Starting phenix.real_space_refine on Mon May 12 09:45:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhd_48274/05_2025/9mhd_48274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhd_48274/05_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_48274/05_2025/9mhd_48274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhd_48274/05_2025/9mhd_48274.map" model { file = "/net/cci-nas-00/data/ceres_data/9mhd_48274/05_2025/9mhd_48274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhd_48274/05_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-5687/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: 6.16, per 1000 atoms: 0.69 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: 2.20 Conformation dependent library (CDL) restraints added in 925.0 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: 0.84 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: 2.13 Time building geometry restraints manager: 2.52 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: 0.010 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.780 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- 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 : 1.030 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: 1.3597 time to fit residues: 183.4780 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 : 0.878 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112383 restraints weight = 9878.433| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.93 r_work: 0.3127 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.980 Fit side-chains REVERT: A 86 GLN cc_start: 0.6417 (mt0) cc_final: 0.6062 (mm-40) REVERT: A 263 ARG cc_start: 0.7349 (ptp-170) cc_final: 0.6879 (ptp-170) REVERT: B 121 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7634 (ttpt) REVERT: C 86 GLN cc_start: 0.6440 (mt0) cc_final: 0.6077 (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: 1.3157 time to fit residues: 191.4297 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 : 0.887 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108494 restraints weight = 9910.792| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.3083 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1161 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= 0.181 Angle : 0.648 8.257 12354 Z= 0.307 Chirality : 0.047 0.323 1400 Planarity : 0.004 0.038 1478 Dihedral : 17.225 155.858 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 : 5.00 % Allowed : 27.02 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.25), residues: 1060 helix: 2.06 (0.21), residues: 590 sheet: 1.25 (0.60), residues: 64 loop : -0.67 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 39 HIS 0.006 0.001 HIS C 11 PHE 0.014 0.001 PHE B 108 TYR 0.025 0.001 TYR C 115 ARG 0.003 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.07268 ( 467) hydrogen bonds : angle 4.23186 ( 1359) covalent geometry : bond 0.00422 ( 9140) covalent geometry : angle 0.64823 (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 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 1.074 Fit side-chains REVERT: A 86 GLN cc_start: 0.6544 (mt0) cc_final: 0.6177 (mm-40) REVERT: A 242 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7785 (mm) REVERT: B 35 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7240 (ttmm) REVERT: B 139 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: D 35 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7241 (ttmm) REVERT: C 86 GLN cc_start: 0.6547 (mt0) cc_final: 0.6181 (mm-40) REVERT: C 242 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7776 (mm) outliers start: 47 outliers final: 22 residues processed: 129 average time/residue: 1.3338 time to fit residues: 182.6198 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 16 ILE 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: 0.9980 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 C 259 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115452 restraints weight = 9892.716| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.98 r_work: 0.3227 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1205 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= 0.117 Angle : 0.522 7.766 12354 Z= 0.253 Chirality : 0.045 0.415 1400 Planarity : 0.003 0.035 1478 Dihedral : 14.769 151.977 1584 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.15 % Allowed : 27.45 % 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 (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: 1.82 (0.25), residues: 1060 helix: 2.34 (0.21), residues: 590 sheet: 1.43 (0.61), residues: 64 loop : -0.58 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.003 0.001 HIS A 259 PHE 0.007 0.001 PHE B 108 TYR 0.014 0.001 TYR C 115 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 467) hydrogen bonds : angle 3.96343 ( 1359) covalent geometry : bond 0.00240 ( 9140) covalent geometry : angle 0.52245 (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 132 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.915 Fit side-chains REVERT: A 86 GLN cc_start: 0.6219 (mt0) cc_final: 0.5952 (mm-40) REVERT: A 130 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7071 (mp) REVERT: B 23 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6325 (ttm-80) REVERT: D 23 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6334 (ttm-80) REVERT: C 86 GLN cc_start: 0.6216 (mt0) cc_final: 0.5951 (mm-40) REVERT: C 130 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7055 (mp) outliers start: 39 outliers final: 21 residues processed: 120 average time/residue: 1.2569 time to fit residues: 160.7099 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 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 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 130 LEU 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 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: 0.5980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.138312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111285 restraints weight = 9989.010| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.98 r_work: 0.3102 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1299 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= 0.179 Angle : 0.569 7.603 12354 Z= 0.282 Chirality : 0.047 0.413 1400 Planarity : 0.004 0.036 1478 Dihedral : 14.076 149.964 1584 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.36 % Allowed : 27.23 % 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 (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: 