Starting phenix.real_space_refine on Tue Apr 29 19:50:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhd_48274/04_2025/9mhd_48274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhd_48274/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mhd_48274/04_2025/9mhd_48274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhd_48274/04_2025/9mhd_48274.map" model { file = "/net/cci-nas-00/data/ceres_data/9mhd_48274/04_2025/9mhd_48274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhd_48274/04_2025/9mhd_48274.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.53, per 1000 atoms: 0.73 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: 2.39 Conformation dependent library (CDL) restraints added in 928.9 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: 0.96 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: 2.24 Time building geometry restraints manager: 2.75 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.630 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (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 TRP 0.012 0.001 TRP A 73 HIS 0.002 0.001 HIS A 11 PHE 0.008 0.001 PHE C 158 TYR 0.015 0.001 TYR C 115 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.16633 ( 467) hydrogen bonds : angle 5.28700 ( 1359) covalent geometry : bond 0.00252 ( 9140) covalent geometry : angle 0.49896 (12354) *********************** 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 : 0.921 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: 1.3845 time to fit residues: 186.3857 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 : 1.062 ------------------------------------------------------------------------------- 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 89 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.138448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112437 restraints weight = 9878.433| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.92 r_work: 0.3129 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0721 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= 0.158 Angle : 0.627 9.359 12354 Z= 0.296 Chirality : 0.047 0.280 1400 Planarity : 0.004 0.034 1478 Dihedral : 22.914 155.504 1640 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.43 % Allowed : 25.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1060 helix: 2.11 (0.21), residues: 592 sheet: 1.39 (0.63), residues: 64 loop : -0.63 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 73 HIS 0.004 0.001 HIS A 11 PHE 0.010 0.001 PHE D 189 TYR 0.021 0.001 TYR A 115 ARG 0.003 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.06566 ( 467) hydrogen bonds : angle 4.27281 ( 1359) covalent geometry : bond 0.00355 ( 9140) covalent geometry : angle 0.62675 (12354) *********************** 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 151 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 1.060 Fit side-chains REVERT: A 86 GLN cc_start: 0.6412 (mt0) cc_final: 0.6059 (mm-40) REVERT: A 263 ARG cc_start: 0.7351 (ptp-170) cc_final: 0.6880 (ptp-170) REVERT: B 121 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: C 86 GLN cc_start: 0.6435 (mt0) cc_final: 0.6073 (mm-40) REVERT: C 263 ARG cc_start: 0.7349 (ptp-170) cc_final: 0.6880 (ptp-170) outliers start: 51 outliers final: 22 residues processed: 137 average time/residue: 1.4596 time to fit residues: 212.1242 Evaluate side-chains 116 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 97 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN C 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108239 restraints weight = 9916.908| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.36 r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1130 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= 0.183 Angle : 0.651 8.093 12354 Z= 0.308 Chirality : 0.047 0.304 1400 Planarity : 0.004 0.039 1478 Dihedral : 17.495 155.880 1588 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.89 % Allowed : 27.34 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1060 helix: 2.05 (0.21), residues: 590 sheet: 1.26 (0.61), residues: 64 loop : -0.67 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 39 HIS 0.006 0.001 HIS C 11 PHE 0.014 0.001 PHE B 108 TYR 0.025 0.002 TYR C 115 ARG 0.003 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.07319 ( 467) hydrogen bonds : angle 4.25472 ( 1359) covalent geometry : bond 0.00430 ( 9140) covalent geometry : angle 0.65125 (12354) *********************** 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 139 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.946 Fit side-chains REVERT: A 86 GLN cc_start: 0.6470 (mt0) cc_final: 0.6102 (mm-40) REVERT: A 242 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 35 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (ttmm) REVERT: B 139 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: D 35 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7175 (ttmm) REVERT: C 86 GLN cc_start: 0.6476 (mt0) cc_final: 0.6109 (mm-40) REVERT: C 242 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7718 (mm) outliers start: 46 outliers final: 21 residues processed: 127 average time/residue: 1.4045 time to fit residues: 189.1940 Evaluate side-chains 118 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 A residue 242 LEU 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 