN C 25 GLN C 208 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110912 restraints weight = 10029.224| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.95 r_work: 0.3144 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9140 Z= 0.214 Angle : 0.594 6.784 12354 Z= 0.299 Chirality : 0.047 0.394 1400 Planarity : 0.004 0.038 1478 Dihedral : 13.379 148.467 1582 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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 aren not related in a simple way. whole: 1.38 (0.25), residues: 1060 helix: 2.04 (0.20), residues: 588 sheet: 1.06 (0.60), residues: 64 loop : -0.81 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.028 0.002 TYR C 115 PHE 0.014 0.002 PHE B 108 TRP 0.012 0.002 TRP C 39 HIS 0.005 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9140) covalent geometry : angle 0.59413 (12354) hydrogen bonds : bond 0.07640 ( 467) hydrogen bonds : angle 4.16749 ( 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 145 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.339 Fit side-chains REVERT: A 86 GLN cc_start: 0.6372 (mt0) cc_final: 0.5966 (mm-40) REVERT: B 23 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6279 (ttm-80) REVERT: B 149 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6359 (mtp85) REVERT: D 23 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6261 (ttm-80) REVERT: D 149 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6371 (mtp85) REVERT: C 86 GLN cc_start: 0.6371 (mt0) cc_final: 0.5965 (mm-40) REVERT: C 242 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7500 (mm) outliers start: 49 outliers final: 25 residues processed: 137 average time/residue: 0.6873 time to fit residues: 99.6373 Evaluate side-chains 122 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 195 LEU 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 103 ILE 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 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 195 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 157 ASN B 192 GLN D 157 ASN D 192 GLN C 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113259 restraints weight = 9960.010| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.97 r_work: 0.3192 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1393 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= 0.132 Angle : 0.503 5.252 12354 Z= 0.254 Chirality : 0.044 0.341 1400 Planarity : 0.004 0.038 1478 Dihedral : 12.697 147.467 1578 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.04 % Allowed : 27.34 % Favored : 68.62 % 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 aren not related in a simple way. whole: 1.63 (0.25), residues: 1060 helix: 2.26 (0.21), residues: 588 sheet: 1.16 (0.60), residues: 64 loop : -0.74 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.017 0.001 TYR A 115 PHE 0.009 0.001 PHE B 108 TRP 0.011 0.002 TRP C 73 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9140) covalent geometry : angle 0.50300 (12354) hydrogen bonds : bond 0.05800 ( 467) hydrogen bonds : angle 3.97309 ( 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 131 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.376 Fit side-chains REVERT: A 86 GLN cc_start: 0.6248 (mt0) cc_final: 0.5975 (mm-40) REVERT: B 23 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6314 (ttm-80) REVERT: D 23 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6307 (ttm-80) REVERT: C 86 GLN cc_start: 0.6253 (mt0) cc_final: 0.5982 (mm-40) REVERT: C 130 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7058 (mp) outliers start: 38 outliers final: 22 residues processed: 121 average time/residue: 0.6759 time to fit residues: 86.8640 Evaluate side-chains 120 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 80 MET Chi-restraints excluded: chain A residue 119 SER 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 103 ILE 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 103 ILE 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 80 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 203 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.137301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109987 restraints weight = 10094.277| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.01 r_work: 0.3106 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9140 Z= 0.152 Angle : 0.519 5.005 12354 Z= 0.264 Chirality : 0.043 0.278 1400 Planarity : 0.004 0.038 1478 Dihedral : 12.433 147.083 1578 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.04 % Allowed : 27.23 % Favored : 68.72 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1060 helix: 2.21 (0.21), residues: 588 sheet: 1.11 (0.61), residues: 64 loop : -0.76 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.023 0.001 TYR C 115 PHE 0.011 0.001 PHE B 108 TRP 0.011 0.002 TRP C 39 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9140) covalent geometry : angle 0.51870 (12354) hydrogen bonds : bond 0.06369 ( 467) hydrogen bonds : angle 3.99254 ( 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 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.350 Fit side-chains REVERT: A 86 GLN cc_start: 0.6339 (mt0) cc_final: 0.6055 (mm-40) REVERT: B 23 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6390 (ttm-80) REVERT: D 23 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6390 (ttm-80) REVERT: C 86 GLN cc_start: 0.6335 (mt0) cc_final: 0.6053 (mm-40) outliers start: 38 outliers final: 25 residues processed: 126 average time/residue: 0.6854 time to fit residues: 91.4716 Evaluate side-chains 127 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 80 MET Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 