1.58 (0.25), residues: 1060 helix: 2.19 (0.21), residues: 588 sheet: 1.25 (0.60), residues: 64 loop : -0.73 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 39 HIS 0.004 0.001 HIS A 11 PHE 0.012 0.001 PHE D 108 TYR 0.026 0.001 TYR A 115 ARG 0.002 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.06942 ( 467) hydrogen bonds : angle 4.09563 ( 1359) covalent geometry : bond 0.00428 ( 9140) covalent geometry : angle 0.56941 (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 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.942 Fit side-chains REVERT: A 80 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7510 (ptp) REVERT: A 86 GLN cc_start: 0.6290 (mt0) cc_final: 0.5955 (mm-40) REVERT: B 23 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6358 (ttm-80) REVERT: B 139 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: B 149 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6394 (mtp180) REVERT: D 23 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6366 (ttm-80) REVERT: D 35 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6927 (ttmm) REVERT: D 149 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6416 (mtp180) REVERT: C 80 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7503 (ptp) REVERT: C 86 GLN cc_start: 0.6301 (mt0) cc_final: 0.5966 (mm-40) outliers start: 41 outliers final: 22 residues processed: 127 average time/residue: 1.3513 time to fit residues: 181.9113 Evaluate side-chains 120 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 A residue 203 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 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 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: 0.7980 chunk 99 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113671 restraints weight = 9823.416| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.97 r_work: 0.3131 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 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 0.030 9140 Z= 0.136 Angle : 0.511 6.513 12354 Z= 0.256 Chirality : 0.044 0.382 1400 Planarity : 0.004 0.036 1478 Dihedral : 13.105 148.449 1584 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.57 % Allowed : 27.23 % 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: 1.67 (0.25), residues: 1060 helix: 2.27 (0.21), residues: 588 sheet: 1.26 (0.60), residues: 64 loop : -0.68 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 73 HIS 0.003 0.001 HIS A 11 PHE 0.009 0.001 PHE B 108 TYR 0.019 0.001 TYR C 115 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 467) hydrogen bonds : angle 3.97159 ( 1359) covalent geometry : bond 0.00304 ( 9140) covalent geometry : angle 0.51116 (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 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.898 Fit side-chains REVERT: A 86 GLN cc_start: 0.6309 (mt0) cc_final: 0.6043 (mm-40) REVERT: B 23 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6369 (ttm-80) REVERT: B 139 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7931 (mm-40) REVERT: D 23 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6367 (ttm-80) REVERT: C 86 GLN cc_start: 0.6311 (mt0) cc_final: 0.6044 (mm-40) outliers start: 43 outliers final: 17 residues processed: 131 average time/residue: 1.3376 time to fit residues: 185.9087 Evaluate side-chains 117 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 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 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: 5.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 D 157 ASN C 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106789 restraints weight = 10166.698| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.02 r_work: 0.3059 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9140 Z= 0.241 Angle : 0.619 6.758 12354 Z= 0.314 Chirality : 0.047 0.346 1400 Planarity : 0.004 0.038 1478 Dihedral : 12.961 147.857 1578 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.89 % Allowed : 26.17 % 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 (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: 1.26 (0.25), residues: 1060 helix: 1.94 (0.20), residues: 588 sheet: 0.91 (0.59), residues: 64 loop : -0.84 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 39 HIS 0.006 0.001 HIS A 11 PHE 0.014 0.002 PHE D 108 TYR 0.030 0.002 TYR A 115 ARG 0.003 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.08164 ( 467) hydrogen bonds : angle 4.21838 ( 1359) covalent geometry : bond 0.00600 ( 9140) covalent geometry : angle 0.61867 (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 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 1.124 Fit side-chains REVERT: A 86 GLN cc_start: 0.6463 (mt0) cc_final: 0.6040 (mm-40) REVERT: B 23 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6329 (ttm-80) REVERT: B 139 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: B 149 ARG cc_start: 0.7377 (ttm110) cc_final: 0.6564 (mtp85) REVERT: D 23 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6323 (ttm-80) REVERT: D 149 ARG cc_start: 0.7387 (ttm110) cc_final: 0.6569 (mtp85) REVERT: C 74 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7740 (tp) REVERT: C 86 GLN cc_start: 0.6458 (mt0) cc_final: 0.6035 (mm-40) outliers start: 46 outliers final: 20 residues processed: 137 average time/residue: 1.4618 time to fit residues: 211.6813 Evaluate side-chains 115 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 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 195 LEU Chi-restraints excluded: chain C residue 196 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.0060 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.131822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103868 restraints weight = 10361.977| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.07 r_work: 0.3119 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9140 Z= 0.168 Angle : 0.542 5.037 12354 Z= 0.277 Chirality : 0.044 0.309 1400 Planarity : 0.004 0.038 1478 Dihedral : 12.680 147.399 1578 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.26 % Allowed : 27.02 % 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: 1.35 (0.25), residues: 1060 helix: 2.04 (0.20), residues: 588 sheet: 0.88 (0.59), residues: 64 loop : -0.84 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 39 HIS 0.004 0.001 HIS A 11 PHE 0.012 0.001 PHE D 108 TYR 0.022 0.001 TYR C 115 ARG 0.002 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.06869 ( 467) hydrogen bonds : angle 4.09717 ( 1359) covalent