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 Chi-restraints excluded: chain C residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.0060 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116504 restraints weight = 9833.775| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.31 r_work: 0.3180 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9140 Z= 0.108 Angle : 0.512 7.772 12354 Z= 0.247 Chirality : 0.044 0.402 1400 Planarity : 0.003 0.035 1478 Dihedral : 14.710 152.136 1584 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.30 % Allowed : 28.51 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.26), residues: 1060 helix: 2.29 (0.21), residues: 602 sheet: 1.48 (0.62), residues: 64 loop : -0.48 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.002 0.001 HIS A 11 PHE 0.006 0.001 PHE B 108 TYR 0.012 0.001 TYR A 115 ARG 0.002 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 467) hydrogen bonds : angle 3.91613 ( 1359) covalent geometry : bond 0.00203 ( 9140) covalent geometry : angle 0.51217 (12354) *********************** 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 126 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.024 Fit side-chains REVERT: A 86 GLN cc_start: 0.6543 (mt0) cc_final: 0.6312 (mm-40) REVERT: A 130 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7361 (mp) REVERT: A 210 MET cc_start: 0.4672 (tpt) cc_final: 0.4435 (mmt) REVERT: C 86 GLN cc_start: 0.6537 (mt0) cc_final: 0.6311 (mm-40) REVERT: C 210 MET cc_start: 0.4679 (tpt) cc_final: 0.4438 (mmt) outliers start: 31 outliers final: 14 residues processed: 115 average time/residue: 1.4579 time to fit residues: 178.2903 Evaluate side-chains 107 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 53 ILE 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 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 VAL 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 16 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106434 restraints weight = 10060.563| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.35 r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 9140 Z= 0.262 Angle : 0.660 8.003 12354 Z= 0.330 Chirality : 0.050 0.424 1400 Planarity : 0.005 0.040 1478 Dihedral : 14.479 150.061 1582 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.79 % Allowed : 26.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1060 helix: 1.91 (0.20), residues: 592 sheet: 1.02 (0.59), residues: 64 loop : -0.80 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 39 HIS 0.005 0.001 HIS A 11 PHE 0.016 0.002 PHE B 108 TYR 0.032 0.002 TYR A 115 ARG 0.003 0.000 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.08535 ( 467) hydrogen bonds : angle 4.29241 ( 1359) covalent geometry : bond 0.00655 ( 9140) covalent geometry : angle 0.65997 (12354) *********************** 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 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.999 Fit side-chains REVERT: A 80 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7884 (ptp) REVERT: A 86 GLN cc_start: 0.6680 (mt0) cc_final: 0.6253 (mm-40) REVERT: B 23 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6516 (ttm170) REVERT: B 35 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7214 (ttmm) REVERT: B 139 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8330 (mm-40) REVERT: B 149 ARG cc_start: 0.7605 (ttm110) cc_final: 0.6774 (mtp85) REVERT: B 157 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7276 (m110) REVERT: D 23 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6574 (ttm170) REVERT: D 35 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7233 (ttmm) REVERT: D 149 ARG cc_start: 0.7607 (ttm110) cc_final: 0.6774 (mtp85) REVERT: D 157 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7301 (m110) REVERT: C 80 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7879 (ptp) REVERT: C 86 GLN cc_start: 0.6668 (mt0) cc_final: 0.6245 (mm-40) outliers start: 45 outliers final: 19 residues processed: 129 average time/residue: 1.3947 time to fit residues: 190.5494 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 157 ASN Chi-restraints excluded: chain B residue 227 LEU 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 157 ASN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 192 GLN D 192 GLN 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 = 0.139876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113233 restraints weight = 9839.426| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1326 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= 0.133 Angle : 0.525 7.339 12354 Z= 0.263 Chirality : 0.045 0.410 1400 Planarity : 0.004 0.035 1478 Dihedral : 13.501 149.252 1578 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.57 % Allowed : 26.