195 LEU 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 103 ILE 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 103 ILE 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 80 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 203 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 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 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 = 0.3661 r_free = 0.3661 target = 0.144832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118644 restraints weight = 9845.779| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.91 r_work: 0.3078 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1453 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= 0.113 Angle : 0.465 4.936 12354 Z= 0.239 Chirality : 0.042 0.212 1400 Planarity : 0.003 0.037 1478 Dihedral : 11.991 146.452 1578 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.62 % Allowed : 27.66 % Favored : 68.72 % 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 aren not related in a simple way. whole: 1.75 (0.26), residues: 1060 helix: 2.38 (0.21), residues: 588 sheet: 1.20 (0.61), residues: 64 loop : -0.70 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 263 TYR 0.015 0.001 TYR A 115 PHE 0.007 0.001 PHE B 108 TRP 0.012 0.001 TRP C 81 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9140) covalent geometry : angle 0.46513 (12354) hydrogen bonds : bond 0.05079 ( 467) hydrogen bonds : angle 3.83046 ( 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 134 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.313 Fit side-chains REVERT: A 86 GLN cc_start: 0.6447 (mt0) cc_final: 0.6192 (mm-40) REVERT: B 22 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 23 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6525 (ttm-80) REVERT: D 22 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6517 (mt-10) REVERT: D 23 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6518 (ttm-80) REVERT: C 86 GLN cc_start: 0.6454 (mt0) cc_final: 0.6196 (mm-40) outliers start: 34 outliers final: 18 residues processed: 127 average time/residue: 0.6633 time to fit residues: 89.2415 Evaluate side-chains 120 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 23 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 103 ILE 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 103 ILE 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 196 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3608 r_free = 0.3608 target = 0.140909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114589 restraints weight = 9928.390| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.92 r_work: 0.3073 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9140 Z= 0.136 Angle : 0.503 7.568 12354 Z= 0.259 Chirality : 0.042 0.176 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.956 146.488 1578 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.09 % Allowed : 28.19 % Favored : 68.72 % 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 aren not related in a simple way. whole: 1.71 (0.26), residues: 1060 helix: 2.34 (0.21), residues: 588 sheet: 1.20 (0.62), residues: 64 loop : -0.71 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 263 TYR 0.020 0.001 TYR A 115 PHE 0.009 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 covalent geometry : bond 0.00309 ( 9140) covalent geometry : angle 0.50274 (12354) hydrogen bonds : bond 0.05731 ( 467) hydrogen bonds : angle 3.85854 ( 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 132 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.6284 (mt0) cc_final: 0.6014 (mm-40) REVERT: A 263 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7105 (ptp-170) REVERT: B 23 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6357 (ttm-80) REVERT: B 123 MET cc_start: 0.6828 (mtp) cc_final: 0.6434 (ptp) REVERT: D 23 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6357 (ttm-80) REVERT: C 86 GLN cc_start: 0.6280 (mt0) cc_final: 0.6013 (mm-40) outliers start: 29 outliers final: 17 residues processed: 127 average time/residue: 0.6808 time to fit residues: 91.5003 Evaluate side-chains 121 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 A residue 263 ARG Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 103 ILE 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 103 ILE 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 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: 0.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.140152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113826 restraints weight = 9911.261| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.93 r_work: 0.3090 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1495 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= 0.148 Angle : 0.513 6.917 12354 Z= 0.266 Chirality : 0.042 0.144 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.949 146.731 1578 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.98 % Allowed : 28.19 % Favored : 68.83 % 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 aren not related in a simple way. whole: 1.65 (0.25), residues: 1060 helix: 2.30 (0.20), residues: 588 sheet: 1.14 (0.61), residues: 64 loop : -0.75 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 263 TYR 0.022 0.001 TYR A 115 PHE 0.011 0.001 PHE B 108 TRP 0.011 0.002 TRP C 39 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9140) covalent geometry : angle 0.51320 (12354) hydrogen bonds : bond 0.06166 ( 467) hydrogen bonds : angle 3.90654 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.30 seconds wall clock time: 53 minutes 54.13 seconds (3234.13 seconds total)