geometry : bond 0.00397 ( 9140) covalent geometry : angle 0.54230 (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 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.095 Fit side-chains REVERT: A 80 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7592 (ptp) REVERT: A 86 GLN cc_start: 0.6323 (mt0) cc_final: 0.5922 (mm-40) REVERT: B 23 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6294 (ttm-80) REVERT: B 139 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8034 (mm-40) REVERT: D 23 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6298 (ttm-80) REVERT: C 74 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7662 (tp) REVERT: C 80 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7588 (ptp) REVERT: C 86 GLN cc_start: 0.6327 (mt0) cc_final: 0.5925 (mm-40) outliers start: 40 outliers final: 22 residues processed: 125 average time/residue: 1.3449 time to fit residues: 178.9991 Evaluate side-chains 121 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 139 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 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 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 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: 0.9980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.145291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119093 restraints weight = 9830.338| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.93 r_work: 0.3083 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9140 Z= 0.109 Angle : 0.464 4.918 12354 Z= 0.239 Chirality : 0.041 0.229 1400 Planarity : 0.004 0.037 1478 Dihedral : 12.022 146.463 1578 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.55 % Allowed : 28.62 % 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 (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: 1.70 (0.26), residues: 1060 helix: 2.34 (0.21), residues: 588 sheet: 0.98 (0.58), residues: 64 loop : -0.70 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.002 0.000 HIS A 11 PHE 0.006 0.001 PHE B 108 TYR 0.013 0.001 TYR A 115 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 467) hydrogen bonds : angle 3.84239 ( 1359) covalent geometry : bond 0.00223 ( 9140) covalent geometry : angle 0.46389 (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 122 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.030 Fit side-chains REVERT: A 80 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7573 (ptp) REVERT: A 86 GLN cc_start: 0.6360 (mt0) cc_final: 0.6120 (mm-40) REVERT: A 263 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7077 (ptp-170) REVERT: B 123 MET cc_start: 0.7075 (mtp) cc_final: 0.6615 (ptp) REVERT: B 139 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8034 (mm-40) REVERT: D 123 MET cc_start: 0.7089 (mtp) cc_final: 0.6597 (ptp) REVERT: C 80 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7572 (ptp) REVERT: C 86 GLN cc_start: 0.6367 (mt0) cc_final: 0.6132 (mm-40) REVERT: C 263 ARG cc_start: 0.7356 (ptp-170) cc_final: 0.6926 (ptp-170) outliers start: 24 outliers final: 11 residues processed: 113 average time/residue: 1.3181 time to fit residues: 158.4941 Evaluate side-chains 114 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 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 71 VAL Chi-restraints excluded: chain C residue 80 MET 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: 0.7980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.140649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114138 restraints weight = 9980.896| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.95 r_work: 0.3068 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1486 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= 0.138 Angle : 0.492 4.985 12354 Z= 0.254 Chirality : 0.042 0.183 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.995 146.588 1578 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.13 % Allowed : 28.94 % 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 (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: 1.68 (0.26), residues: 1060 helix: 2.32 (0.21), residues: 588 sheet: 1.01 (0.59), residues: 64 loop : -0.69 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 81 HIS 0.003 0.001 HIS A 11 PHE 0.010 0.001 PHE D 108 TYR 0.021 0.001 TYR C 115 ARG 0.002 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.05887 ( 467) hydrogen bonds : angle 3.89944 ( 1359) covalent geometry : bond 0.00313 ( 9140) covalent geometry : angle 0.49206 (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 121 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.887 Fit side-chains REVERT: A 80 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7463 (ptp) REVERT: A 86 GLN cc_start: 0.6217 (mt0) cc_final: 0.5981 (mm-40) REVERT: B 22 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6373 (mt-10) REVERT: B 139 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7936 (mm-40) REVERT: C 80 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7472 (ptp) REVERT: C 86 GLN cc_start: 0.6227 (mt0) cc_final: 0.5993 (mm-40) REVERT: C 263 ARG cc_start: 0.7358 (ptp-170) cc_final: 0.6866 (ptp-170) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 1.3685 time to fit residues: 166.7024 Evaluate side-chains 115 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 67 SER Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 MET 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: 0.9980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 C 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118379 restraints weight = 9893.177| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.91 r_work: 0.3095 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9140 Z= 0.117 Angle : 0.474 7.715 12354 Z= 0.246 Chirality : 0.041 0.150 1400 Planarity : 0.004 0.037 1478 Dihedral : 11.795 146.515 1578 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 28.83 % 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 (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: 1.77 (0.26), residues: 1060 helix: 2.40 (0.21), residues: 588 sheet: 1.07 (0.59), residues: 64 loop : -0.69 (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 D 108 TYR 0.016 0.001 TYR C 115 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 467) hydrogen bonds : angle 3.81754 ( 1359) covalent geometry : bond 0.00250 ( 9140) covalent geometry : angle 0.47356 (12354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5907.86 seconds wall clock time: 102 minutes 37.22 seconds (6157.22 seconds total)