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1060 helix: 2.16 (0.20), residues: 590 sheet: 1.13 (0.59), residues: 64 loop : -0.70 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 81 HIS 0.003 0.001 HIS A 11 PHE 0.011 0.001 PHE B 108 TYR 0.020 0.001 TYR A 115 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 467) hydrogen bonds : angle 4.05385 ( 1359) covalent geometry : bond 0.00282 ( 9140) covalent geometry : angle 0.52528 (12354) *********************** 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 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.893 Fit side-chains REVERT: A 86 GLN cc_start: 0.6132 (mt0) cc_final: 0.5806 (mm-40) REVERT: B 23 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6306 (ttm-80) REVERT: D 23 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6283 (ttm-80) REVERT: C 86 GLN cc_start: 0.6132 (mt0) cc_final: 0.5807 (mm-40) outliers start: 43 outliers final: 18 residues processed: 127 average time/residue: 1.2844 time to fit residues: 173.3336 Evaluate side-chains 113 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 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 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 119 SER Chi-restraints excluded: chain C residue 195 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 25 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.135668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109086 restraints weight = 10059.869| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.94 r_work: 0.3090 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9140 Z= 0.259 Angle : 0.641 7.408 12354 Z= 0.324 Chirality : 0.049 0.389 1400 Planarity : 0.005 0.040 1478 Dihedral : 13.330 148.369 1578 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.32 % Allowed : 25.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1060 helix: 1.84 (0.20), residues: 592 sheet: 0.82 (0.59), residues: 64 loop : -0.89 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 39 HIS 0.006 0.001 HIS C 11 PHE 0.014 0.002 PHE D 108 TYR 0.031 0.002 TYR A 115 ARG 0.002 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.08456 ( 467) hydrogen bonds : angle 4.27549 ( 1359) covalent geometry : bond 0.00646 ( 9140) covalent geometry : angle 0.64127 (12354) *********************** 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 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 1.230 Fit side-chains REVERT: A 74 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7746 (tp) REVERT: A 86 GLN cc_start: 0.6502 (mt0) cc_final: 0.6034 (mm-40) REVERT: A 242 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7637 (mm) REVERT: B 23 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6344 (ttm170) REVERT: B 149 ARG cc_start: 0.7386 (ttm110) cc_final: 0.6568 (mtp85) REVERT: D 23 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6359 (ttm170) REVERT: D 149 ARG cc_start: 0.7396 (ttm110) cc_final: 0.6578 (mtp85) REVERT: C 74 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (tp) REVERT: C 80 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7699 (ptp) REVERT: C 86 GLN cc_start: 0.6507 (mt0) cc_final: 0.6034 (mm-40) REVERT: C 242 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7636 (mm) outliers start: 50 outliers final: 26 residues processed: 135 average time/residue: 1.6212 time to fit residues: 232.3864 Evaluate side-chains 122 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 195 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 242 LEU 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 53 MET 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 74 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108964 restraints weight = 10211.164| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.01 r_work: 0.3031 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1446 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= 0.134 Angle : 0.513 5.403 12354 Z= 0.261 Chirality : 0.044 0.347 1400 Planarity : 0.004 0.037 1478 Dihedral : 12.761 147.741 1578 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.15 % Allowed : 26.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1060 helix: 2.15 (0.20), residues: 590 sheet: 0.93 (0.58), residues: 64 loop : -0.78 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 73 HIS 0.003 0.001 HIS A 11 PHE 0.010 0.001 PHE D 108 TYR 0.018 0.001 TYR A 115 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 467) hydrogen bonds : angle 4.01717 ( 1359) covalent geometry : bond 0.00290 ( 9140) covalent geometry : angle 0.51282 (12354) *********************** 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 132 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.036 Fit side-chains REVERT: A 74 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7716 (tp) REVERT: A 80 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7633 (ptp) REVERT: A 86 GLN cc_start: 0.6237 (mt0) cc_final: 0.5877 (mm-40) REVERT: A 210 MET cc_start: 0.4587 (tpt) cc_final: 0.4383 (mmt) REVERT: B 23 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6406 (ttm-80) REVERT: D 23 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6380 (ttm-80) REVERT: C 74 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7730 (tp) REVERT: C 86 GLN cc_start: 0.6230 (mt0) cc_final: 0.5887 (mm-40) REVERT: C 263 ARG cc_start: 0.7290 (ptp-170) cc_final: 0.6906 (ptp-170) outliers start: 39 outliers final: 20 residues processed: 124 average time/residue: 1.4297 time to fit residues: 188.5316 Evaluate side-chains 118 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 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 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 74 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 195 LEU 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 18 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 192 GLN D 192 GLN C 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112661 restraints weight = 10037.501| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.02 r_work: 0.3055 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1455 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= 0.123 Angle : 0.481 4.979 12354 Z= 0.247 Chirality : 0.042 0.246 1400 Planarity : 0.004 0.037 1478 Dihedral : 12.156 146.558 1578 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.30 % Allowed : 27.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1060 helix: 2.31 (0.21), residues: 590 sheet: 0.97 (0.59), residues: 64 loop : -0.74 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.003 0.001 HIS A 11 PHE 0.008 0.001 PHE D 108 TYR 0.017 0.001 TYR A 115 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.05407 ( 467) hydrogen bonds : angle 3.87676 ( 1359) covalent geometry : bond 0.00268 ( 9140) covalent geometry : angle 0.48100 (12354) *********************** 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: 31 poor density : 97 time to evaluate : 0.951 Fit side-chains REVERT: A 80 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7478 (ptp) REVERT: A 86 GLN cc_start: 0.6228 (mt0) cc_final: 0.5998 (mm-40) REVERT: A 263 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6947 (ptp-170) REVERT: B 23 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6361 (ttm-80) REVERT: B 123 MET cc_start: 0.6909 (mtp) cc_final: 0.6417 (ptp) REVERT: D 23 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6356 (ttm-80) REVERT: D 157 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6674 (m110) REVERT: C 74 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 86 GLN cc_start: 0.6211 (mt0) cc_final: 0.5969 (mm-40) outliers start: 31 outliers final: 16 residues processed: 121 average time/residue: 1.3337 time to fit residues: 171.3978 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 : 0.879 ------------------------------------------------------------------------------- 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 195 LEU 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 103 ILE Chi-restraints excluded: chain D residue 157 ASN 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 195 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 98 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 C 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110549 restraints weight = 10166.507| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1471 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= 0.123 Angle : 0.478 4.950 12354 Z= 0.247 Chirality : 0.042 0.200 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.977 146.505 1578 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.87 % Allowed : 27.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1060 helix: 2.38 (0.21), residues: 588 sheet: 1.01 (0.59), residues: 64 loop : -0.75 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.003 0.001 HIS A 11 PHE 0.008 0.001 PHE B 108 TYR 0.018 0.001 TYR A 115 ARG 0.002 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.05447 ( 467) hydrogen bonds : angle 3.84634 ( 1359) covalent geometry : bond 0.00269 ( 9140) covalent geometry : angle 0.47822 (12354) ********************** 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 126 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.928 Fit side-chains REVERT: A 80 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7454 (ptp) REVERT: A 86 GLN cc_start: 0.6256 (mt0) cc_final: 0.5985 (mm-40) REVERT: B 23 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6355 (ttm-80) REVERT: D 23 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6346 (ttm-80) REVERT: D 123 MET cc_start: 0.6827 (mtp) cc_final: 0.6454 (ptp) REVERT: D 157 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6638 (m110) REVERT: C 86 GLN cc_start: 0.6266 (mt0) cc_final: 0.5997 (mm-40) REVERT: C 130 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6995 (mp) outliers start: 27 outliers final: 17 residues processed: 121 average time/residue: 1.3644 time to fit residues: 175.3668 Evaluate side-chains 121 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 103 ILE Chi-restraints excluded: chain D residue 157 ASN 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 195 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 38 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118550 restraints weight = 9892.804| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.93 r_work: 0.3160 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9140 Z= 0.112 Angle : 0.463 4.914 12354 Z= 0.240 Chirality : 0.041 0.155 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.724 146.386 1578 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.55 % Allowed : 28.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1060 helix: 2.44 (0.21), residues: 588 sheet: 0.98 (0.59), residues: 64 loop : -0.75 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.003 0.001 HIS A 259 PHE 0.008 0.001 PHE B 108 TYR 0.017 0.001 TYR C 115 ARG 0.007 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.05113 ( 467) hydrogen bonds : angle 3.79135 ( 1359) covalent geometry : bond 0.00239 ( 9140) covalent geometry : angle 0.46276 (12354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6321.71 seconds wall clock time: 110 minutes 45.50 seconds (6645.50 seconds total)